10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2018

OR

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from              to

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

(510) 450-0761

(Address and telephone number of principal executive offices)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuance to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer.

Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	o	Smaller reporting company	x
Emerging growth company	o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  o    No  x

Shares outstanding of the Registrant's common stock:

Class	Outstanding as of August 10, 2018
Common Stock, $0.0001 par value per share	50,368,507

AMYRIS, INC.

TABLE OF CONTENTS

		Page
PART I
Item 1.	Financial Statements (unaudited)	3
	Condensed Consolidated Balance Sheets as of June 30, 2018 and December 31, 2017	3
	Condensed Consolidated Statements of Operations for the Three and Six Months Ended June 30, 2018 and 2017	4
	Condensed Consolidated Statements of Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2018 and 2017	5
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2018 and 2017	6
	Notes to Condensed Consolidated Financial Statements	8
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	32
Item 3.	Quantitative and Qualitative Disclosures about Market Risk	43
Item 4.	Controls and Procedures	43
PART II
Item 1.	Legal Proceedings	45
Item 1A.	Risk Factors	45
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	46
Item 3.	Defaults Upon Senior Securities	46
Item 6.	Exhibits	47
SIGNATURES

2

PART I

ITEM 1. FINANCIAL STATEMENTS

AMYRIS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)

(In thousands, except shares and per share amounts)	June 30,  2018			December 31,  2017
Assets
Current assets:
Cash and cash equivalents	$	14,050		$	57,059
Restricted cash		1,846			2,994
Short-term investments		130			—
Accounts receivable, net of allowance of $642 as of June 30, 2018 and December 31, 2017		26,814			24,281
Unbilled receivable		12,683			9,340
Inventories		6,632			5,408
Prepaid expenses and other current assets		4,687			5,525
Total current assets		66,842			104,607
Property, plant and equipment, net		15,300			13,892
Unbilled receivable, noncurrent		9,747			7,940
Restricted cash, noncurrent		959			959
Recoverable taxes from Brazilian government entities		1,057			1,445
Other assets		24,747			22,640
Total assets	$	118,652		$	151,483
Liabilities, Mezzanine Equity and Stockholders' Deficit
Current liabilities:
Accounts payable	$	19,206		$	15,921
Accrued and other current liabilities		20,101			29,402
Deferred revenue		9,643			4,880
Debt, current portion		59,987			36,924
Related party debt, current portion		49,669			20,019
Total current liabilities		158,606			107,146
Long-term debt, net of current portion		43,642			61,893
Related party debt, net of current portion		18,104			46,541
Derivative liabilities		138,695			119,978
Other noncurrent liabilities		8,581			10,632
Total liabilities		367,628			346,190
Commitments and contingencies (Note 9)
Mezzanine equity:
Contingently redeemable common stock (Note 5)		5,000			5,000
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of June 30, 2018 and December 31, 2017, and 19,334 and 22,171 shares issued and outstanding as of June 30, 2018 and December 31, 2017, respectively		—			—
Common stock - $0.0001 par value, 250,000,000 shares authorized as of June 30, 2018 and December 31, 2017; 50,340,680 and 45,637,433 shares issued and outstanding as of June 30, 2018 and December 31, 2017, respectively		5			5
Additional paid-in capital		1,086,814			1,048,274
Accumulated other comprehensive loss		(42,818	)		(42,156	)
Accumulated deficit		(1,298,914	)		(1,206,767	)
Total Amyris, Inc. stockholders’ deficit		(254,913	)		(200,644	)
Noncontrolling interest		937			937
Total stockholders' deficit		(253,976	)		(199,707	)
Total liabilities, mezzanine equity and stockholders' deficit	$	118,652		$	151,483

See the accompanying notes to the unaudited condensed consolidated financial statements.

3

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2018			2017			2018			2017
Revenue:
Renewable products (includes related party revenue of $144, $0, $295 and $0, respectively)	$	6,633		$	9,892		$	11,828		$	17,929
Licenses and royalties (includes related party revenue of $6,887, $0, $18,287 and $0, respectively)		6,887			5,497			18,324			5,752
Grants and collaborations (includes related party revenue of $1,737, $149, $3,127 and $149, respectively)		9,674			10,290			16,040			14,979
Total revenue (includes related party revenue of $8,768, $149, $21,709 and $149, respectively)		23,194			25,679			46,192			38,660
Cost and operating expenses:
Cost of products sold		5,984			17,279			11,299			30,047
Research and development		15,287			14,249			34,100			28,956
Sales, general and administrative		20,189			15,949			38,946			28,799
Total cost and operating expenses		41,460			47,477			84,345			87,802
Loss from operations		(18,266	)		(21,798	)		(38,153	)		(49,142	)
Other income (expense):
Interest expense		(8,824	)		(9,303	)		(17,029	)		(21,486	)
Gain (loss) from change in fair value of derivative instruments		24,365			35,775			(39,548	)		38,114
Gain upon extinguishment of derivative liability		1,857			—			1,857			—
Loss upon extinguishment of debt		(26	)		(3,624	)		(26	)		(3,528	)
Other income (expense), net		2,427			(120	)		2,936			(440	)
Total other income (expense), net		19,799			22,728			(51,810	)		12,660
Income (loss) before income taxes		1,533			930			(89,963	)		(36,482	)
Provision for income taxes		—			(310	)		—			(269	)
Net income (loss) attributable to Amyris, Inc.		1,533			620			(89,963	)		(36,751	)
Less deemed dividend on capital distribution to related parties		—			(8,648	)					(8,648	)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		—			(562	)					(562	)
Less cumulative dividends on Series A and B preferred stock		(399	)		(1,675	)		(794	)		(1,675	)
Less earnings allocated to participating securities		(67	)		—			—			—
Net income (loss) attributable to Amyris, Inc. common stockholders	$	1,067		$	(10,265	)	$	(90,757	)	$	(47,636	)
Net income (loss) per share attributable to common stockholders, basic	$	0.02		$	(0.44	)	$	(1.71	)	$	(2.24	)
Net loss per share attributable to common stockholders, diluted	$	(0.29	)	$	(0.44	)	$	(1.71	)	$	(2.24	)
Weighted-average shares of common stock outstanding used in computing net income (loss) per share of common stock, basic		54,932,411			23,155,874			53,076,975			21,226,013
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted		60,729,736			23,155,874			53,076,975			21,226,013

See the accompanying notes to the unaudited condensed consolidated financial statements.

4

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS)

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2018			2017			2018			2017
Comprehensive income (loss):
Net income (loss) attributable to Amyris, Inc.	$	1,533		$	620		$	(89,963	)	$	(36,751	)
Foreign currency translation adjustment, net of tax		(525	)		(1,422	)		(662	)		(1,099	)
Total comprehensive income (loss) attributable to Amyris, Inc.	$	1,008		$	(802	)	$	(90,625	)	$	(37,850	)

See the accompanying notes to the unaudited condensed consolidated financial statements.

5

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)

	Six Months Ended June 30,
(In thousands)	2018			2017
Cash flows from operating activities
Net loss	$	(89,963	)	$	(36,751	)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss (gain) from change in fair value of derivative liabilities		39,548			(38,115	)
Amortization of debt discount		6,587			7,637
Stock-based compensation		3,178			2,684
Depreciation and amortization		2,944			5,550
Loss (gain) on disposal of property, plant and equipment		942			(161	)
Loss on foreign currency exchange rates		271			63
Loss upon extinguishment of debt		26			3,528
Gain on extinguishment of derivative liability		(1,857	)		—
Gain on change in fair value of equity investment		(1,717	)		—
Receipt of equity in connection with collaboration arrangements revenue		—			(2,660	)
Changes in assets and liabilities:
Accounts receivable		(2,027	)		(3,509	)
Unbilled receivables		(5,150	)		—
Inventories		(1,313	)		409
Prepaid expenses and other assets		(1,072	)		(4,220	)
Accounts payable		2,681			(1,739	)
Accrued and other liabilities		(10,031	)		7,943
Deferred revenue		3,959			(838	)
Net cash used in operating activities		(52,994	)		(60,179	)
Cash flows from investing activities
Purchases of property, plant and equipment		(4,207	)		(264	)
Increase in short-term investments		(157	)		(85	)
Net cash used in investing activities		(4,364	)		(349	)
Cash flows from financing activities
Proceeds from issuance of debt		34,611			12,455
Proceeds from issuance of common stock upon exercise of warrants		14,549			—
Proceeds from issuance of common stock in private placement		1,416			—
Proceeds from exercises of ESPP purchases		270			—
Proceeds from exercises of common stock options		248			69
Principal payments on debt		(37,037	)		(24,372	)
Principal payments on capital leases		(593	)		(764	)
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units		(185	)		(110	)
Proceeds from issuance of convertible preferred stock		—			50,661
Net cash provided by financing activities		13,279			37,939
Effect of exchange rate changes on cash, cash equivalents and restricted cash		(78	)		7
Net decrease in cash, cash equivalents and restricted cash		(44,157	)		(22,582	)
Cash, cash equivalents and restricted cash at beginning of period		61,012			32,433
Cash, cash equivalents and restricted cash at end of the period	$	16,855		$	9,851
Reconciliation of cash, cash equivalents and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$	14,050		$	5,078
Restricted cash, current		1,846			3,815
Restricted cash, noncurrent		959			958
Total cash, cash equivalents and restricted cash	$	16,855		$	9,851

See the accompanying notes to the unaudited condensed consolidated financial statements.

6

AMYRIS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS, Continued

(Unaudited)

	Six Months Ended June 30,
(In thousands)	2018		2017
Supplemental disclosures of cash flow information:
Cash paid for interest	$	8,035	$	4,526
Supplemental disclosures of non-cash investing and financing activities:
Settlement of derivative liability into equity	$	9,536	$	—
Accrued interest added to debt principal	$	1,894	$	1,745
Acquisition of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	744	$	1,189
Financing of equipment	$	642	$	138
Issuance of convertible preferred stock upon conversion of debt	$	—	$	40,204
Issuance of common stock upon conversion of debt	$	—	$	28,702
Issuance of common stock for settlement of debt principal and interest payments	$	—	$	3,233
Financing of insurance premium under notes payable	$	—	$	191

See the accompanying notes to the unaudited condensed consolidated financial statements.

7

AMYRIS, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavors & Fragrances markets. The Company's proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company's biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. The Company has successfully used its technology to develop and produce six distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the 10-K, from which the condensed consolidated balance sheet as of December 31, 2017 is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP), for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, since they are interim statements, the accompanying condensed consolidated financial statements do not include all of the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are not necessarily indicative of results for a full year.

Liquidity

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations for at least the next 12 months following the issuance of these financial statements. As of June 30, 2018, the Company had negative working capital of $105.9 million, excluding cash and cash equivalents and short-term investments (compared to negative working capital of $59.6 million as of December 31, 2017), and an accumulated deficit of $1.3 billion.

As of June 30, 2018, the Company's debt (including related party debt), net of deferred discount and issuance costs of $25.5 million, totaled $171.4 million, of which $109.7 million is classified as current and $23.2 million is mandatorily convertible into equity and within the control of the Company. The Company's debt service obligations through August 31, 2019 are $114.5 million, including $15.8 million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness and cross-default clauses. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of the Company's outstanding indebtedness.

Cash and cash equivalents of $14.1 million as of June 30, 2018 are not sufficient to fund expected future negative cash flows from operations and cash debt service obligations through one year following the issuance of these financial statements. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that these financial statements are issued. The financial statements do not include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to extend existing debt maturities by restructuring a majority of its convertible debt, which is uncertain and outside the control of the Company, in addition to the mandatory conversion of certain debt obligations into equity, which conversion is within the control of the Company. Further, the Company's operating plan for the next 12 months from the date of issuance of these financial statements contemplates a significant reduction in its net operating cash outflows as compared to the previous 12 months, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) significantly increased royalty revenues (previously referred to as value share revenues), (iii) reduced cost of products sold as a percentage of renewable products revenue due to anticipated procurement and production efficiencies, and (iv) cash inflows from grants and collaborations. Finally, during the second half of 2018, the Company plans to obtain project financing for the construction of a new specialty ingredients manufacturing facility in Brazil. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it may be forced to liquidate its assets or obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all.

8

Significant Accounting Policies

Note 1, "Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the 10-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. Except as noted below for the adoption of Accounting Standards Codification (“ASC”) Topic 606 (“ASC 606”), Revenue from Contracts with Customers, and Accounting Standards Update (“ASU”) 2016-01, Financial Instruments-Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities, there have been no material changes to the Company's significant accounting policies and estimates during the three and six months ended June 30, 2018.

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer and recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does not incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators among others when determining whether it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does not meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note 10, "Significant Revenue Agreements" in Part II, Item 8 of the 10-K.

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. The Company’s renewable products are delivered to customers from the Company’s facilities with shipping terms typically specifying F.O.B. shipping point.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts may contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

9

The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does not have the ability to direct the product to a different customer. It is at this point that we have right to payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do not include rights of return. Returns are accepted only if the product does not meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception and revenue is estimated and recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends.

When the Company’s intellectual property license is not the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

10

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services: The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaborators with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include one or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment.

The Company generally invoices its collaborators on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Deferred revenue arises from amounts received in advance of performing the research and development activities and is recognized as revenue in future periods as the performance obligations are satisfied.

Grants: The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

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For descriptions of the Company's other significant accounting policies, see the Company's Annual Report on Form 10-K for the year ended December 31, 2017.

Recent Accounting Pronouncements

(a) Recent Accounting Standards, Pronouncements or Updates Recently Adopted

In the six months ended June 30, 2018, the Company adopted these new accounting standards or updates:

Revenue Recognition The Company adopted ASC 606 with a date of initial application of January 1, 2018. As a result, the Company has changed its accounting policy for revenue recognition as detailed above in “Significant Accounting Policies”. The Company applied ASC 606 using the modified retrospective approach by recognizing the cumulative effect of initially applying ASC 606 to all contracts not completed as of the date of adoption as an adjustment to the opening balance of accumulated deficit at January 1, 2018. Therefore, the comparative information has not been adjusted and continues to be reported under the legacy revenue recognition guidance of ASC 605, "Revenue Recognition".

The Company applied ASC 606 using a practical expedient for contracts that were modified before the application date, which allowed us to determine an aggregate effect of all modifications that occurred before January 1, 2018, when determining the satisfied and unsatisfied performance obligations, the transaction price, and allocating that transaction price to the performance obligations instead of retrospectively restating the contracts for such contract modifications.

The cumulative effect of initially applying ASC 606 resulted in an increase to accumulated deficit at January 1, 2018 of approximately $0.8 million. The increase in accumulated deficit arose primarily from a $0.8 million increase of deferred revenue related to the effects of measuring and allocating the transaction price to the performance obligations under ASC 606 compared to the legacy guidance of ASC 605. The most significant change in accounting policy is the Company now estimates royalty revenues from licenses of the Company’s intellectual property and recognizes estimated royalty revenues at a point in time when the Company sells its renewable products to its customers (if the sales-based royalty exception does not apply) or when the licensee sells its products to its customer (if the sales-based royalty exception does apply). Also, the transaction price for royalty revenues is reduced for variable incentive payments that may be payable by the Company to customers.

The following table presents the amounts by which revenue is affected in the current reporting period by the application of ASC 606 as compared with the legacy guidance that was in effect before the accounting change. No other consolidated statements of operations financial statement line items were impacted by the adoption of ASC 606.

	Three Months Ended June 30, 2018							Six Months Ended June 30, 2018
(In thousands)	As Reported		Adjustments			Amounts Without the Adoption of ASC 606		As Reported		Adjustments			Amounts Without the Adoption of ASC 606
Renewable products	$	6,633	$	—		$	6,633	$	11,828	$	—		$	11,828
Licenses and royalties		6,887		(4,980	)		1,907		18,324		(15,747	)		2,577
Grants and collaborations		9,674		(2,039	)		7,635		16,040		(2,265	)		13,775
Total revenue from all customers	$	23,194	$	(7,019	)	$	16,175	$	46,192	$	(18,012	)	$	28,180

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Financial Instruments In January 2016, the Financial Accounting Standards Board (FASB) issued ASU 2016-01, Financial Instruments-Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities, which changes the accounting for equity investments, financial liabilities under the fair value option, and the presentation and disclosure requirements for financial instruments. The Company adopted ASU 2016-01 on January 1, 2018 and, as a result, has changed its accounting policy to account for investments in equity securities (other than those accounted for using the equity method of accounting) at fair value with changes in fair value recognized in net income. The Company applied the modified retrospective approach by recognizing a $1.4 million cumulative effect adjustment as an increase to the opening balance of accumulated deficit at January 1, 2018 representing an unrealized loss measured as the difference between the fair value and the cost basis of the Company’s equity investments as of January 1, 2018 previously accounted for using the cost method of accounting.

Classification of Cash Flow Elements In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments, which affects the classification of certain cash receipts and cash payments on the statement of cash flows. ASU 2016-15 resulted in a change in cash flow classification of debt prepayment or extinguishment costs. Prior to the adoption of ASU 2016-15, the Company classified gains or losses upon extinguishment of debt as an operating activity in the statements of cash flows. ASU 2016-15 became effective January 1, 2018 on a retrospective basis. Upon the Company's adoption of ASU 2016-15, such gains or losses are now classified in statements of cash flows as a financing activity.

Restricted Cash in Statement of Cash Flows In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230): Restricted Cash, which requires that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The accounting standard update became effective January 1, 2018 using a retrospective transition method for each period presented. Upon adoption, ASU 2016-18 has resulted in a change in the presentation of restricted cash in the statement of cash flows for current and prior periods presented.

Derecognition of Nonfinancial Assets In February 2017, the FASB issued ASU 2017-05, Other Income—Gains and Losses from the Derecognition of Nonfinancial Assets (Subtopic 610-20): Clarifying the Scope of Asset Derecognition Guidance and Accounting for Partial Sales of Nonfinancial Assets, which requires entities to apply certain recognition and measurement principles in ASC 606 when they derecognize nonfinancial assets, and in substance, nonfinancial assets, and the counterparty is not a customer. The guidance applies to: (1) contracts to transfer to a noncustomer a nonfinancial asset or group of nonfinancial assets, or an ownership interest in a consolidated subsidiary that does not meet the definition of a business and is not a not-for-profit activity; and (2) contributions of nonfinancial assets that are not a business to a joint venture or other noncontrolled investee. The accounting standard update became effective January 1, 2018 on a modified retrospective basis. Adoption of this ASU did not impact the Company's consolidated financial position, results of operations or cash flows.

Staff Accounting Bulletin No 118 - Tax Cuts and Jobs Act of 2017 On December 22, 2017, the Tax Cuts and Jobs Act of 2017 (the Act) was signed into law, making significant changes to the Internal Revenue Code. Changes include, but are not limited to, a corporate tax rate decrease from 35% to 21%, the transition of U.S. international taxation from a worldwide tax system to a territorial system, and a one-time transition tax on the mandatory deemed repatriation of cumulative foreign earnings as of December 31, 2017.

Based on the Company’s current operations it is anticipated that the only significant current impact of the Act for the Company will be the reduction in the U.S. corporate tax rate. The Act reduces the corporate tax rate to 21 percent, effective January 1, 2018. In December 2017, Staff Accounting Bulletin No. 118 (SAB 118) was issued to address the application of U.S. GAAP in situations when a registrant does not have the necessary information available, prepared, or analyzed in reasonable detail to complete the accounting for certain income tax effects of the Tax Act. As of June 30, 2018, due to the complexities of the new law, the Company has not yet completed its accounting for all the tax effects of the Tax Act, but has made a reasonable estimate of the effects on the Company's existing deferred tax balances. In all cases, the Company will continue to make and refine its calculations as additional analysis is completed. In addition, the Company's provisional estimate of the effects on its existing deferred tax balances may also be adjusted as the Company gains a more thorough understanding of the tax law during the one-year measurement period allowed under SAB 118. Additionally, the Act created a new requirement that certain income, referred to as "Global Intangible Low-Taxed Income" (GILTI) earned by controlled foreign corporations (CFCs) must be included currently in the gross income of the CFCs’ U.S. shareholder. The Company’s selection of an accounting policy with respect to the new GILTI tax rules will depend, in part, on analyzing its global income to determine whether it expects to have future U.S. inclusions in taxable income related to GILTI and, if so, what the impact is expected to be. As of June 30, 2018, the Company has not made a policy decision regarding whether to record deferred taxes on GILTI.

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(b) Recent Accounting Standards Pronouncements or Updates Not Yet Effective as of Period End

Leases In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842), with fundamental changes as to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The accounting standard update will be effective beginning in the first quarter of fiscal 2019 using a modified retrospective approach, which requires lessees and lessors to recognize and measure leases at the beginning of the earliest period presented. The Company is in the initial stages of evaluating the impact of the new standard on its accounting policies, processes and system requirements. The Company anticipates that the standard may have a material impact on the Company’s condensed consolidated balance sheets due to the requirement to recognize leased right-of-use assets and corresponding liabilities related to leases on the Company’s condensed consolidated balance sheets, but is still evaluating whether the standard might have a material impact on the Company’s other condensed consolidated financial statements.

Financial Instruments with "Down Round" Features In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging (Topic 815): Accounting for Certain Financial Instruments with Down Round Features. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update will be effective beginning in the first quarter of fiscal 2019 using a modified retrospective approach. The Company is in the initial stages of evaluating the impact of the new standard on its consolidated financial statements.

Non-employee Stock-based Compensation In June 2018, the FASB issued ASU 2018-07, Improvements to Nonemployee Share-Based Payment Accounting, which more closely aligns the accounting for employee and nonemployee stock-based compensation. Under the new standard, companies will no longer be required to value non-employee awards differently from employee awards. This accounting standard update will be effective beginning in the first quarter of fiscal 2019 using a modified retrospective approach. The Company anticipates that the new standard will not materially impact the Company's consolidated financial statements.

Use of Estimates

The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the periods presented. Actual results could differ from these estimates, and such differences may be material to the financial statements.

Reclassifications

Certain prior period amounts have been reclassified to conform to the current period presentation in the Company’s condensed consolidated financial statements and the accompanying notes to the condensed consolidated financial statements. The condensed consolidated statements of operations previously presented license fee revenue in combination with grants and collaborations revenue, and royalties (formerly referred to as “value share”) were previously presented in combination with renewable products revenue. Licenses and royalties revenue is presented as a separate line within the condensed consolidated statements of operations. The reclassifications reflect the growth in the Company’s business model of licensing its technology and earning royalties from customers utilizing the Company’s technology in the products it produces and sells. The reclassifications had no impact on total revenue.

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In the statements of cash flows, the prior period has been restated to reflect accounting standards changes for reporting (i) restricted cash, and (ii) debt extinguishment costs, in statements of cash flows.

2. Balance Sheet Details

Accounts Receivable, Net

Accounts receivable, net is comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable	$	9,567	$	18,953
Related party accounts receivable		17,247		5,328
	$	26,814	$	24,281

Inventories

Inventories are stated at the lower of cost or net realizable value and are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Raw materials	$	823	$	819
Work-in-process		1,147		364
Finished goods		4,662		4,225
Inventories	$	6,632	$	5,408

Property, Plant and Equipment, Net

Property, plant and equipment, net is comprised of the following:

(In thousands)	June 30, 2018			December 31, 2017
Machinery and equipment	$	46,755		$	49,277
Leasehold improvements		40,571			40,036
Computers and software		10,497			9,555
Furniture and office equipment, vehicles and land		3,463			3,415
Construction in progress		18,583			17,438
		119,869			119,721
Less: accumulated depreciation and amortization		(104,569	)		(105,829	)
Property, plant and equipment, net	$	15,300		$	13,892

Property, plant and equipment, net includes $4.8 million and $4.2 million of machinery and equipment under capital leases as of June 30, 2018 and December 31, 2017, respectively. Accumulated amortization of assets under capital leases totaled $1.9 million and $1.6 million as of June 30, 2018 and December 31, 2017, respectively.

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During the three and six months ended June 30, 2018, the Company capitalized $1.2 million and $1.6 million, respectively, of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use.

Depreciation and amortization expense, including amortization of assets under capital leases, was $1.4 million and $2.7 million for the three months ended June 30, 2018 and 2017, respectively, and $2.9 million and $5.6 million for the six months ended June 30, 2018 and 2017, respectively.

Other Assets

Other assets are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Contingent consideration	$	8,151	$	8,151
Prepaid royalty		7,285		7,409
Deposits		3,662		2,462
Equity investment in SweeGen		3,570		3,233
Goodwill		560		560
Other		1,519		825
Other assets	$	24,747	$	22,640

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Payroll and related expenses	$	7,074	$	7,238
Accrued interest		2,325		8,213
SMA relocation accrual		3,417		3,587
Tax-related liabilities		2,305		5,837
Professional services		1,400		1,894
Other		3,580		2,633
Total accrued and other current liabilities	$	20,101	$	29,402

3. Fair Value Measurement

Assets and Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize assets and liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

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(In thousands)	June 30, 2018								December 31, 2017
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Money market funds	$	—	$	—	$	—	$	—	$	53,199	$	—	$	—	$	53,199
Certificates of deposit		130		—		—		130		7,813		—		—		7,813
Equity investment in SweeGen		—		3,570		—		3,570		—		—		—		—
Total assets measured and recorded at fair value	$	130	$	3,570	$	—	$	3,700	$	61,012	$	—	$	—	$	61,012
Liabilities
Embedded derivatives in connection with the issuance of debt and equity instruments	$	—	$	—	$	6,560	$	6,560	$	—	$	—	$	4,203	$	4,203
Freestanding derivative instruments in connection with the issuance of equity instruments		—		—		132,135		132,135		—		—		115,775		115,775
Total liabilities measured and recorded at fair value	$	—	$	—	$	138,695	$	138,695	$	—	$	—	$	119,978	$	119,978

There were no transfers between levels during the periods presented.

Equity Investment in SweeGen

The Company holds 850,115 unregistered shares of SweeGen, Inc. common stock received as payment in connection with a December 2016 revenue agreement between the Company and Phyto Tech Corp. (d/b/a Blue California). At June 30, 2018, the fair value of the shares was $3.6 million, determined based on the over-the-counter market (OTCMKTS) trading price of the SweeGen shares (Level 2). For the three and six months ended June 30, 2018, the Company recorded unrealized gains of $1.4 million and $1.7 million, respectively, for changes in fair value of the shares. The Company adopted ASU 2016-01 on January 1, 2018 and now accounts for its equity investment in SweeGen at fair value, with changes in fair value recognized in net income; see "Recent Accounting Pronouncements" in Note 1, “Basis of Presentation and Summary of Significant Accounting Policies” above. The fair value of the SweeGen shares is included in Other Assets in the condensed consolidated balance sheets.

Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt and equity instruments, measured at fair value using significant unobservable inputs (Level 3):

(In thousands)	Equity-related Derivative Liability			Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2017	$	112,368		$	7,610	$	119,978
Loss from change in fair value of derivative liabilities		34,650			6,709		41,359
Derecognition upon extinguishment of derivative liabilities		(22,642	)		—		(22,642	)
Balance at June 30, 2018	$	124,376		$	14,319	$	138,695

The derivative liabilities recognized in connection with the issuance of equity and debt instruments represent the fair value of the make-whole provisions of the Series A and B Preferred Stock as well as the cash and anti-dilution warrants issued concurrently with the Series A, B and D Preferred Stock (see Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 10-K), and conversion options, conversion price adjustment features and down round provisions associated with the R&D Note, Temasek Funding Warrant, Tranche Notes, 2014 144A Notes and 2015 144A Notes (see Note 4, “Debt” and Note 6, "Stockholders' Deficit" in Part II, Item 8 of the 10-K).

The market-based assumptions and estimates used in applying a Monte Carlo simulation approach and Black-Scholes-Merton option value approach for valuing the derivative liabilities in connection with debt and equity instruments include amounts in the following ranges and amounts:

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	June 30, 2018			June 30, 2017
Risk-free interest rate	1.97%	-	2.85%	1.68%	-	2.40%
Risk-adjusted yields	15.10%	-	25.23%	18.40%	-	28.53%
Stock price volatility	45%	-	75%	45%	-	80%
Probability of change in control	0%	-	5%		5%
Stock price		$6.39			$3.75
Credit spread	12.96%	-	22.98%	16.63%	-	26.70%
Estimated conversion dates	2018	-	2025	2018	-	2025

The valuation of the embedded derivatives in connection with the issuance of debt and equity instruments and freestanding derivative instruments in connection with the issuance of equity instruments can be significantly affected by changes in valuation assumptions. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. A third-party valuation specialist assisted in determining estimates of fair value.

See Note 6, "Stockholders' Deficit", for more information about the derecognition upon extinguishment of derivative liabilities in connection with the April 2018 warrants exercise.

Changes in Fair Value

Changes in the fair value of assets or liabilities measured at fair value on a recurring basis are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable, credit facilities and convertible notes are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of loans payable and credit facilities using observable market-based inputs (Level 2) and estimates the fair value of convertible notes based on rates currently offered for instruments with similar maturities and terms (Level 3). The fair values and carrying values of the Company's debt were as follows:

(In thousands)	June 30, 2018				December 31, 2017
	Fair Value		Carrying Value		Fair Value		Carrying Value
Total debt	$	165,844	$	171,402	$	156,900	$	165,377

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4. Debt

Net carrying amounts of debt are as follows:

	June 30, 2018								December 31, 2017
(In thousands)	Principal		Unamortized Debt Discount			Net Balance			Principal		Unamortized Debt Discount			Net Balance
Nonrelated Party
Convertible notes
2015 Rule 144A convertible notes	$	37,887	$	(4,576	)	$	33,311		$	37,887	$	(6,872	)	$	31,015
2014 Rule 144A convertible notes		24,004		(2,023	)		21,981			24,004		(3,170	)		20,834
December 2017 convertible note		—		—			—			5,000		(25	)		4,975
August 2013 financing convertible notes		4,416		(2,541	)		1,875			4,009		(2,918	)		1,091
		66,307		(9,140	)		57,167			70,900		(12,985	)		57,915
Loans payable and credit facilities
GACP term loan facility		36,000		(1,596	)		34,404			—		—			—
Senior secured loan facility		—		—			—			28,566		(253	)		28,313
Ginkgo notes		12,000		(4,599	)		7,401			12,000		(4,983	)		7,017
Other loans payable		5,696		(1,234	)		4,462			6,463		(1,277	)		5,186
Other credit facilities		195		—			195			381		—			381
		53,891		(7,429	)		46,462			47,410		(6,513	)		40,897
Subtotal nonrelated party		120,198		(16,569	)		103,629			118,310		(19,498	)		98,812
Related Party
Related party convertible notes
August 2013 financing convertible notes		23,199		432			23,631			21,711		897			22,608
2014 Rule 144A convertible notes		24,705		(2,423	)		22,282			24,705		(3,784	)		20,921
R&D note		3,700		—			3,700			3,700		(18	)		3,682
		51,604		(1,991	)		49,613			50,116		(2,905	)		47,211
Related party loans payable
DSM note		25,000		(6,896	)		18,104			25,000		(8,039	)		16,961
Other DSM loan		56		—			56			393		—			393
February 2016 private placement		—		—			—			2,000		—			2,000
		25,056		(6,896	)		18,160			27,393		(8,039	)		19,354
Subtotal related party		76,660		(8,887	)		67,773			77,509		(10,944	)		66,565
Total debt		196,858		(25,456	)		171,402			195,819		(30,442	)		165,377
Less: current portion							(109,656	)							(56,943	)
Long-term debt, net of current portion						$	61,746							$	108,434

During the six months ended June 30, 2018, aside from debt payments (including payments-in-kind), the following debt transactions occurred:

• Senior Secured Loan Facility Repayment: On June 29, 2018, the Company repaid in full the $27.3 million outstanding principal balance owed under the Senior Secured Loan Facility.

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• GACP Term Loan Facility: On June 29, 2018, the Company, certain of the Company’s subsidiaries and GACP Finance Co., LLC (GACP) entered into a Loan and Security Agreement (the LSA) to borrow $36.0 million (the GACP Term Loan Facility). The LSA also provides for an incremental secured term loan facility in an aggregate principal amount of up to $35.0 million (the Incremental GACP Term Loan Facility and, together with the GACP Term Loan Facility, the GACP Term Loan Facilities), subject to certain conditions and approvals, to fund the construction of a custom-built manufacturing facility in Brazil. The majority of the net proceeds from the GACP Term Loan Facility were used to repay all amounts outstanding under the Senior Secured Loan Facility between the Company and Stegodon. The remaining net proceeds were used on July 2, 2018 to repay amounts outstanding under the R&D Note at maturity.   Loans under the GACP Term Loan Facilities have a maturity date of July 1, 2021; provided, that if the Company has not (i) met certain financial conditions on or prior to January 7, 2019 or (ii) refinanced the 2015 144A Notes and 2014 144A Notes with indebtedness that has a maturity date which is later than July 1, 2021 or converted such notes into equity prior to January 12, 2019, then the maturity date will be January 12, 2019. The GACP Term Loan Facilities will amortize beginning on July 1, 2019 in quarterly installments equal to 2.5% of the original loan amounts, with the remaining principal balance payable on the maturity date. Loans under the GACP Term Loan Facilities will accrue interest at a rate per annum equal to the sum of (i) the greater of (A) the U.S. prime rate as reported in the Wall Street Journal and (B) 4.0%, plus (ii) 6.25%, payable monthly. The GACP Term Loan Facilities are guaranteed by the subsidiaries of the Company party to the LSA and collateralized by first-priority liens on substantially all the Company’s and such subsidiaries’ assets, including intellectual property, subject to certain exceptions. The LSA includes customary terms, covenants and restrictions, including mandatory prepayments upon the occurrence of certain events, including asset sales, casualty events, incurrence of additional indebtedness and borrowing base deficiencies, subject to certain exceptions and reinvestment rights. The LSA contains three financial covenants: minimum revenue, liquidity and asset coverage ratio.   The Company paid origination fees at closing equal to 4%, or $1.4 million, of the funded amount of the GACP Term Loan Facility and other closing costs totaling $0.2 million, plus an agency fee of $25,000 per quarter during the term of the GACP Term Loan Facilities. The $1.6 million of issuance costs will be amortized using the effective interest method over the expected 3-year loan term.

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of June 30, 2018 are as follows:

Years ending December 31 (In thousands)	Convertible Notes			Loans Payable			Credit Facilities			Related Party Convertible Notes			Related Party Loans Payable			Total
2018 (remaining six months)	$	2,580		$	3,323		$	1,878		$	4,503		$	1,306		$	13,590
2019		69,334			1,627			5,912			25,508			2,500			104,881
2020		—			1,626			7,289			—			2,500			11,415
2021		—			1,627			32,551			—			27,500			61,678
2022		—			13,417			—			—			—			13,417
Thereafter		—			2,528			—			—			—			2,528
Total future minimum payments		71,914			24,148			47,630			30,011			33,806			207,509
Less: amount representing interest		(5,160	)		(6,453	)		(11,434	)		(1,606	)		(8,750	)		(33,403	)
Add: amount mandatorily convertible into common stock upon maturity		—			—			—			24,802			—			24,802
Less: future interest accruals to be converted to principal		(447	)		—			—			(1,603	)		—			(2,050	)
Present value of minimum debt payments		66,307			17,695			36,196			51,604			25,056			196,858
Less: current portion of debt principal		(66,307	)		(2,714	)		(196	)		(51,604	)		(56	)		(120,877	)
Noncurrent portion of debt principal	$	—		$	14,981		$	36,000		$	—		$	25,000		$	75,981

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5. Mezzanine Equity

Mezzanine equity is comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Contingently redeemable common stock	$	5,000	$	5,000

Mezzanine equity at June 30, 2018 and December 31, 2017 is comprised of proceeds from shares of common stock sold on May 10, 2016 to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount not less than the proceeds from the stock sale to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party, the shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%.

6. Stockholders' Deficit

Warrants

In connection with various debt and equity transactions (see Note 4, "Debt" and Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 10-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrant activity for the six months ended June 30, 2018:

Transaction	Number Outstanding as of December 31, 2017		Additional Warrants Issued		Exercises			Number Outstanding as of June 30, 2018
July 2015 private placement		81,197		—		—			81,197
July 2015 related party debt exchange		2,082,010		—		—			2,082,010
February 2016 related party private placement		171,429		—		—			171,429
May 2017 warrants (Series A and B preferred stock)		18,042,568		—		(3,801,330	)		14,241,238
August 2017 DSM offering (Series B preferred stock)		3,968,116		—		—			3,968,116
August 2017 Vivo offering (Series D preferred stock)		5,575,118		—		—			5,575,118
Tranche 1 new cash warrants		—		3,616,174		—			3,616,174
Other		1,406		—		—			1,406
		29,921,844		3,616,174		(3,801,330	)		29,736,688

For the six months ended June 30, 2018, net proceeds were $14.5 million from the issuance of common stock upon exercise of 3,801,330 warrants.

Warrants Exercises and New Warrant Issuance

On April 12, 2018, certain holders of the May 2017 Warrants (see Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 10-K) exercised their May 2017 Cash Warrants to purchase 3,616,174 shares of common stock for net proceeds to the Company of $14.5 million and surrendered their May 2017 Dilution Warrants. Upon exercise of such May 2017 Cash Warrants and surrender of such May 2017 Dilution Warrants, certain derivative liabilities representing certain anti-dilution rights embedded in the May 2017 Warrants were effectively settled. Concurrent with the exercise of the May 2017 Cash Warrants and surrender of such May 2017 Dilution Warrants, the Company issued new warrants to these same holders to purchase 3,616,174 shares of common stock, exercisable at a price of $7.00 per share. The new warrants were fully exercisable upon issuance, with an expiration date of July 12, 2019. The new warrants do not provide the holders with anti-dilution protection. Consequently, the new warrants were treated as additional consideration to the May 2017 Warrant holders in exchange for their anti-dilution rights embedded in the original May 2017 Warrants. The Company used the Black-Scholes-Merton option pricing model to determine the fair value of the new warrants, which resulted in a fair value of $9.4 million. Black-Scholes-Merton input assumptions were as follows: volatility of 90%, risk-free rate of 2.16%, expected term of 1.25 years, expected dividend yield of $0, exercise price of $7.00, and Company stock price on issue date of $6.80. As a result of this exchange transaction, the Company recorded a $1.9 million net gain on the extinguishment of the related derivative liability during the three months ended June 30, 2018. This net gain was comprised of an $11.3 million gain on derecognition of the derivative liability and a $9.4 million loss on issuance of the new warrant.

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At Market Issuance Sales Agreement

On March 8, 2016, the Company entered into an At Market Issuance Sales Agreement (the ATM Sales Agreement) with FBR Capital Markets & Co. and MLV & Co. LLC (the Agents) under which the Company may issue and sell shares of its common stock having an aggregate offering price of up to $50.0 million (the ATM Shares) from time to time through the Agents, acting as its sales agents, under the Company's Registration Statement on Form S-3 (File No. 333-203216), effective April 15, 2015. Sales of the ATM Shares through the Agents may be made by any method that is deemed an "at the market offering" as defined in Rule 415 under the Securities Act of 1933, as amended, including by means of ordinary brokers' transactions at market prices, in block transactions, or as otherwise agreed by the Company and the Agents. The Company will pay the applicable Agent a commission rate of up to 3.0% of the gross proceeds from the sale of any ATM Shares sold through such Agent under the ATM Sales Agreement. The ATM Sales Agreement includes no commitment by other parties to purchase ATM Shares the Company offers for sale.

During the three and six months ended June 30, 2018, the Company issued and sold 191,639 and 205,168 shares of common stock under the ATM Sales Agreement, at average prices of $6.91 and $6.90 per share, respectively, resulting in total net proceeds to the Company of $1.4 million. The ATM Sales Agreement expired on April 15, 2018, and as a result, zero remained available for issuance under the ATM Sales Agreement as of June 30, 2018.

7. Variable-interest Entities and Unconsolidated Investments

Consolidated Variable-interest Entity

The table below reflects the carrying value of the Aprinnova JV's (see Note 7, “Variable-interest Entities and Unconsolidated Investments” in Part II, Item 8 of the 10-K) assets and liabilities, for which the Company is the primary beneficiary at June 30, 2018:

(In thousands)	June 30, 2018		December 31, 2017
Assets	$	37,133	$	36,781
Liabilities	$	1,873	$	3,187

The Aprinnova JV's creditors have recourse only to the assets of the Aprinnova JV.

During the three and six months ended June 30, 2018 and 2017, there was no activity in noncontrolling interest.

Unconsolidated Investments

The Company's unconsolidated investments are summarized as follows:

				Carrying Value of Investment on Condensed Consolidated Balance Sheets
(Amounts in thousands)	Amyris Equity Ownership %			June 30, 2018		December 31, 2017
Equity-method investments:
Novvi LLC		20	%	$	—	$	—
Total Amyris BioSolutions B.V.		25	%	$	—	$	—
Other unconsolidated equity investment:
SweeGen, Inc.		3	%	$	3,570	$	3,233

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8. Net Loss per Share Attributable to Common Stockholders

For the three months ended June 30, 2017 and the six months ended June 30, 2018 and June 30, 2017, basic net loss per share attributable to common stockholders was the same as diluted net loss per share attributable to common stockholders because the inclusion of all potentially dilutive securities outstanding was antidilutive. For the three months ended June 30, 2018, income was allocated to participating Series B and Series D preferred shares, as they participate in profits. As the adjustments to net income due to the presumed conversion of dilutive securities created a net loss position for the three months ended June 30, 2018 on a diluted basis, there was no allocation to participating securities for diluted EPS, as the participating securities do not participate in losses.

The following table presents the calculation of basic and diluted net loss per share attributable to common stockholders:

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2018			2017			2018			2017
Numerator:
Net income (loss) attributable to Amyris, Inc.	$	1,533		$	620		$	(89,963	)	$	(36,751	)
Less deemed dividend on capital distribution to related parties		—			(8,648	)		—			(8,648	)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		—			(562	)		—			(562	)
Less cumulative dividends on Series A and B preferred stock		(399	)		(1,675	)		(794	)		(1,675	)
Less earnings allocated to participating securities		(67	)		—			—			—
Net income (loss) attributable to Amyris, Inc. common stockholders, basic		1,067			(10,265	)		(90,757	)		(47,636	)
Earnings allocated to participating securities		67			—			—			—
Gain from change in fair value of dilutive common stock warrants		(13,421	)		—			—			—
Interest on dilutive convertible debt		357			—			—			—
Accretion of debt discount		(99	)		—			—			—
Gain from change in fair value of derivative instruments		(5,765	)		—			—			—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(17,794	)	$	(10,265	)	$	(90,757	)	$	(47,636	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic		54,932,411			23,155,874			53,076,975			21,226,013
Basic income (loss) per share	$	0.02		$	(0.44	)	$	(1.71	)	$	(2.24	)
Weighted-average shares of common stock outstanding		54,932,411			23,155,874			53,076,975			21,226,013
Effect of dilutive convertible debt		2,709,323			—			—			—
Effect of dilutive common stock warrants		3,088,002			—			—			—
Weighted-average common stock equivalents used in computing net loss per share of common stock, diluted		60,729,736			23,155,874			53,076,975			21,226,013
Diluted loss per share	$	(0.29	)	$	(0.44	)	$	(1.71	)	$	(2.24	)

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The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been antidilutive:

	Three Months Ended June 30,				Six Months Ended June 30,
	2018		2017		2018		2017
Period-end stock options to purchase common stock		5,424,330		997,275		5,424,330		997,275
Convertible promissory notes (1)		5,695,615		6,270,734		8,390,819		6,270,734
Period-end common stock warrants		18,177,362		16,871,700		24,341,772		16,871,700
Period-end restricted stock units		5,211,584		666,336		5,211,584		666,336
Period-end preferred stock		4,053,905		-		4,053,905		-
Total potentially dilutive securities excluded from computation of diluted net loss per share		38,562,796		24,806,045		47,422,410		24,806,045

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

9. Commitments and Contingencies

Commitments

Future minimum payments under the Company's lease obligations as of June 30, 2018 are as follows (in thousands):

Years ending December 31: (In thousands)	Capital Leases			Operating Leases		Total Lease Obligations
2018 (remaining six months)	$	424		$	4,941	$	5,365
2019		451			8,755		9,206
2020		125			7,017		7,142
2021		—			7,241		7,241
2022		—			7,414		7,414
Thereafter		—			3,281		3,281
Total future minimum payments	$	1,000		$	38,649	$	39,649
Less: amount representing interest		(49	)
Present value of minimum lease payments		951
Less: current portion		(583	)
Long-term portion	$	368

Guarantor Arrangements

In November 2010, the Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel; see Note 4, "Debt" in Part II, Item 8 of the 10-K. The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee as of June 30, 2018 and December 31, 2017 was R$6.0 million (US$1.6 million and US$1.8 million, respectively) based on exchange rates at each date.

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note 13, “Divestiture” in Part II, Item 8 of the 10-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

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The Company and a number of the Company’s current officers and directors are parties to four separate purported shareholder derivative complaints based on allegedly misleading statements and/or omissions made in connection with the Company’s securities filings (the Derivative Complaints). The Derivative Complaints seek to recover, on the Company's behalf, unspecified damages purportedly sustained by the Company and also seek a series of changes to the Company’s corporate governance policies, restitution to the Company from the individual defendants, and an award of attorneys’ fees. Two of the Derivative Complaints were filed in the U.S. District Court for the Northern District of California (together, the Federal Derivative Cases). On December 21, 2017, the defendants filed a motion to dismiss the Federal Derivative Cases, which was granted on March 9, 2018. On March 29, 2018, the plaintiffs filed an amended complaint, and on May 4, 2018 the defendants filed a motion to dismiss the amended complaint. On July 23, 2018, the court granted defendants’ motion to dismiss the amended complaint with prejudice and entered judgment in favor of the defendants. The remaining two Derivative Complaints were filed in the Superior Court for the State of California and are in the initial pleadings stage. The Company believes the Derivative Complaints lack merit and intends to continue to defend itself vigorously. Given the early stage of these proceedings, it is not yet possible to reliably determine any potential liability that could result from this matter. See Part II, Item 1, “Legal Proceedings” in this Quarterly Report on Form 10-Q for more details.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management's expectations, the Company's consolidated financial statements for the relevant reporting period could be materially adversely affected.

10. Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

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	Three Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	2,339	$	—	$	4,624	$	6,963	$	1,902	$	2,663	$	7,379	$	11,944
Europe		2,987		6,887		4,314		14,188		749		202		2,786		3,737
Asia		1,113		—		—		1,113		7,161		2,632		125		9,918
South America		194		—		736		930		80		—		—		80
Other		—		—		—		—		—		—		—		—
	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892	$	5,497	$	10,290	$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	4,301	$	—	$	5,832	$	10,133	$	2,998	$	2,673	$	9,369	$	15,040
Europe		5,421		18,324		7,815		31,560		3,307		446		5,359		9,112
Asia		1,791		—		1,000		2,791		11,468		2,633		251		14,352
South America		215		—		1,393		1,608		144		—		—		144
Other		100		—		—		100		12		—		—		12
	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Significant Revenue Agreements

In connection with significant revenue agreements (also see Note 10, “Significant Revenue Agreements” in Part II, Item 8 of the 10-K), the Company recognized the following revenues for the three and six months ended June 30, 2018 and 2017:

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	Three Months Ended June 30,
(In thousands)	2018									2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total			Renewable Products			Licenses and Royalties			Grants and Collaborations			Total
DSM - related party	$	—	$	6,887	$	1,737	$	8,624		$	—		$	—		$	149		$	149
Givaudan		2,109		—		1,358		3,467			—			—			1,500			1,500
Firmenich		—		—		1,219		1,219			—			202			2,137			2,339
Nenter		—		—		—		—			4,016			2,633			—			6,649
DARPA		—		—		4,191		4,191			—			—			4,671			4,671
Subtotal revenue from significant revenue agreements		2,109		6,887		8,505		17,501			4,016			2,835			8,457			15,308
Revenue from all other customers		4,524		—		1,169		5,693			5,876			2,662			1,833			10,371
Total revenue from all customers	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892		$	5,497		$	10,290		$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	—	$	18,287	$	3,127	$	21,414	$	—	$	—	$	149	$	149
Givaudan		3,184		—		2,859		6,043		619		—		3,000		3,619
Firmenich		207		37		2,486		2,730		998		446		3,211		4,655
Nenter		—		—		1,000		1,000		6,324		2,633		—		8,957
DARPA		—		—		5,038		5,038		—		—		5,642		5,642
Subtotal revenue from significant revenue agreements		3,391		18,324		14,510		36,225		7,941		3,079		12,002		23,022
Revenue from all other customers		8,437		—		1,530		9,967		9,988		2,673		2,977		15,638
Total revenue from all customers	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional. Contract assets are presented as Unbilled Receivables on the consolidated balance sheets.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has not passed to the customer. Contract liabilities are presented as deferred revenue on the consolidated balance sheets.

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Trade receivables related to revenue from contracts with customers are included in accounts receivable on the consolidated balance sheets, net of the allowance for doubtful accounts. Trade accounts receivable are recorded at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company for sale of goods or the performance of services.

Contract Balances

The following table provides information about unbilled receivables, deferred revenue, and accounts receivable from contracts with customers:

(In thousands)	June 30, 2018			December 31, 2017
Unbilled receivable, current	$	12,683		$	9,340
Unbilled receivable, noncurrent	$	9,747		$	7,940
Deferred revenue, current	$	9,643		$	4,880
Deferred revenue, noncurrent	$	383	(1)	$	383	(1)
Accounts receivable, net	$	26,814		$	24,281

⁽¹⁾     As of June 30, 2018 and December 31, 2017, deferred revenue, noncurrent is presented in Other Noncurrent Liabilities in the consolidated balance sheets because of its insignificance.

Unbilled receivables, current, as of June 30, 2018 relate to satisfied performance obligations that the Company has not invoiced to the customer and, as of December 31, 2017, primarily relate to the Company’s right to consideration from DSM for minimum future royalties which the Company received cash of $9,250,000 during the three months ended June 30, 2018. Unbilled receivables, noncurrent, relate to the Company’s right to consideration from DSM for minimum future royalties. The Company’s right to cash receipt for these minimum royalty amounts occurs on or before December 31, 2019.

Deferred revenue, current increased by $4.8 million at June 30, 2018 resulting from a $0.8 million increase upon adoption of ASC 606 on January 1, 2018 plus the net amount of collaboration and royalty revenues invoiced in excess of amounts recognized as revenue, less $3.3 million of revenue recognized during the six months ended June 30, 2018 that was included in deferred revenue at the beginning of the period.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of June 30, 2018.

(In thousands)	June 30, 2018
Remaining 2018	$	4,032
2019		6,338
2020		6,338
2021 and thereafter		572
Total from all customers	$	17,280

In accordance with the disclosure provisions of ASC 606, the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of one year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, approximately $12.4 million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

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11. Related Party Transactions

Related Party Debt

See Note 4. Debt, for related party debt balances as of June 30, 2018 and December 31, 2017.

Related Party Accounts Receivable and Unbilled Receivables

Related party accounts receivable and unbilled receivables as of June 30, 2018 and December 31, 2017 were as follows:

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable, net:
DSM	$	15,829	$	3,483
Novvi		472		1,607
Total		384		238
	$	16,685	$	5,328
Unbilled receivable, current:
DSM	$	12,683	$	9,340
Unbilled receivable, noncurrent:
DSM	$	9,747	$	7,940

Related Party Joint Ventures

See Note 7, "Variable-interest Entities and Unconsolidated Investments" above and in Part II, Item 8 of the 10-K for information about the Company's:

• Aprinnova joint venture with Nikko, and

• TAB joint venture with Total

12. Stock-based Compensation

The Company’s stock option activity and related information for the six months ended June 30, 2018 was as follows:

	Quantity of Stock Options			Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years		Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2017		1,338,367		$	33.40		7.7	$	97
Granted		4,192,476		$	5.12
Exercised		(43,055	)	$	3.68
Forfeited or expired		(63,458	)	$	29.29
Outstanding - June 30, 2018		5,424,330		$	11.83		9.2	$	8,541
Vested or expected to vest after June 30, 2018		4,981,859		$	12.42		9.2	$	7,790
Exercisable at June 30, 2018		949,237		$	42.07		6.7	$	1,119

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The Company’s restricted stock units (RSUs) activity and related information for the six months ended June 30, 2018 was as follows:

	Quantity of Restricted Stock Units			Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2017		683,554		$	8.62		1.40
Awarded		4,712,787		$	5.27
RSUs released		(144,572	)	$	11.18
RSUs forfeited		(37,879	)	$	7.01
Outstanding - June 30, 2018		5,213,890		$	5.53		2.03
Vested or expected to vest after June 30, 2018		4,927,426		$	5.54		2.00

Stock-based compensation expense related to options and RSUs granted to employees and non-employees during the three and six months ended June 30, 2018 and 2017 was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Research and development	$	333	$	441	$	696	$	925
Sales, general and administrative		1,567		597		2,482		1,759
Total stock-based compensation expense	$	1,900	$	1,038	$	3,178	$	2,684

As of June 30, 2018, there was unrecognized compensation expense of $36.0 million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of 3.7 years.

The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,						Six Months Ended June 30,
	2018			2017			2018			2017
Expected dividend yield		—	%		—	%		—	%		—	%
Risk-free interest rate		2.7	%		1.8	%		2.7	%		1.8	%
Expected term (in years)		6.86			5.38			6.85			5.38
Expected volatility		79.6	%		85.7	%		79.7	%		85.7	%

In May 2018, shareholders approved amendments to the Company's 2010 Equity Incentive Plan (EIP) to (i) increase the number of shares of common stock available for grant and issuance thereunder by 9 million shares and (ii) increase the annual per-participant award limit thereunder to 4 million shares.

Also in May 2018, shareholders approved an amendment to the Company's 2010 Employee Stock Purchase Plan (ESPP) to increase the maximum number of shares of common stock that may be issued over the term of the ESPP by 1 million shares.

In May 2018, the Company granted its chief executive officer performance-based stock options (PSOs) to purchase 3,250,000 shares. PSOs are equity awards with the final number of PSOs that may vest determined based on the Company’s performance against pre-established EBITDA milestones and Amyris stock price milestones. The EBITDA milestones are measured from the grant date through December 31, 2021, and the stock price milestones are measured from the grant date through December 31, 2022. The PSOs vest in four tranches contingent upon the achievement of both the EBITDA milestones and stock price milestones for each respective tranche, and the chief executive officer’s continued employment with the Company. Over the measurement periods, the number of PSOs that may be issued and the related stock-based compensation expense that is recognized is adjusted upward or downward based upon the probability of achieving the EBITDA milestones. Depending on the probability of achieving the EBITDA milestones and stock price milestones and certification of achievement of those milestones for each vesting tranche by the Company’s Board of Directors or Compensation Committee, the PSOs issued could be from zero to 3,250,000 stock options, with an exercise price of $5.08 per share.

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Stock-based compensation expense for this award will be recognized using a graded-vesting approach over the service period beginning at the grant date thru December 31, 2022, as the Company’s management has determined that certain EBITDA milestones are probable of achievement as of June 30, 2018, The Company utilized a Monte Carlo simulation model to estimate the grant date fair value of each tranche of the award which totaled $5.1 million. Approximately, $0.1 million of compensation expense was recognized for this award for the three and six months ended June 30, 2018. The assumptions used to estimate the fair value of this award with performance and market vesting conditions were as follows:

Stock Option Award with Performance and Market Vesting Conditions
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility		70	%
Risk-free interest rate		2.75	%
Dividend yield		0.0	%

13. Subsequent Events

R&D Note Repayment

On July 2, 2018, the Company repaid the R&D Note (see Note 4, "Debt" above and Note 4, "Debt" and Note 18, “Subsequent Events” in Part II, Item 8 of the 10-K) in full at maturity. The principal amount was $3.7 million.

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ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis should be read in conjunction with our condensed consolidated financial statements and the related notes that appear elsewhere in this Quarterly Report on Form 10-Q. These discussions contain forward-looking statements reflecting our current expectations that involve risks and uncertainties which are subject to safe harbors under the Securities Act of 1933, as amended (the Securities Act), and the Securities Exchange Act of 1934 (the Exchange Act). These forward-looking statements include, but are not limited to, statements concerning our strategy of achieving a significant reduction in net cash outflows in 2018 and 2019, aspects of our future operations, our future financial position, including the expected extension of debt maturities and obtaining project financing for a new manufacturing facility, revenues and projected costs, expectations regarding demand and acceptance for our technologies, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item 1A, “Risk Factors” in this Quarterly Report on Form 10-Q, in Part I, Item 1A, “Risk Factors” in our Annual Report on Form 10-K for the fiscal year ended December 31, 2017 and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

Overview and Recent Developments

Amyris, Inc. (the Company, Amyris, we, us or our) is a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably sourced products into the Health & Wellness, Clean Beauty, and Flavors & Fragrances markets. Our proven technology platform enables us to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. We have successfully used our technology to develop and produce seven distinct molecules at commercial volumes.

We believe that industrial biotechnology represents a third industrial revolution, bringing together biology and engineering to generate new, more sustainable materials to meet the growing global demand for bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We continue to build demand for our current portfolio of products through an extensive sales network provided by our collaboration partners that represent the leading companies in the world for our target market sectors. We also have a small group of direct sales and distributors who support our Clean Beauty market. Via our partnership model, our partners invest in the development of each molecule to bring it from the lab to commercial scale and use their extensive sales force to sell our ingredients and formulations to their customers as part of their core business. We capture long-term revenue both through the production and sale of the molecule to our partners and through royalty revenues (previously referred to as value share) from our partners' product sales to their customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic acid, which is a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free licenses to allow Sanofi-Aventis to produce artemisinic acid using our technology. Building on our success with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell sustainable alternatives to a broad range of markets.

We focused our initial development efforts primarily on the production of Biofene®, our brand of renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through fermentation using engineered microbes. Our farnesene derivatives are sold in more than 1,000 products as nutraceuticals, skincare products, fragrances, solvents, polymers, and lubricant ingredients. The commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development process in the lab and drive manufacturing costs down. This investment has enabled our technology platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began manufacturing additional molecules for the Flavors & Fragrances industry; in 2015 we began investing to expand our capabilities to other small molecule chemical classes beyond terpenes via our collaboration with the Defense Advanced Research Projects Agency (DARPA), and in 2016 we expanded into proteins.

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We have invested over $500 million in infrastructure and technology to create microbes that produce molecules from sugar or other feedstocks at commercial scale. This platform has been used to design, build, optimize, and upscale strains producing seven distinct molecules, leading to more than 15 commercial ingredients used in over 1,000 consumer products. Our time to market for molecules has decreased from seven years to less than a year for our most recent molecule, mainly due to our ability to leverage the technology platform we have built.

Our technology platform has been in active use since 2008 and has been integrated with our commercial production since 2011, creating an organism development process that we believe makes us an industry leader in the successful scale-up and commercialization of biotech-produced ingredients. The key performance characteristics of our platform that we believe differentiate us include our proprietary computational tools, strain construction tools, screening and analytics tools, and advanced lab automation and data integration. Having this fully integrated with our large scale manufacturing process and capability enables us to always engineer with the end specification and requirements guiding our technology. Our state-of-the-art infrastructure includes industry-leading strain engineering and lab automation located in Emeryville, California, pilot scale production facilities in Emeryville, California and Campinas, Brazil, a demonstration-scale facility in Campinas, Brazil and a commercial-scale production facility in Leland, North Carolina, which is owned and operated by our Aprinnova joint venture to convert our Biofene into squalane and other final products.

Several years ago, we made the strategic decision to transition our business model from collaborating and commercializing molecules in low margin commodity markets to higher margin specialty markets. We began the transition by first commercializing and supplying farnesene-derived squalene as a cosmetic ingredient sold to formulators and distributors. We also entered into collaboration and supply agreements for the development and commercialization of molecules within the Flavors & Fragrances and Cosmetic Ingredients markets where we utilize our strain generation technology to develop molecules that meet the customer’s rigorous specifications.

During this transition, we solidified the business model of partnering with our customers to create sustainable, high performing, low-cost molecules that replace an ingredient in their supply chain, commercially scale and manufacture those molecules, and share in the profits earned by our customers once our customer sells its product into these specialty markets. These three steps constitute our collaboration revenues, renewable product revenues, and royalty revenues (previously referred to as value share revenues).

During 2017, we completed several development agreements with DSM and others for new products such as Vitamin A, a human nutrition molecule and others. We plan to bring two to three new molecules a year to commercial production.

In the first half of 2017, management made the decision to monetize the use of one of our lower margin molecules, farnesene, in certain fields of use (e.g., the human and animal health and nutrition field) while retaining any associated royalties. We began discussions with our partners and ultimately made the decision to license farnesene to DSM for use in these fields, which we announced in November 2017. During the discussions with DSM, management also made the decision to sell to DSM our manufacturing facility, Brotas, which we completed on December 28, 2017.

Brotas 1 was built to batch manufacture one commodity product at a time (originally for high-volume production of biofuels, a business the Company has exited), which is an inefficient manufacturing process that is not suited for the high margin specialty markets in which we operate today. We currently manufacture nine specialty products and will be increasing the number of specialty products we manufacture by two to three products a year. The inefficiencies we experienced included having to idle the facility for two weeks at a time to prepare for the next product batch manufacture. These inefficiencies caused our cost of goods sold to be significantly higher. With the sale of Brotas 1, we expect that our gross margins will markedly improve due to the reduction in manufacturing costs caused by these inefficiencies. Additionally, we currently are constructing our new facility in Brazil, which will allow for the manufacture of five products concurrently and over 10 different products annually. Concurrent with the sale of Brotas 1, we contracted with DSM for the use of Brotas 1 to manufacture products for us to fulfill our product supply commitments to our customers until the new production facility is completed in 2019. In addition, in 2019, we plan to resume construction of a production facility in Pradópolis, Brazil that we partially built prior to 2013. This facility will support production of our alternative sweetener products.

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As discussed above, on December 28, 2017, we completed the sale of Amyris Brasil, which operated our Brotas 1 production facility, to DSM and concurrently entered into a series of commercial agreements and a credit agreement with DSM. At closing, we received $33.0 million in cash for the capital stock of Amyris Brasil, which is subject to certain post-closing working capital adjustments and reimbursements from DSM contingent on DSM’s utilization of certain Brazilian tax benefits it acquired with its purchase of Amyris Brasil. We used $12.6 million of the cash proceeds received to repay certain indebtedness of Amyris Brasil. The total fair value of the consideration in connection with the sales agreement for Amyris Brasil was $56.9 million and resulted in a pretax gain of $5.7 million from continuing operations.

Concurrent with the sale of Amyris Brasil, we entered into a series of commercial agreements with DSM including (i) a license agreement to DSM of its farnesene product for DSM to use in the Vitamin E, Lubricant, and Flavors & Fragrances specialty markets; (ii) a value share agreement that DSM will pay specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene under the Nenter Supply Agreement assigned to DSM; (iii) a performance agreement to perform research and development to optimize farnesene for production and sale of farnesene products; and (iv) a transition services agreement where we provide finance, legal, logistics, and human resource services to support the Brotas 1 facility under DSM ownership for a six-month period with a DSM option to extend for six additional months. At closing, DSM paid to us a nonrefundable license fee of $27.5 million and a nonrefundable minimum royalty revenue payment (previously referred to as value share) of $15.0 million. DSM will also pay the Company nonrefundable minimum royalty amounts in 2018 and 2019. The future nonrefundable minimum annual royalty payments were determined to be fixed and determinable with a fair value of $17.8 million, and were included as part of the total arrangement consideration subject to allocation of this overall multiple-element divestiture transaction. See Note 10, “Significant Revenue Agreements”, in our Annual Report on Form 10-K for the fiscal year ended December 31, 2017 (the 10-K) for a full listing and details of agreements entered into with DSM. Additionally, we entered into a $25.0 million credit agreement with DSM that we used to repay all outstanding amounts under the Guanfu Note; see Note 4, “Debt” in the 10-K.

In the second quarter of 2018, we successfully demonstrated our industrial process at full scale to produce a high-purity, zero calorie, natural sweetener from sugar cane. The molecule we are producing from sugar cane, Reb M, is recognized as the leading natural sweetener but is found in very limited quantities when derived from the Stevia plant and has many impurities from the Stevia plant that leave an unacceptable taste in the mouth of the consumer. The Reb M we produce from sugar cane is more sustainable, lower cost and has a specific technical profile that is advantaged in taste and total process economics for blends and formulations. Initial feedback on our samples has been very positive due to this unique sweetness profile and the lack of the undesired taste impact of Stevia plant sourced and other fermentation and bio transformation Reb products on the market. Our FDA Generally Regarded As Safe (GRAS) filing has been initiated and we will have commercial quantities of product produced at the Brotas facility by the end of the year.

In June 2018, we and our contract manufacturer, Antibióticos de León (“ADL”), executed an amendment to our January 2018 production agreement, thereby providing us additional tank capacity at ADL’s production facility in León, Spain. This amendment was necessary to provide additional, cost-effective manufacturing capability to meet higher than expected product demand from its partners. The amended agreement includes a commitment to running a certain number of batches at ADL’s production facility from the period September 1, 2018 through December 31, 2019 for up to four of our products.

On June 29, 2018, we closed a $36 million term loan with Great American Capital Partners, LLC (GACP), a subsidiary of B. Riley Capital Management, LLC, an SEC Registered Investment Advisor and wholly-owned subsidiary of B. Riley Financial, Inc. The term loan matures on July 1, 2021, subject to certain early maturity conditions. Cash proceeds from the term loan were used to pay off the Company’s senior secured loan facility with Stegodon and the related party R&D Note with Total Raffinage Chimie SA. The term loan also includes an additional $35 million accordion credit facility that provides us with another option for financing construction of a production facility, if necessary. See Note 4. Debt in the Condensed Consolidated Financial Statements included in Part I of this Form 10-Q for more information.

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In the second quarter of 2018, we executed an agreement for a significant project consortium in Europe with the Universidade Católica Portuguesa (UCP) Porto Campus and AICEP Portugal Global (AICEP). UCP is a university system, including the leading biotech school in Portugal, and operates 15 research centers. AICEP is an independent public entity of the Government of Portugal, focused in encouraging the best foreign companies to invest in Portugal. In conjunction with this agreement, we opened a subsidiary in Porto, Portugal. The primary purpose of this subsidiary is to conduct a research and development project together with Escola Superior de Biotecnologia o Universidade Católica Portuguese. This subsidiary will be the second R&D center of Amyris and will be responsible for certain areas of research, namely valorization of fermentation residues and wastes and the advancement of the Company's Artificial Intelligence (AI) and Informatics platform.

The overall multi-year project is valued up to approximately $50 million including investment funding and incentives allotted across the parties involved. Amyris believes this is the largest biotechnology grant ever awarded in Portugal and one of the largest ever approved by the AICEP for commercial applications. Amyris has sole responsibility for commercialization and majority ownership of all intellectual property (IP) generated.

Also in the second quarter of 2018, we announced plans to partner with BGI Genomics, one of the world’s largest genomics companies to apply our respective synthetic biology platforms in a new joint venture to discover, develop and commercialize human microbiome-targeting health and nutrition products in Greater China. The joint venture seeks to combine Amyris’ best-in-class science and technology with BGI’s gene sequencing expertise, data and analytics. The goal will be to develop health products for the Greater China market using natural products including traditional Chinese medicinal ingredients produced with sustainable resources and through Amyris’ proprietary clean fermentation capabilities.

Sales and Revenue

We recognize revenue from product sales, license fees and royalties, and grants and collaborations.

We have research and development collaboration arrangements for which we receive payments from our collaborators, which include The Defense Advanced Research Projects Agency (DARPA), affiliates of Koninklijke DSM N.V. (DSM), Firmenich SA (Firmenich), Givaudan International SA (Givaudan), and others. Some of our collaboration arrangements provide for advance payments to us in consideration for grants of exclusivity or research efforts that we will perform, and others require us to achieve milestones prior to receiving payments. In addition, all of our non-government partnerships include commercial terms for the supply of molecules we successfully upscale and produce at commercial volumes, and we expect such partnerships will contribute revenues from product sales and royalties (previously referred to as value share) if and when such molecules are commercialized. See Note 10, “Revenue Recognition” in Part I, Item 1 of this Quarterly Report on Form 10-Q, and Note 10, “Significant Revenue Agreements” in Part II, Item 8 of the 10-K for more details.

We are continuing to identify new opportunities to apply our technology and deliver sustainable access to key molecules. As a result, we have a pipeline that is expected to commercialize two to three new molecules each year over the coming years with a sweetener, and a flavor and a fragrance molecule expected to be commercialized in 2018. We are currently finalizing the commercial terms for the molecules we expect to commercialize in 2018, including our Reb-M product that is a superior sweetener and sugar replacement for food and beverages. We currently manufacture nine specialty products and will be increasing the number of specialty products we manufacture by two to three products a year.

As part of the DSM acquisition of our farnesene-for-Vitamin-E business, we will receive a royalty payment on all Nenter sales of Vitamin E utilizing farnesene produced and sold by DSM from our technology. DSM will pay us minimum royalties totaling $33 million for 2018, 2019 and 2020, the first three years of the agreement. These minimum royalty payments are creditable against future royalties due should the total royalties from Nenter not meet or exceed the minimum.

We have several other molecules in our development pipeline with partners including DSM, Givaudan and Firmenich that we expect will contribute revenues from product sales and royalties (previously referred to as value share) when they are commercialized.

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Critical Accounting Policies and Estimates

Management's discussion and analysis of results of operations and financial condition are based on the Company's consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the U.S. (U.S. GAAP). We believe that the critical accounting policies described in this section are those that significantly impact our financial condition and results of operations and require the most difficult, subjective or complex judgements, often as a result of the need to make estimates about the effects of matters that are inherently uncertain. Because of this uncertainty, actual results may vary from these estimates.

Our most critical accounting estimates include:

• recognition of revenue involving arrangements with multiple revenue-generating activities; and

• the valuation of financial instruments including embedded derivatives and freestanding financial instruments such as warrants, which impact gains or losses on derivatives, the carrying value of debt, preferred stock, interest expense and deemed dividends.

For more information about our critical accounting estimates and policies, see Note 1, "Basis of Presentation and Summary of Significant Accounting Policies" in Part I, Item 1 of this Quarterly Report on Form 10-Q and Part II, Item 8 of the 10-K.

Results of Operations

On August 6, 2018, we filed a Current Report on Form 8-K, Items 2.02 and 9.01, and a press release related to our unaudited preliminary financial results for the three and six months ended June 30, 2018.  In that Form 8-K, we disclosed total revenue of $24.8 million and $47.8 million for the three and six months ended June 30, 2018, respectively, and deferred revenue of $7.9 million as of June 30, 2018.  In the unaudited Condensed Consolidated Financial Statements presented in Part I, Item 1 of this Form 10-Q, we disclose total revenue of $23.2 million and $46.2 million for the three and six months ended June 30, 2018, respectively, and deferred revenue of $9.6 million as of June 30, 2018. We anticipate the increase in deferred revenue will be recognized in revenue over the next three quarters.

Revenue

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Revenue
Renewable products	$	6,633	$	9,892	$	11,828	$	17,929
Licenses and royalties		6,887		5,497		18,324		5,752
Grants and collaborations		9,674		10,290		16,040		14,979
Total revenue	$	23,194	$	25,679	$	46,192	$	38,660

Three Months Ended June 30, 2018 and 2017

Total revenue decreased by 10% to $23.2 million for the three months ended June 30, 2018, compared to the same period in 2017. The decrease was primarily due to a $3.3 million decrease in renewable products revenue due to discontinuing low margin product sales, partly offset by an increase in revenue from licenses and royalties. A $1.4 million increase in licenses and royalties revenue was due to royalty revenue from DSM, and a $0.6 million decrease in collaborations revenue was primarily due to Biogen.

Renewable products revenue decreased by 33% to $6.6 million for the three months ended June 30, 2018, compared to the same period in 2017. The decrease was attributable to the assignment of certain farnesene supply agreements to DSM and discontinuing low margin product sales, partly offset by increases in sales of our Biossance and Neossance products.

Licenses and royalties revenue increased by 25% to $6.9 million for the three months ended June 30, 2018, compared to the same period in 2017, due to royalty revenues from DSM.

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Grants and collaborations revenue decreased by 6% to $9.7 million for the three months ended June 30, 2018, compared to the same period in 2017, primarily due to no collaboration revenue from Biogen.

Six Months Ended June 30, 2018 and 2017

Total revenue increased by 19% to $46.2 million for the six months ended June 30, 2018, compared to the same period in 2017, primarily due to a $12.6 million increase in licenses and royalties revenue due to royalty revenue from DSM, and a $1.1 million increase in collaborations revenue, primarily from DSM.

Renewable products revenue decreased by 34% to $11.8 million for the six months ended June 30, 2018, compared to the same period in 2017. The decline was attributable to the assignment of certain farnesene supply agreements to DSM and discontinuing low margin product sales, partially offset by increases in sales of our Biossance and Neossance products.

Licenses and royalties revenue increased by 219% to $18.3 million for the six months ended June 30, 2018, compared to the same period in 2017, due to royalty revenues from DSM.

Grants and collaborations revenue increased by 7% to $16.0 million for the six months ended June 30, 2018, compared to the same period in 2017, primarily due to increases in collaboration revenues from DSM, partially offset by decreases from DARPA and Biogen.

Costs and Operating Expenses

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Cost and operating expenses
Cost of products sold	$	5,984	$	17,279	$	11,299	$	30,047
Research and development		15,287		14,249		34,100		28,956
Sales, general and administrative		20,189		15,949		38,946		28,799
Total cost and operating expenses	$	41,460	$	47,477		84,345	$	87,802

Cost of Products Sold

Cost of products sold includes the costs of raw materials, labor and overhead, amounts paid to contract manufacturers, inventory write-downs resulting from applying lower of cost or net realizable value inventory adjustments, and costs related to production scale-up. Because of our product mix, our overall cost of products sold does not necessarily increase or decrease proportionately with changes in our renewable product revenues.

Three Months Ended June 30, 2018 and 2017

Cost of products sold decreased by 65% to $6.0 million for the three months ended June 30, 2018, compared to the same period in 2017, primarily due to the (i) December 2017 sale of our Brotas production facility to DSM, which substantially reduced our fixed production costs, (ii) the assignment of certain farnesene supply agreements to DSM with a resulting 33% decrease in renewable products revenue, and (iii) our discontinuing manufacturing of low-margin products.

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Six Months Ended June 30, 2018 and 2017

Cost of products sold decreased by 62% to $11.3 million for the six months ended June 30, 2018, compared to the same period in 2017, primarily due to (i) December 2017 sale of our Brotas production facility to DSM, which substantially reduced our fixed production costs, (ii) the assignment of certain farnesene supply agreements to DSM with a resulting 34% decrease in renewable products revenue, and (iii) our discontinuing manufacturing of low-margin products.

Research and Development Expenses

Three Months Ended June 30, 2018 and 2017

Research and development expenses increased by 7% to $15.3 million for the three months ended June 30, 2018, compared to the same period in 2017, due to increases in headcount to support new product development and one-time costs related to product development. During the three months ended June 30, 2018, we capitalized $1.2 million of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use.

Six Months Ended June 30, 2018 and 2017

Research and development expenses increased by 18% to $34.1 million for the six months ended June 30, 2018, compared to the same period in 2017, due to increases in headcount to support new product development and one-time costs related to product development. During the six months ended June 30, 2018, we capitalized $1.6 million of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use.

Sales, General and Administrative Expenses

Three Months Ended June 30, 2018 and 2017

Sales, general and administrative expenses increased by 27% to $20.2 million for the three months ended June 30, 2018, compared to the same period in 2017, primarily due to increases in headcount to support our growth and expansion, and professional services costs.

Six Months Ended June 30, 2018 and 2017

Sales, general and administrative expenses increased by 35% to $38.9 million for the six months ended June 30, 2018, compared to the same period in 2017, primarily due to increases in headcount to support our growth and expansion, and professional services costs.

Other (Expense) Income, Net

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands)	2018			2017			2018			2017
Other income (expense)
Interest expense	$	(8,824	)	$	(9,303	)	$	(17,029	)	$	(21,486	)
Gain (loss) from change in fair value of derivative instruments		24,365			35,775			(39,548	)		38,114
Gain upon extinguishment of derivative liability		1,857			—			1,857			—
Loss upon extinguishment of debt		(26	)		(3,624	)		(26	)		(3,528	)
Other income (expense), net		2,427			(120	)		2,936			(440	)
Total other income (expense), net	$	19,799		$	22,728		$	(51,810	)	$	12,660

Three Months Ended June 30, 2018 and 2017

Total other income, net was $19.8 million for the three months ended June 30, 2018, compared to total other income, net of $22.7 million for the same period in 2017. The $2.9 million decrease was primarily due to an $11.4 million decrease in gain on change in fair value of derivative instruments, offset by the decrease in debt extinguishment loss and by increases in gain upon extinguishment of derivative liability associated with certain May 2017 warrant exercises and new warrant issuances that occurred in the second quarter 2018. Also offsetting the decrease was a mark-to-market gain of $1.4 million related to our equity investment in SweeGen, which in 2017 was carried at cost, and a foreign currency gain of $0.9 million. These gains are reflected in the Other income (expense), net line in the table above.

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Six Months Ended June 30, 2018 and 2017

Total other expense, net was $51.8 million for the six months ended June 30, 2018, compared to total other income, net of $12.7 million for the same period in 2017. The $64.5 million change was primarily due to a $39.5 million loss on change in fair value of derivative instruments in 2018, compared to a $38.1 million gain on change in fair value of derivative instruments in 2017. The loss from change in fair value of derivative instruments for the six months ended June 30, 2018 was the result of a significant increase in derivative instruments issued subsequent to March 31, 2017, and a 70% increase in our stock price during the six months ended June 30, 2018. This increase in loss was offset by decreases in interest expense due to a decrease in average debt balances and loss upon debt extinguishment, the gain upon extinguishment of derivative liability due to the warrant exchange that occurred in Q2 2018, a mark-to-market gain of $1.7 million related to our equity investment in SweeGen, which in 2017 was carried at cost, and a foreign currency gain of $1.1 million.

Provision for Income Taxes

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Provision for income taxes	$	—	$	310	$	—	$	269

Three Months Ended June 30, 2018 and 2017

For the three months ended June 30, 2018, we recorded a provision for income taxes of $0, and for the three months ended June 30, 2017, we recorded a provision for income taxes of $0.3 million. The provision for the three months ended June 30, 2017 consisted of an accrual of Brazilian withholding tax on intercompany interest, offset by an income tax benefit in continuing operations related to foreign exchange movement in other comprehensive income. Other than the above-mentioned amounts, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

Six Months Ended June 30, 2018 and 2017

For the six months ended June 30, 2018, we recorded a provision for income taxes of $0, and for the six months ended June 30, 2017, we recorded a provision for income taxes of $0.3 million. The provision for the six months ended June 30, 2017 consisted of an accrual of Brazilian withholding tax on intercompany interest, offset by an income tax benefit in continuing operations related to foreign exchange movement in other comprehensive income. Other than the above-mentioned amounts, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

Liquidity and Capital Resources

(In thousands)	June 30,  2018			December 31,  2017
Working capital deficit, excluding cash and cash equivalents and short-term investments	$	(105,944	)	$	(59,598	)
Cash and cash equivalents	$	14,050		$	57,059
Debt and capital lease obligations	$	172,353		$	166,318
Accumulated deficit	$	(1,298,914	)	$	(1,206,767	)

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	Six Months Ended June 30,
(In thousands)	2018			2017
Net cash provided by (used in):
Operating activities	$	(52,994	)	$	(60,179	)
Investing activities	$	(4,364	)	$	(349	)
Financing activities	$	13,279		$	37,939

Liquidity. We have incurred significant operating losses since our inception, and we expect to continue to incur losses and negative cash flows from operations through at least the next 12 months following issuance of the financial statements. As of June 30, 2018, we had negative working capital, excluding cash and cash equivalents and short-term investments, of $105.9 million, (compared to negative working capital (excluding cash) of $59.6 million as of December 31, 2017), an accumulated deficit of $1.3 billion, and cash and cash equivalents of $14.1 million (compared to $57.1 million as of December 31, 2017).

As of June 30, 2018, our debt (including related party debt), net of deferred discount and issuance costs of $25.5 million, totaled $171.4 million, of which $109.7 million is classified as current and $23.2 million is mandatorily convertible into equity and within our control. Our debt service obligations through August 31, 2019 are $114.5 million (excluding $23.2 million of principal that will be mandatorily converted into common stock upon maturity), including $15.8 million of anticipated cash interest payments. Our debt agreements contain various covenants, including certain restrictions on our business that could cause us to be at risk of defaults, such as restrictions on additional indebtedness and cross-default clauses. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of a substantial portion of our outstanding indebtedness.

Our consolidated financial statements as of and for the three months ended June 30, 2018 have been prepared on the basis that we will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. Due to the factors described above, there is substantial doubt about our ability to continue as a going concern within one year after the date that these financial statements are issued. Our ability to continue as a going concern will depend, in large part, on our ability to begin achieving positive cash flows from operations within the next 12 months, to extend existing debt maturities, which is uncertain, and to complete the mandatory conversion of certain debt obligations into equity, which conversion is within the control of the Company. The financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition. In addition, if we are unable to continue as a going concern, we may be unable to meet our obligations under our existing debt facilities, which could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and we may be forced to liquidate our assets. In such a scenario, the values we receive for our assets in liquidation or dissolution could be significantly lower than the values reflected in our financial statements.

Our operating plan for the next 12 months contemplates a significant reduction in our net cash outflows, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) significantly increased royalty revenues (previously referred to as value share revenues), (iii) reduced production costs as a result of anticipated efficiencies, and (iv) cash inflows from grants and collaborations. In addition, during the second half of 2018, we plan to obtain project financing for the construction of a new specialty ingredients manufacturing facility in Brazil.

If we are unable to generate sufficient cash contributions from product sales, licenses and royalties, and payments from existing and new collaboration partners, and new financing commitments due to contractual restrictions and covenants, we may need to obtain additional funding from equity or debt financings, which may not occur in a timely manner or on reasonable terms, if at all, agree to burdensome covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable.

If we do not achieve our planned operating results, our ability to continue as a going concern would be jeopardized and we may need to take the following actions to support our liquidity needs during the next 12 months:

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• Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts;

• Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors;

• Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects; and

• Closely monitor our working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

We expect to fund operations for the foreseeable future with cash and investments currently on hand, cash inflows from collaborations, grants, product sales, license and royalties and equity and debt financings, to the extent necessary. Some of our research and development collaborations are subject to risk that we may not meet milestones. Future equity and debt financings, if needed, are subject to the risk that we may not be able to secure financing in a timely manner or on reasonable terms, if at all. Our planned working capital and capital expenditure needs for the remainder of 2018 are dependent on significant inflows of cash from renewable product sales, license and royalties and existing collaboration partners, as well as additional funding from new collaborations.

For details, see the following Notes in “Notes to Condensed Consolidated Financial Statements” included in this Quarterly Report on Form 10-Q and/or in “Notes to Consolidated Financial Statements” included in the 10-K:

• Note 4, "Debt"

• Note 5, "Mezzanine Equity"

• Note 6, "Stockholders' Deficit"

Cash Flows during the Six Months Ended June 30, 2018 and 2017

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are costs related to the production and sale of our products and personnel-related expenditures, offset by cash received from renewable product sales, licenses and royalties, and grants and collaborations.

For the six months ended June 30, 2018, net cash used in operating activities was $53.0 million, consisting primarily of our $90.0 million net loss, partially offset by $49.9 million of non-cash adjustments that were primarily comprised of a $39.5 million loss on change in fair value of derivative instruments, $6.6 million of debt discount amortization, $3.2 million of stock-based compensation and $2.9 million of depreciation and amortization on property, plant and equipment. Additionally, there was a $13.0 million decrease in working capital.

For the six months ended June 30, 2017, net cash used in operating activities was $60.2 million consisting primarily of our $36.8 million net loss and a $2.0 million increase in working capital, partly offset by non-cash adjustments primarily comprised of a $38.1 million non-cash gain from the change in fair value of derivative instruments, $7.6 million of debt discount amortization and $5.6 million of depreciation and amortization on property, plant and equipment, and a $3.5 million loss on debt extinguishment.

Cash Flows from Investing Activities

Our investing activities consist primarily of capital expenditures and changes in short-term investments.

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For the six months ended June 30, 2018, net cash used in investing activities was $4.4 million, primarily comprised of purchases of property, plant and equipment, which included $1.6 million of capitalized internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use.

For the six months ended June 30, 2017, net cash used in investing activities was $0.3 million, primarily comprised of $0.3 million of purchases of property, plant and equipment.

Cash Flows from Financing Activities

For the six months ended June 30, 2018, net cash provided by financing activities was $13.3 million, primarily due to $34.6 million of net proceeds from debt issuance and $14.5 million of net proceeds from issuance of common stock upon the exercise of warrants, partly offset by $37.0 million of debt principal payments.

For the six months ended June 30, 2017, net cash provided by financing activities was $37.9 million, primarily due to $50.7 million of net proceeds from issuance of convertible preferred stock and $12.5 million of net proceeds from debt issuance, partly offset by $24.4 million of debt principal payments.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any material off-balance sheet arrangements, as defined under the rules of the Securities and Exchange Commission, such as relationships with unconsolidated entities or financial partnerships, which are often referred to as structured finance or special purpose entities, established for the purpose of facilitating financing transactions that are not required to be reflected on our condensed consolidated financial statements.

Contractual Obligations

The following is a summary of our contractual obligations as of June 30, 2018:

Year Ended December 31,  (In thousands)	Total		2018		2019		2020		2021		2022		Thereafter
Principal payments on debt (1)	$	174,106	$	6,492	$	93,545	$	3,830	$	55,843	$	12,255	$	2,141
Interest payments on debt (2)		33,402		7,098		11,336		7,584		5,835		1,162		387
Operating leases		38,649		4,941		8,755		7,017		7,241		7,414		3,281
Principal payments on capital leases		951		400		429		122		—		—		—
Interest payments on capital leases		49		25		22		2		—		—		—
Purchase obligations (3)		7,035		1,592		2,800		2,643		—		—		—
Total	$	254,192	$	20,548	$	116,887	$	21,198	$	68,919	$	20,831	$	5,809

____________________

⁽¹⁾ Principal payments on debt shown above include a total of $23.2 million in 2018 and 2019 subject to a Maturity Treatment Agreement, which will be converted to common stock at maturity, subject to there being no default under the terms of the debt.

⁽²⁾ Does not include any obligations related to make-whole interest or down-round provisions. The fixed interest rates are more fully described in Note 4, "Debt" in Part 1, Item 1 of this Quarterly Report on Form 10-Q and Part II, Item 8 of the 10-K.

⁽³⁾ Purchase obligations include noncancelable contractual obligations.

Recently Issued Accounting Standards Not Yet Adopted

See Note 1, “Basis of Presentation and Summary of Significant Accounting Policies” in Part I, Item 1 of this Quarterly Report on Form 10-Q for a discussion of recently issued accounting standards not yet adopted.

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ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The market risk inherent in our market risk sensitive instruments and positions is the potential loss arising from adverse changes in: commodity market prices, foreign currency exchange rates and interest rates as described below.

Interest Rate Risk

Our exposure to market risk for changes in interest rates relates primarily to our investment portfolio and our outstanding debt obligations, including embedded derivatives therein. We generally invest our cash in investments with short maturities or with frequent interest reset terms. Accordingly, our interest income fluctuates with short-term market conditions. As of June 30, 2018, our investment portfolio consisted of certificates of deposit, which are highly liquid. Due to the short-term nature of our investment portfolio, we do not believe that an immediate 10% increase in interest rates would have a material effect on the fair value of our portfolio. Since we believe we have the ability to liquidate our investment portfolio, we expect that our operating results or cash flows would not be materially affected by a sudden change in market interest rates on the portfolio.

As of June 30, 2018, 82% of our outstanding debt is in fixed rate instruments. The remaining 18% of our outstanding debt is comprised of variable-rate loans under the GACP secured term loan facility, for which the interest rate is based on the U.S. prime rate, subject to a rate floor (see Note 4, “Debt” in Part 1, Item 1 of this Quarterly Report on Form 10-Q for details). As a result, changes in interest rates could affect interest expense and payments in relation to that component of our debt.

In addition, changes in interest rates may significantly change the fair value of our derivative liabilities (see Note 3, "Fair Value Measurement" in Notes to Condensed Consolidated Financial Statements included in this Quarterly Report on Form 10-Q).

Foreign Currency Risk

Most of our sales contracts are denominated in U.S. dollars, and therefore our revenues are not currently subject to significant foreign currency risk.

The functional currency of our consolidated Brazilian subsidiary is the local currency (Brazilian real), in which recurring business transactions occur. We do not use currency exchange contracts as hedges against our investment in that subsidiary.

Our permanent investment in Brazil was $24.7 million as of June 30, 2018 ($17.8 million as of December 31, 2017), using the exchange rate at each date. A hypothetical 10% adverse change in Brazilian real exchange rates would have had an adverse impact to Other Comprehensive Loss of $2.5 million as of June 30, 2018 ($1.8 million as of December 31, 2017).

We have also evaluated foreign currency exposure in relation to our other non-U.S. Dollar denominated assets and liabilities and determined that there would be an immaterial effect on our results of operations from 10% exchange rate fluctuations between those currencies and the U.S. Dollar.

ITEM 4. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Under the rules of the Securities and Exchange Commission (the SEC), “disclosure controls and procedures” (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934 (the Exchange Act)) are controls and other procedures that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the rules and forms of the SEC. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in our reports that we file or submit under the Exchange Act is accumulated and communicated to our management, including our Chief Executive Officer (CEO) and Chief Financial Officer (CFO), as appropriate, to allow timely decisions regarding required disclosure.

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At June 30, 2018, our management, with the participation of our CEO and CFO, evaluated the effectiveness of our disclosure controls and procedures. Based on that evaluation, our management, including our CEO and CFO, concluded that our disclosure controls and procedures were not effective as of June 30, 2018. This conclusion was based on the material weakness in our internal control over financial reporting described in Part II, Item 9A “Controls and Procedures” of our Annual Report on Form 10-K for the fiscal year ended December 31, 2017 (the 10-K). The material weakness has not been remediated as of June 30, 2018.

A material weakness is a deficiency, or combination of deficiencies, in internal control over financial reporting such that there is a reasonable possibility that a material misstatement of the company’s annual or interim consolidated financial statements will not be prevented or detected on a timely basis. If not remediated, the material weakness in our internal control over financial reporting described in the 10-K could result in a material misstatement of our annual or interim consolidated financial statements that would not be prevented or detected on a timely basis.

Changes in Internal Control over Financial Reporting

During the fiscal quarter ended June 30, 2018, we completed our assessment and analysis of key control deficiencies and began to implement additional review controls over routine transactions and more robust review procedures over our more complex and non-routine transactions. We continue to address and supplement our resource needs with qualified personnel possessing the appropriate level of technical accounting expertise and we continue to make progress in addressing the material weakness in our internal control over financial reporting described in the 10-K. Otherwise, there were no changes in our internal control over financial reporting during the fiscal quarter ended June 30, 2018 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. We are taking further actions to remediate the material weakness in our internal control over financial reporting and will report on those actions in upcoming Quarterly and Annual Reports on Form 10-Q and 10-K, respectively.

Limitations on the Effectiveness of Controls and Procedures

Our management, including our CEO and CFO, does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent or detect all errors and all fraud. A control system, no matter how well-designed and operated, can provide only reasonable, not absolute, assurance that the control system’s objectives will be met. The design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Further, because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, have been detected. The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Projections of any evaluation of the effectiveness of controls to future periods are subject to risks. Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures.

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PART II

ITEM 1. LEGAL PROCEEDINGS

On April 20, 2017, a securities class action complaint (the Securities Class Action Complaint) was filed against the Company and its CEO, John G. Melo, and CFO, Kathleen Valiasek, in the U.S. District Court for the Northern District of California (Case No. 3:17-cv-02210-WHO). The Securities Class Action Complaint sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company’s common stock between March 2, 2017 and April 17, 2017. The Securities Class Action Complaint alleged securities law violations based on statements made by the Company in its earnings press release issued on March 2, 2017 and Form 12b-25 filed with the Securities and Exchange Commission on April 3, 2017. On September 21, 2017, an order of dismissal was entered on the plaintiff’s notice of voluntary dismissal without prejudice.

Subsequent to the filing of the Securities Class Action Complaint, four separate purported shareholder “derivative” complaints were filed based on substantially the same facts as the Securities Class Action Complaint (the Derivative Complaints). The Derivative Complaints named Amyris, Inc. as a nominal defendant and named a number of the Company’s then-current officers and directors as additional defendants. . The lawsuits seek to recover, on the Company's behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and/or omissions made in connection with the Company’s securities filings. The Derivative Complaints also seek a series of changes to the Company’s corporate governance policies, restitution to the Company from the individual defendants, and an award of attorneys’ fees.  Two of the Derivative Complaints were filed in the U.S. District Court for the Northern District of California (together, the Federal Derivative Cases): Bonner v. John Melo, et al., Case No. 4:17-cv-04719, filed August 15, 2017, and Goldstein v. John Melo, et al., Case No. 3:17-cv-04927, filed on August 24, 2017. On September 19, 2017, an order was entered consolidating the Federal Derivative Cases into a single consolidated action, captioned: In re Amyris, Inc., Shareholder Derivative Litigation, Lead Case No. 2:15-cv-04719, and ordering the plaintiffs to file a consolidated complaint or designate an operative complaint by November 3, 2017. On November 3, 2017, the plaintiffs in the Federal Derivative Cases filed a Notice of Designation of Operative Complaint, designating the complaint filed in the Bonner case as the operative complaint. On December 21, 2017, the defendants filed a motion to dismiss the Federal Derivative Cases; and on March 9, 2018, the Court granted defendants’ motion to dismiss. On March 29, 2018, the plaintiffs filed an Amended Complaint with the Court. On May 4, 2018, the defendants filed a motion to dismiss the Amended Complaint; and on July 23, 2018, the Court granted defendants’ motion to dismiss the amended complaint with prejudice and entered judgment in favor of the defendants. The remaining two Derivative Complaints were filed in the Superior Court for the State of California (together, the State Derivative Cases): Gutierrez v. John G. Melo, et al., Case. No. BC 665782, filed on June 20, 2017, in the Superior Court for the County of Los Angeles, and Soleimani v. John G. Melo, et al., Case No. RG 17865966, filed on June 29, 2017, in the Superior Court for the County of Alameda. On August 31, 2017, the Gutierrez case was transferred to the Superior Court for the State of California, County of Alameda and assigned a case number, RG17876383. The State Derivative Cases are in the initial pleadings stage. We believe the claims lack merit and intend to continue to defend ourselves vigorously. Given the nature of these proceedings, it is not yet possible to reliably determine any potential liability that could result from this matter.

ITEM 1A. RISK FACTORS

The risks described in Part I, Item 1A, "Risk Factors" in our Annual Report on Form 10-K for the fiscal year ended December 31, 2017 (the 10-K) could materially and adversely affect our business, financial condition and results of operations, and the trading price of our common stock could decline. These risk factors do not identify all risks that we face; our operations could also be affected by factors that are not presently known to us or that we currently consider to be immaterial to our operations. Due to risks and uncertainties, known and unknown, our past financial results may not be a reliable indicator of future performance, and historical trends should not be used to anticipate results or trends in future periods. The “Risk Factors” section of the 10-K remains current in all material respects.

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ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

On April 12, 2018, we issued warrants to purchase an aggregate of 3,616,174 shares of our common stock (the April 2018 Warrants), exercisable at a price of $7.00 per share and for a term of fifteen months, to certain holders of the May 2017 Warrants (see Note 6, “Stockholders’ Deficit” in Part II, Item 8 of the 10-K), in exchange for such holders exercising for cash their May 2017 Cash Warrants, representing an aggregate of 3,616,174 shares issued and gross proceeds to the Company of $15.9 million, and surrendering their May 2017 Dilution Warrants, which were not currently exercisable for any shares, for cancellation, pursuant to warrant exercise agreements (the Warrant Exercise Agreements) entered into with such holders. The April 2018 Warrants do not contain any non-standard anti-dilution protection and only permit “cashless” exercise after six months, and only to the extent that there is no effective registration statement covering the shares issuable upon exercise.. In addition, in connection with the Warrant Exercise Agreements, the Company and the holders entered into separate letter agreements (the Leak-Out Agreements), pursuant to which each holder agreed, subject to certain exceptions, not to dispose of shares of our common stock on any trading day in an amount greater than such holder’s pro rata share of 30% of the daily average composite trading volume of our common stock for such trading day for a period of thirty trading days.

Oppenheimer & Co. Inc. acted as placement agent in connection with the issuance of the April 2018 Warrants. The April 2018 Warrants were issued in private placements pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (the Securities Act), and Regulation D promulgated under the Securities Act. The investors acquired the April 2018 Warrants for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and are accredited investors as defined in Rule 501 of Regulation D promulgated under Section 3(b) of the Securities Act. These holders had adequate access, through their relationships with us, to information about us.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

None.

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ITEM 6. EXHIBITS

Exhibit No.		Description
	4.01	Eighth Amendment, dated May 30, 2018, to Loan and Security Agreement, dated March 29, 2014, between registrant and Stegodon Corporation, as assignee of Hercules Capital, Inc.
	4.02	Fourth Amendment, dated May 31, 2018, to 12% Senior Convertible Note issued March 21, 2016 (RS-10) by registrant to Total Energies Nouvelles Activités USA
	4.03	Form of April 2018 Warrant
	10.01	Form of Warrant Exercise Agreement
	10.02	Form of Leak-Out Agreement
	10.03	2010 Equity Incentive Plan, as amended, and forms of award agreements thereunder
	10.04	2010 Employee Stock Purchase Plan, as amended, and form of subscription agreement thereunder
	10.05	Performance Stock Option Award Agreement, dated May 29, 2018, between the registrant and John Melo
	10.06	Amendment #1, dated May 30, 2018, to Executive Severance Plan Participation Agreement, dated December 18, 2013, between the registrant and John Melo
	10.07	Loan and Security Agreement, dated June 29, 2018, by and among the registrant, certain subsidiaries of the registrant and GACP Finance Co., LLC
	31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	32.01 *	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
	32.02 *	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
	101. INS	XBRL Instance Document
	101. SCH	XBRL Taxonomy Extension Schema Document
	101. CAL	XBRL Taxonomy Extension Calculation Linkbase Document
	101. DEF	XBRL Taxonomy Extension Definition Linkbase Document
	101. LAB	XBRL Taxonomy Extension Label Linkbase Document
	101. PRE	XBRL Taxonomy Extension Presentation Linkbase Document

* This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act. 

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this Quarterly Report on Form 10-Q to be signed on its behalf by the undersigned, thereunto duly authorized.

	AMYRIS, INC.
By:	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer (Principal Executive Officer)
	August 14, 2018
By:	/s/ Kathleen Valiasek
	Kathleen Valiasek
	Chief Financial Officer   (Principal Financial Officer)
	August 14, 2018

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EX-4.01

EXHIBIT 4.01

Eighth Amendment To Loan And Security Agreement

This EIGHTH AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”), dated as of May 30, 2018, is among AMYRIS, INC., a Delaware corporation (the “Parent”), and each of its Subsidiaries that has delivered a Joinder Agreement (as defined herein) (each a “Subsidiary Guarantor” and collectively, the “Subsidiary Guarantors” and together with Parent, collectively, “Borrower”), the several banks and other financial institutions or entities from time to time parties to this Agreement (collectively, referred to as “Lender”) and STEGODON CORPORATION, a Delaware corporation, as successor-in-interest to Hercules Technology Growth Capital, Inc., a Maryland corporation, in its capacity as administrative agent for itself and the Lender (in such capacity, the “Agent”).

Recitals

A.WHEREAS, Parent, Subsidiary Guarantors, Lender and Agent have previously entered into that certain Loan and Security Agreement, dated as of March 29, 2014, as previously amended on June 12, 2014, March 31, 2015, October 12, 2015, November 30, 2015, May 9, 2016, June 24, 2016, June 29, 2016, July 18, 2016, October 5, 2016, October 6, 2016, October 27, 2016, November 29, 2016, December 5, 2016, December 14, 2016, December 17, 2016, December 30, 2016, January 10, 2017, April 13, 2017, November 13, 2017, December 28, 2017, and March 30, 2018 (as further amended from time to time, the “Loan Agreement”), pursuant to which, among other things, Lender has provided certain term loans and other financial accommodations to Borrower;

B.WHEREAS, Borrower desires to amend the Loan Agreement by extending the date for a principal payment in the amount of $5,500,000 due under the terms of the Loan Agreement from May 31, 2018 to July 2, 2018; and

C.WHEREAS, Agent and the Lenders are willing to so amend the Loan Agreement as more specifically set forth herein, subject to the terms and conditions contained herein.

Now, Therefore, for good and valuable consideration (the receipt and sufficiency of which are hereby acknowledged), in reliance upon the representations and warranties made in support thereof and contained herein, the parties hereto agree as follows:

1.Defined Terms. Each capitalized term used but not otherwise defined herein has the meaning ascribed thereto in the Loan Agreement.

2.Amendments to Loan and Security Agreement. Subject to the satisfaction of the conditions precedent set forth in Section 3 of this Amendment and effective as of the Eighth Amendment Effective Date (notwithstanding the date of execution of this Amendment), the Loan Agreement is hereby amended as follows:

(a)Section 1.1 (Definitions). The Loan Agreement is hereby amended by inserting the following definition to appear alphabetically in Section 1.1 thereof:

“      “July 2018 Principal Payment” is defined in Section 2.2(d)(ii)(y).”

(b)Section 2.2(d) (Payments). The Loan Agreement is hereby amended by amending Section 2.2(d)(ii)(y) in its entirety and replacing it with the following:

“     (y) on or prior to July 2, 2018, a principal payment of $5,500,000 (the “July 2018 Principal Payment”), which payment shall be applied to the principal amount of Secured Obligations then outstanding. The date on which such payment is received by Agent shall be the “2018 Principal Payment Date”.”

3.Conditions to Effectiveness. The provisions of this Amendment shall become effective on the date, which date (if ever) shall be on or prior to May 31, 2018, that all of the following conditions precedent have been satisfied (the “Eighth Amendment Effective Date”):

(a)Agent shall have received a pdf copy of this Amendment, duly executed and delivered by Parent and the Subsidiary Guarantor;

(b)Each of the representations and warranties of Borrower in Section 4 of this Amendment shall be true, correct and accurate in all material respects as of the Eighth Amendment Effective Date;

(c)No Material Adverse Effect has occurred;

(d)Agent shall have received either (i) a secretary’s certificate certifying as to the Borrower’s charter documents, authorizations and incumbency matters in form and substance satisfactory to Agent, or (ii) a confirmation satisfactory to Agent in its sole discretion that the Borrower’s charter documents, authorizations and incumbency have not changed since previously delivered to Agent;

(e)No Event of Default exists under the Loan Agreement or any Loan Document;

(f)Borrower shall have paid to Agent’s counsel all legal fees and out-of-pocket expenses incurred in connection with the Loan Documents and this Amendment; and

(g)All legal matters incident to the execution and delivery of this Amendment shall be satisfactory to Agent and its counsel.

4.Representations, Warranties and Agreements. Borrower hereby represents, warrants and agrees in favor of Agent and Lender as follows:

(a)No Event of Default has occurred and is continuing (or would result from the amendment of the Loan Agreement contemplated hereby);

(b)The execution, delivery and performance by Borrower of this Amendment have been duly authorized by all necessary corporate and/or other action and do not and will not require any registration with, consent or approval of, notice to or action by, any Person in order to be effective and enforceable. Each of the Loan Agreement and the other Loan Documents to which Borrower is a party constitutes and continues to constitute the legally, valid and binding obligation of Borrower, in each case enforceable against Borrower in accordance with its terms;

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(c)All of the representations and warranties of Borrower contained in the Loan Agreement and the other Loan Documents are true and correct in all material respects on and as of the date hereof and will be true and correct on the Eighth Amendment Effective Date (except to the extent that such representations and warranties specifically refer to an earlier date, in which case they shall be true and correct in all material respects as of such earlier date, and in each case, without duplication of any materiality qualifiers);

(d)No Material Adverse Effect has occurred;

(e)Borrower is entering into this Amendment on the basis of such Person’s own business judgment, without reliance upon Agent or Lender; and

(f)Borrower acknowledges and agrees that the execution and delivery by Agent and Lender of this Amendment shall not be deemed to create a course of dealing or otherwise obligate Agent or Lender to execute similar agreements under the same or similar circumstances in the future. Neither Agent nor Lender has any obligation to Borrower or any other Person to further amend provisions of the Loan Agreement or the other Loan Documents. Other than as specifically contemplated hereby, all of the terms, covenants and provisions of the Loan Agreement (and the other Loan Documents) are and shall remain in full force and effect.

5.Amendment Fee. As consideration for this Amendment, Borrower shall pay to Agent an amendment fee equal to $100,000.00 (the “Amendment Fee”), for the ratable benefit of the Lenders, which fee shall be fully earned on the Eighth Amendment Effective Date and due and payable on July 2, 2018. The Amendment Fee shall not be refunded or repaid to Borrower under any circumstances; provided, that the Amendment Fee shall be forgiven by the Agent and the Lenders if Borrower shall have indefeasibly paid the July 2018 Principal Payment in full in cash on or prior to July 2, 2018.

6.General Provisions.

(a)Upon the effectiveness of this Amendment, all references in the Loan Agreement and in the other Loan Documents to the Loan Agreement shall refer to the Loan Agreement as modified hereby. This Amendment shall be deemed incorporated into, and a part of, the Loan Agreement. This Amendment is a Loan Document. THIS AMENDMENT IS EXPRESSLY SUBJECT TO THE PROVISIONS OF SECTION 11.8 (GOVERNING LAW), SECTION 11.9 (CONSENT TO JURISDICTION AND VENUE) AND SECTION 11.10 (MUTUAL WAIVER OF JURY TRIAL; JUDICIAL REFERENCE) OF THE LOAN AGREEMENT, WHICH PROVISIONS ARE INCORPORATED HEREIN AND MADE APPLICABLE HERETO BY THIS REFERENCE.

(b)This Amendment is made pursuant to Section 11.3(b) and 11.7 of the Loan Agreement and shall be binding upon and inure to the benefit of the parties hereto and thereto and their respective successors and assigns. No third party beneficiaries are intended in connection with this Amendment.

(c)This Amendment may be executed in counterparts (and by different parties hereto in different counterparts), each of which shall constitute an original, but all of which when taken together shall constitute a single contract. Delivery of an executed counterpart of a signature page of this Amendment by telecopy or other electronic means shall be effective as delivery of a manually executed counterpart of this Amendment.

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(d)Each provision of this Amendment shall be severable from every other provision of this Amendment for the purpose of determining the legal enforceability of any specific provision.

(e)Borrower shall promptly pay to Agent’s counsel all attorneys’ fees and expenses incurred in connection with the preparation, negotiation and closing of this Amendment.

(f)The appearing parties herein declare that all the terms and conditions of the Loan Agreement continue to remain, as herein amended, in full force and effect and by these presents the appearing parties hereby ratify, reaffirm and confirm all the terms and conditions of the Loan Agreement and further declare that it is their express intention that the transactions set forth in this Amendment shall in no way, manner or form be construed or be interpreted as an extinctive novation of any of the obligations and agreements set forth in the Loan Agreement.

[Document continues with signature pages.]

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IN WITNESS WHEREOF, the parties hereto have caused this Eighth Amendment to Loan and Security Agreement to be duly executed and delivered as of the date first written above.

AMYRIS, INC.

By:  /s/ Kathleen Valiasek

Print Name: Kathleen Valiasek

Title: Chief Financial Officer

AMYRIS FUELS, LLC

By:  /s/ Kathleen Valiasek

Print Name: Kathleen Valiasek

Title: Chief Financial Officer

AGENT:

STEGODON CORPORATION

Signature: /s/ Austin Che

Print Name: Austin Che

Title: President

LENDER:

STEGODON CORPORATION

Signature: /s/ Austin Che

Print Name: Austin Che

Title: President

EX-4.02

EXHIBIT 4.02

FOURTH AMENDMENT TO 12% SENIOR CONVERTIBLE NOTE (RS-10)

This Fourth Amendment to 12% Senior Convertible Note (RS-10) (this “Amendment”) is made and entered into as of May 31st, 2018, by and between Amyris, Inc., a Delaware corporation (the “Company”), and Total Raffinage Chimie S.A., as assignee of Total Energies Nouvelles Activités USA (the “Investor”).

RECITALS

WHEREAS, on March 21, 2016 the Company issued to the Investor a Senior Convertible Note (RS-10) in the principal amount of $3,700,000, as amended by (i) that First Amendment to 1.5% Senior Convertible Note (RS-10) dated February 27, 2017, (ii) that Second Amendment to 1.5% Senior Convertible Note (RS-10) dated May 12, 2017 and (iii) that Third Amendment to 1.5% Senior Convertible Note (RS-10) dated March 30, 2018 (as amended, the “Note”).

WHEREAS, the Company and the Investor desire to further amend the Note as set forth herein.

WHEREAS, pursuant to Section 7 of the Note, the Note may be amended with the written consent of the Company and the Investor.

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties hereby agree as follows:

1. Amendment of Section 2(a) of the Note. Section 2(a) of the Note is hereby deleted in its entirety and replaced with the following:

(a)                  Interest. This Note shall bear interest (i) from the Issue Date to May 15, 2017 on the Face Amount at a rate per annum equal to 1.50% (subject to Section 4(k)) and (ii) from May 16, 2017 to the Final Maturity Date on the Face Amount at a rate per annum equal to 12.00% (subject to Section 4(k)). Interest on this Note shall accrue daily and be due and payable in arrears on (i) December 31, 2017, (ii) March 31, 2018, (iii) May 31, 2018 and (iv) the Final Maturity Date, and at such other times as may be specified herein. All computations of interest shall be made on the basis of a 360-day year and actual days elapsed (which results in more interest being paid than if computed on the basis of a 365-day year). Notwithstanding the foregoing, if an Event of Default shall have occurred and be continuing this Note shall bear interest on the Face Amount at a rate per annum equal to 13.50% (as may be further adjusted pursuant to Section 4(k)).

2. Amendment of Section 2(b) of the Note. Section 2(b) of the Note is hereby deleted in its entirety and replaced with the following:

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(b)                  Scheduled Payment of Principal. Unless paid, converted or cancelled and extinguished earlier in accordance with the terms hereof, the Company shall deliver to the Investor cash in the amount of the Face Amount, together with all accrued and unpaid interest on this Note, on July 2, 2018 (the “Final Maturity Date”) and this Note shall be retired and canceled.

3. Full Force and Effect. Except as expressly modified by this Amendment, the terms of the Note shall remain in full force and effect.

4. Integration. This Amendment and the Note constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

5. Counterparts; Facsimile. This Amendment may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf), and delivery of any signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other party.

[Remainder of Page intentionally left blank]

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IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

AMYRIS, INC.

By: /s/ Kathleen Valiasek

Name: Kathleen Valiasek

Title: Chief Financial Officer

[Signature Page to Fourth Amendment to R&D Note]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

Total Raffinage Chimie S.A.

By: /s/ Nathalie Brunelle

Name: Nathalie Brunelle

Title: Deputy CEO

[Signature Page to Fourth Amendment to R&D Note]

EX-10.04

EXHIBIT 10.04

AMYRIS, INC.

2010 Employee Stock Purchase Plan

As Amended May 22, 2018

1.        Establishment of Plan. Amyris, Inc. (the “Company”) proposes to grant options for purchase of the Company’s Common Stock to eligible employees of the Company and its Participating Corporations (as hereinafter defined) pursuant to this Employee Stock Purchase Plan (as amended, this “Plan”). For purposes of this Plan, “Parent” and “Subsidiary” shall have the same meanings as “parent corporation” and “subsidiary corporation” in Sections 424(e) and 424(f), respectively, of the Internal Revenue Code of 1986, as amended (the “Code”), and “Corporate Group” shall refer collectively to the Company and all its Parents and Subsidiaries. “Participating Corporations” are the Company and any Parents or Subsidiaries that the Board of Directors of the Company (the “Board”) designates from time to time as corporations that shall participate in this Plan. The Company intends this Plan to qualify as an “employee stock purchase plan” under Section 423 of the Code (including any amendments to or replacements of such Section), and this Plan shall be so construed. Any term not expressly defined in this Plan but defined for purposes of Section 423 of the Code shall have the same definition herein. Subject to Section 14, a total of 11,241 shares of the Company’s Common Stock is reserved for issuance under this Plan. In addition, on each January 1 for each calendar year after the Effective Date, the aggregate number of shares of the Company’s Common Stock reserved for issuance under the Plan shall be increased automatically by the lesser of one (1%) percent of the number of shares of the Company’s Common Stock issued and outstanding on each December 31 immediately prior to the date of increase or (ii) such number of shares of the Company’s Common determined by the Board or the Committee provided that the aggregate number of shares issued over the term of this Plan shall not exceed 1,666,666 shares of Common Stock.

2.        Purpose. The purpose of this Plan is to provide eligible employees of the Company and Participating Corporations with a means of acquiring an equity interest in the Company through payroll deductions, to enhance such employees’ sense of participation in the affairs of the Company and Participating Corporations, and to provide an incentive for continued employment.

3.        Administration. The Plan will be administered by the Compensation Committee of the Board or by the Board (either referred to herein as the “Committee”). Subject to the provisions of this Plan and the limitations of Section 423 of the Code or any successor provision in the Code, all questions of interpretation or application of this Plan shall be determined by the Committee and its decisions shall be final and binding upon all Participants. The Committee will have full and exclusive discretionary authority to construe, interpret and apply the terms of the Plan, to determine eligibility and decide upon any and all claims filed under the Plan. Every finding, decision and determination made by the Committee will, to the full extent permitted by law, be final and binding upon all parties. Notwithstanding any provision to the contrary in this Plan, the Committee may adopt rules and/or procedures relating to the operation and administration of the Plan to accommodate requirements of local law and procedures outside of the United States. Members of the Committee shall receive no compensation for their services in connection with the administration of this Plan, other than standard fees as established from time to time by the Board for services rendered by Board members serving on Board committees. All expenses incurred in connection with the administration of this Plan shall be paid by the Company.

4.        Eligibility. Any employee of the Company or the Participating Corporations is eligible to participate in an Offering Period (as hereinafter defined) under this Plan except the following:

(a) employees who are not employed by the Company or a Participating Corporation prior to the beginning of such Offering Period or prior to such other time period as specified by the Committee; except that employees who are employed on the Effective Date of the Registration Statement filed by the Company with the Securities and Exchange Commission (the “SEC”) under the Securities Act of 1933, as amended (the “Securities Act”) registering the initial public offering of the Company’s Common Stock shall be eligible to participate in the First Offering Period;

(b) employees who are customarily employed for twenty (20) hours or less per week;

(c) employees who are customarily employed for five (5) months or less in a calendar year;

(d) employees who, together with any other person whose stock would be attributed to such employee pursuant to Section 424(d) of the Code, own stock or hold options to purchase stock possessing five percent (5%) or more of the total combined voting power or value of all classes of stock of the Company or any of its Participating Corporations or who, as a result of being granted an option under this Plan with respect to such Offering Period, would own stock or hold options to purchase stock possessing five percent (5%) or more of the total combined voting power or value of all classes of stock of the Company or any of its Participating Corporations;

(e) employees who do not meet any other eligibility requirements that the Committee may choose to impose (within the limits permitted by the Code);

(f) employees who have been an employee of the Company for less than one (1) month prior to the first day of an Offering Period (except as set forth in (a) above); and

(g) individuals who provide services to the Company or any of its Participating Corporations as independent contractors who are reclassified as common law employees for any reason except for federal income and employment tax purposes.

5.        Offering Dates.

(a) The offering periods of this Plan (each, an “Offering Period”) may be of up to twelve (12) months duration (except the Initial Offering Period, which may be longer than twelve (12) months as described below) and shall commence and end at the times designated by the Committee. Each Offering Period shall consist of two six month purchase periods (each a “Purchase Period”) during which payroll deductions of Participants are accumulated under this Plan.

(b) The initial Offering Period shall commence on the date on which the Registration Statement covering the initial public offering of shares of the Company’s Common Stock is declared effective by the U.S. Securities and Exchange Commission (the “Effective Date”), and shall end on November 15th of the year following the Effective Date. The initial Offering Period shall consist of a single Purchase Period. Thereafter, a twelve-month Offering Period shall commence on each May 16^th and November 16^th, with each such Offering Period also consisting of two six-month Purchase Periods.

(c) The first business day of each Offering Period is referred to as the “Offering Date,” however, for the initial Offering Period this shall be the Effective Date. The last business day of each Purchase Period is referred to as the “Purchase Date.” The Committee shall have the power to change the terms of this Section 5 as provided in Section 25 below.

6.        Participation in this Plan.

(a) Any employee who is an eligible employee determined in accordance with Section 4 immediately prior to the initial Offering Period will be automatically enrolled in the initial Offering Period under this Plan. With respect to subsequent Offering Periods, any eligible employee determined in accordance with Section 4 will be eligible to participate in this Plan, subject to the requirement of Section 6(b) hereof and the other terms and provisions of this Plan. Eligible employees who meet the eligibility requirements set forth in Section 4 and who are either automatically enrolled in the initial offering period or who elect to participate in the this Plan pursuant to Section 6(b) are referred to herein as a “Participant” or collectively as “Participants.”

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(b)        Notwithstanding the foregoing, (i) an eligible employee may elect to decrease the number of shares of Common Stock that such employee would otherwise be permitted to purchase for the initial Offering Period under the Plan and/or purchase shares of Common Stock for the initial Offering Period through payroll deductions by delivering a subscription agreement to the Company within thirty (30) days after the filing of an effective registration statement pursuant to Form S-8 and (ii) the Committee may set a later time for filing the subscription agreement authorizing payroll deductions for all eligible employees with respect to a given Offering Period. With respect to Offering Periods after the initial Offering Period, a Participant may elect to participate in this Plan by submitting a subscription agreement prior to the commencement of the Offering Period (or such earlier date as the Committee may determine) to which such agreement relates.

(c)       Once an employee becomes a Participant in an Offering Period, then such Participant will automatically participate in the Offering Period commencing immediately following the last day of such prior Offering Period unless the Participant withdraws or is deemed to withdraw from this Plan or terminates further participation in the Offering Period as set forth in Section 11 below. Such Participant is not required to file any additional subscription agreement in order to continue participation in this Plan.

7.        Grant of Option on Enrollment. Becoming a Participant with respect to an Offering Period will constitute the grant (as of the Offering Date) by the Company to such Participant of an option to purchase on the Purchase Date up to that number of shares of Common Stock of the Company determined by a fraction, the numerator of which is the amount accumulated in such Participant’s payroll deduction account during such Purchase Period and the denominator of which is the lower of (i) eighty-five percent (85%) of the fair market value of a share of the Company’s Common Stock on the Offering Date (but in no event less than the par value of a share of the Company’s Common Stock), or (ii) eighty-five percent (85%) of the fair market value of a share of the Company’s Common Stock on the Purchase Date (but in no event less than the par value of a share of the Company’s Common Stock) provided, however, that for the Purchase Period within the initial Offering Period the numerator shall be fifteen percent (15%) of the Participant’s compensation for such Purchase Period and provided, further, that the number of shares of the Company’s Common Stock subject to any option granted pursuant to this Plan shall not exceed the lesser of (x) the maximum number of shares set by the Committee pursuant to Section 10(b) below with respect to the applicable Purchase Date, or (y) the maximum number of shares which may be purchased pursuant to Section 10(a) below with respect to the applicable Purchase Date. The fair market value of a share of the Company’s Common Stock shall be determined as provided in Section 8 below.

8.        Purchase Price. The purchase price per share at which a share of Common Stock will be sold in any Offering Period shall be eighty-five percent (85%) of the lesser of:

(a) The fair market value on the Offering Date; or

(b) The fair market value on the Purchase Date.

The term “fair market value” means, as of any date, the value of a share of the Company’s Common Stock determined as follows:

(i) if such Common Stock is publicly traded and is then listed on a national securities exchange, its closing price on the date of determination on the principal national securities exchange on which the Common Stock is listed or admitted to trading as reported in The Wall Street Journal or such other source as the Board or the Committee deems reliable; or

(ii) if such Common Stock is publicly traded but is neither listed or admitted to trading on a national securities exchange, the average of the closing bid and asked prices on the date of determination as reported in The Wall Street Journal or such other source as the Board or the Committee deems reliable; or

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(iii) with respect to the initial Offering Period, “fair market value” on the Offering Date shall be the price at which shares of Common Stock are offered to the public pursuant to the Registration Statement covering the initial public offering of shares of the Company’s Common Stock; and

(iv) if none of the foregoing is applicable, by the Board or the Committee in good faith.

9.        Payment of Purchase Price; Payroll Deduction Changes; Share Issuances.

(a) The purchase price of the shares is accumulated by regular payroll deductions made during each Offering Period. The deductions are made as a percentage of the Participant’s compensation in one percent (1%) increments not less than one percent (1%), nor greater than fifteen percent (15%) or such lower limit set by the Committee. Compensation shall mean all compensation categorized by the Company as total compensation including base salary or regular hourly wages, overtime, holiday, vacation and sick pay and shift premiums and excluding, to the extent permitted by Code Section 423, bonuses, salary continuation, relocation assistance payments, geographical hardship pay, noncash prizes and awards, automobile allowances, severance type payments, and nonqualified deferred executive compensation (including amounts attributable to equity compensation), provided, however, that for purposes of determining a Participant’s compensation, any election by such Participant to reduce his or her regular cash remuneration under Sections 125 or 401(k) of the Code shall be treated as if the Participant did not make such election. Payroll deductions shall commence on the first payday following the last Purchase Date (first payday following the effective date of filing with the U.S. Securities and Exchange Commission a securities registration statement for the Plan with respect to the initial Offering Period) and shall continue to the end of the Offering Period unless sooner altered or terminated as provided in this Plan.

(b) A Participant may increase or decrease the rate of payroll deductions during an Offering Period by filing with the Company a new authorization for payroll deductions, with the new rate to become effective for the next payroll period commencing after the Company’s receipt of the authorization and continuing for the remainder of the Offering Period unless changed as described below. Such change in the rate of payroll deductions may be made at any time during an Offering Period, under rules determined by the Committee. A Participant may increase or decrease the rate of payroll deductions for any subsequent Offering Period by filing with the Company a new authorization for payroll deductions prior to the beginning of such Offering Period, or such other time period as specified by the Committee.

(c) A Participant may reduce his or her payroll deduction percentage to zero during an Offering Period by filing with the Company a request for cessation of payroll deductions. Such reduction shall be effective beginning with the next payroll period after the Company’s receipt of the request and no further payroll deductions will be made for the duration of the Offering Period. Payroll deductions credited to the Participant’s account prior to the effective date of the request shall be used to purchase shares of Common Stock of the Company in accordance with Section (e) below. A reduction of the payroll deduction percentage to zero shall be treated as such Participant’s withdrawal from such Offering Period, and the Plan, effective as of the day after the next Purchase Date following the filing date of such request with the Company.

(d) All payroll deductions made for a Participant are credited to his or her account under this Plan and are deposited with the general funds of the Company. No interest accrues on the payroll deductions. All payroll deductions received or held by the Company may be used by the Company for any corporate purpose, and the Company shall not be obligated to segregate such payroll deductions.

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(e) On each Purchase Date, so long as this Plan remains in effect and provided that the Participant has not submitted a signed and completed withdrawal form before that date which notifies the Company that the Participant wishes to withdraw from that Offering Period under this Plan and have all payroll deductions accumulated in the account maintained on behalf of the Participant as of that date returned to the Participant, the Company shall apply the funds then in the Participant’s account to the purchase of whole shares of Common Stock reserved under the option granted to such Participant with respect to the Offering Period to the extent that such option is exercisable on the Purchase Date. The purchase price per share shall be as specified in Section 8 of this Plan. Any amount remaining in a Participant’s account on a Purchase Date which is less than the amount necessary to purchase a full share of the Company’s Common Stock shall be carried forward, without interest, into the next Purchase Period or Offering Period, as the case may be. In the event that this Plan has been oversubscribed, all funds not used to purchase shares on the Purchase Date shall be returned to the Participant, without interest. No Common Stock shall be purchased on a Purchase Date on behalf of any employee whose participation in this Plan has terminated prior to such Purchase Date.

(f) As promptly as practicable after the Purchase Date, the Company shall issue shares for the Participant’s benefit representing the shares purchased upon exercise of his or her option.

(g) During a Participant’s lifetime, his or her option to purchase shares hereunder is exercisable only by him or her. The Participant will have no interest or voting right in shares covered by his or her option until such option has been exercised.

10.        Limitations on Shares to be Purchased.

(a) No Participant shall be entitled to purchase stock under any Offering Period at a rate which, when aggregated with such Participant’s rights to purchase stock, that are also outstanding in the same calendar year(s) (whether under other Offering Periods or other employee stock purchase plans of the Corporate Group), exceeds $25,000 in fair market value, determined as of the Offering Date, (or such other limit as may be imposed by the Code) for each calendar year in which such Offering Period is in effect (hereinafter the “Maximum Share Amount”). The Company shall automatically suspend the payroll deductions of any Participant as necessary to enforce such limit provided that when the Company automatically resumes such payroll deductions, the Company must apply the rate in effect immediately prior to such suspension.

(b) The Committee may, in its sole discretion, set a lower maximum number of shares which may be purchased by any Participant during any Offering Period than that determined under Section 10(a) above, which shall then be the Maximum Share Amount for subsequent Offering Periods; provided, however, in no event shall a Participant be permitted to purchase more than 3,000 Shares during any one Offering Period, irrespective of the Maximum Share Amount set forth in (a) and (b) hereof. If a new Maximum Share Amount is set, then all Participants must be notified of such Maximum Share Amount prior to the commencement of the next Offering Period for which it is to be effective. The Maximum Share Amount shall continue to apply with respect to all succeeding Offering Periods unless revised by the Committee as set forth above.

(c) If the number of shares to be purchased on a Purchase Date by all Participants exceeds the number of shares then available for issuance under this Plan, then the Company will make a pro rata allocation of the remaining shares in as uniform a manner as shall be reasonably practicable and as the Committee shall determine to be equitable. In such event, the Company shall give written notice of such reduction of the number of shares to be purchased under a Participant’s option to each Participant affected.

(d) Any payroll deductions accumulated in a Participant’s account which are not used to purchase stock due to the limitations in this Section 10, and not covered by Section 9(e), returned to the Participant as soon as practicable after the end of the applicable Purchase Period..

11.        Withdrawal.

(a) Each Participant may withdraw from an Offering Period under this Plan by signing and delivering to the Company a written notice to that effect on a form provided for such purpose by the Company. Such withdrawal may be elected at any time prior to the end of an Offering Period, or such other time period as specified by the Committee.

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(b) Upon withdrawal from this Plan, the accumulated payroll deductions shall be returned to the withdrawn Participant, without interest, and his or her interest in this Plan shall terminate. In the event a Participant voluntarily elects to withdraw from this Plan, he or she may not resume his or her participation in this Plan during the same Offering Period, but he or she may participate in any Offering Period under this Plan which commences on a date subsequent to such withdrawal by filing a new authorization for payroll deductions in the same manner as set forth in Section 6 above for initial participation in this Plan.

12.       Termination of Employment. Termination of a Participant’s employment for any reason, including retirement, death, disability, or the failure of a Participant to remain an eligible employee of the Company or of a Participating Corporation, immediately terminates his or her participation in this Plan. In such event, accumulated payroll deductions credited to the Participant’s account will be returned to him or her or, in the case of his or her death, to his or her legal representative, without interest. For purposes of this Section 12, an employee will not be deemed to have terminated employment or failed to remain in the continuous employ of the Company or of a Participating Corporation in the case of sick leave, military leave, or any other leave of absence approved by the Company; provided that such leave is for a period of not more than ninety (90) days or reemployment upon the expiration of such leave is guaranteed by contract or statute.

13.        Return of Payroll Deductions. In the event a Participant’s interest in this Plan is terminated by withdrawal, termination of employment or otherwise, or in the event this Plan is terminated by the Board, the Company shall deliver to the Participant all accumulated payroll deductions credited to such Participant’s account. No interest shall accrue on the payroll deductions of a Participant in this Plan.

14.        Capital Changes. If the number of outstanding Shares is changed by a stock dividend, recapitalization, stock split, reverse stock split, subdivision, combination, reclassification or similar change in the capital structure of the Company, without consideration, then the Committee shall adjust the number and class of Common Stock that may be delivered under the Plan, the purchase price per share and the number of shares of Common Stock covered by each option under the Plan which has not yet been exercised, and the numerical limits of Sections 1 and 10 shall be proportionately adjusted, subject to any required action by the Board or the stockholders of the Company and in compliance with applicable securities laws; provided that fractions of a Share will not be issued.

15.        Nonassignability. Neither payroll deductions credited to a Participant’s account nor any rights with regard to the exercise of an option or to receive shares under this Plan may be assigned, transferred, pledged or otherwise disposed of in any way (other than by will, the laws of descent and distribution or as provided in Section 22 below) by the Participant. Any such attempt at assignment, transfer, pledge or other disposition shall be void and without effect.

16.        Use of Participant Funds and Reports. The Company may use all payroll deductions received or held by it under the Plan for any corporate purpose, and the Company will not be required to segregate Participant payroll deductions. Until Shares are issued, Participants will only have the rights of an unsecured creditor. Each Participant shall receive promptly after the end of each Purchase Period a report of his or her account setting forth the total payroll deductions accumulated, the number of shares purchased, the per share price thereof and the remaining cash balance, if any, carried forward to the next Purchase Period or Offering Period, as the case may be.

17.        Notice of Disposition. Each Participant shall notify the Company in writing if the Participant disposes of any of the shares purchased in any Offering Period pursuant to this Plan if such disposition occurs within two (2) years from the Offering Date or within one (1) year from the Purchase Date on which such shares were purchased (the “Notice Period”). The Company may, at any time during the Notice Period, place a legend or legends on any certificate representing shares acquired pursuant to this Plan requesting the Company’s transfer agent to notify the Company of any transfer of the shares. The obligation of the Participant to provide such notice shall continue notwithstanding the placement of any such legend on the certificates.

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18.        No Rights to Continued Employment. Neither this Plan nor the grant of any option hereunder shall confer any right on any employee to remain in the employ of the Company or any Participating Corporation, or restrict the right of the Company or any Participating Corporation to terminate such employee’s employment.

19.        Equal Rights And Privileges. All eligible employees shall have equal rights and privileges with respect to this Plan so that this Plan qualifies as an “employee stock purchase plan” within the meaning of Section 423 or any successor provision of the Code and the related regulations. Any provision of this Plan which is inconsistent with Section 423 or any successor provision of the Code shall, without further act or amendment by the Company, the Committee or the Board, be reformed to comply with the requirements of Section 423. This Section 19 shall take precedence over all other provisions in this Plan.

20.        Notices. All notices or other communications by a Participant to the Company under or in connection with this Plan shall be deemed to have been duly given when received in the form specified by the Company at the location, or by the person, designated by the Company for the receipt thereof.

21.        Term; Stockholder Approval. This Plan will become effective on the Effective Date. This Plan, as amended, shall be approved by the stockholders of the Company, in any manner permitted by applicable corporate law, within twelve (12) months before or after the date this Plan is adopted by the Board. No purchase of shares that are subject to such stockholder approval before becoming available under this Plan shall occur prior to stockholder approval of such shares and the Board or Committee may delay any Purchase Date and postpone the commencement of any Offering Period subsequent to such Purchase Date as deemed necessary or desirable to obtain such approval. This Plan shall continue until the earlier to occur of (a) termination of this Plan by the Board (which termination may be effected by the Board at any time pursuant to Section 25 below), (b) issuance of all of the shares of Common Stock reserved for issuance under this Plan, or (c) the tenth anniversary of the first Purchase Date under the Plan.

22.        Designation of Beneficiary.

(a) A Participant may file a written designation of a beneficiary who is to receive any shares and cash, if any, from the Participant’s account under this Plan in the event of such Participant’s death subsequent to the end of a Purchase Period but prior to delivery to him of such shares and cash. In addition, a Participant may file a written designation of a beneficiary who is to receive any cash from the Participant’s account under this Plan in the event of such Participant’s death prior to a Purchase Date.

(b) Such designation of beneficiary may be changed by the Participant at any time by written notice. In the event of the death of a Participant and in the absence of a beneficiary validly designated under this Plan who is living at the time of such Participant’s death, the Company shall deliver such shares or cash to the executor or administrator of the estate of the Participant, or if no such executor or administrator has been appointed (to the knowledge of the Company), the Company, in its discretion, may deliver such shares or cash to the spouse or to any one or more dependents or relatives of the Participant, or if no spouse, dependent or relative is known to the Company, then to such other person as the Company may designate.

23.        Conditions Upon Issuance of Shares; Limitation on Sale of Shares. Shares shall not be issued with respect to an option unless the exercise of such option and the issuance and delivery of such shares pursuant thereto shall comply with all applicable provisions of law, domestic or foreign, including, without limitation, the Securities Act, the Securities Exchange Act of 1934, as amended, the rules and regulations promulgated thereunder, and the requirements of any stock exchange or automated quotation system upon which the shares may then be listed, and shall be further subject to the approval of counsel for the Company with respect to such compliance.

24.        Applicable Law. The Plan shall be governed by the substantive laws (excluding the conflict of laws rules) of the State of Delaware.

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25.        Amendment or Termination. The Committee, in its sole discretion, may amend, suspend, or terminate the Plan, or any part thereof, at any time and for any reason. If the Plan is terminated, the Committee, in its discretion, may elect to terminate all outstanding Offering Periods either immediately or upon completion of the purchase of shares of Common Stock on the next Purchase Date (which may be sooner than originally scheduled, if determined by the Committee in its discretion), or may elect to permit Offering Periods to expire in accordance with their terms (and subject to any adjustment pursuant to Section 14). If an Offering Period is terminated prior to its previously-scheduled expiration, all amounts then credited to Participants’ accounts for such Offering Period, which have not been used to purchase shares of the Company’s Common Stock, shall be returned to those Participants (without interest thereon, except as otherwise required under local laws) as soon as administratively practicable. Further, the Committee will be entitled to change the Purchase Periods and Offering Periods, limit the frequency and/or number of changes in the amount withheld during an Offering Period, permit contributions to be increased or decreased, establish the exchange ratio applicable to amounts withheld in a currency other than U.S. dollars, permit payroll withholding in excess of the amount designated by a Participant in order to adjust for delays or mistakes in the administration of the Plan, establish reasonable waiting and adjustment periods and/or accounting and crediting procedures to ensure that amounts applied toward the purchase of the Company’s Common Stock for each Participant properly correspond with amounts withheld from the Participant’s base salary or regular hourly wages, and establish such other limitations or procedures as the Committee determines in its sole discretion advisable which are consistent with the Plan. Such actions will not require stockholder approval or the consent of any Participants. However, no amendment shall be made without approval of the stockholders of the Company (obtained in accordance with Section 21 above) within twelve (12) months of the adoption of such amendment (or earlier if required by Section 21) if such amendment would: (a) increase the number of shares that may be issued under this Plan; or (b) change the designation of the employees (or class of employees) eligible for participation in this Plan.

26.        Corporate Transactions.

(a) In the event of a Corporate Transaction (as defined below), each outstanding right to purchase Company Common Stock will be assumed or an equivalent option substituted by the successor corporation or a parent or a subsidiary of the successor corporation. In the event that the successor corporation refuses to assume or substitute for the purchase right, the Offering Period with respect to which such purchase right relates will be shortened by setting a new Purchase Date (the “New Purchase Date”) and will end on the New Purchase Date. The New Purchase Date shall occur on or prior to the consummation of the Corporate Transaction.

(b) “Corporate Transaction” means the occurrence of any of the following events: (i) any “person” (as such term is used in Sections 13(d) and 14(d) of the Exchange Act) becomes the “beneficial owner” (as defined in Rule 13d-3 of the Exchange Act), directly or indirectly, of securities of the Company representing fifty percent (50%) or more of the total voting power represented by the Company’s then outstanding voting securities; or (ii) the consummation of the sale or disposition by the Company of all or substantially all of the Company’s assets; or (iii) the consummation of a merger or consolidation of the Company with any other corporation, other than a merger or consolidation which would result in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting securities of the surviving entity or its parent) at least fifty percent (50%) of the total voting power represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately after such merger or consolidation.

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Amyris, Inc. (THE “COMPANY”) 2010 EMPLOYEE STOCK PURCHASE PLAN (“ESPP”) ENROLLMENT/CHANGE FORM                    

SECTION 1: ACTIONS	CHECK DESIRED ACTION: ¨           Enroll in the ESPP ¨           Change Contribution Percentage ¨           Discontinue Contributions	AND COMPLETE SECTIONS: 2 + 3 + 4 + 6 2 + 4 + 6 2 + 5 + 6
SECTION 2:	Name:		Department:
PERSONAL DATA	Home Address:
	Social Security No.: ¨ ¨ ¨ - ¨ ¨ - ¨ ¨ ¨ ¨
SECTION 3: ENROLL	I hereby elect to participate in the ESPP, effective at the beginning of the next Offering Period (or with the first Offering Period). I elect to purchase shares of the Common Stock of the Company pursuant to the ESPP. I understand that the stock certificate(s) for the shares purchased on my behalf will be issued in street name and deposited directly into my brokerage account. I hereby agree to take all steps, and sign all forms, required to establish an account with [                    ] for this purpose. My participation will continue as long as I remain eligible, unless I withdraw from the ESPP by filing a new Enrollment/Change Form with the Company. I understand that I must notify the Company of any disposition of shares purchased under the ESPP.
SECTION 4: ELECT CONTRIBUTION PERCENTAGE	I hereby authorize the Company to withhold from each of my paychecks such amount as is necessary to equal at the end of the applicable Offering Period     % of my compensation (as defined in the ESPP) paid during such Offering Period as long as I continue to participate in the ESPP. That amount will be applied to the purchase of shares of the Company’s Common Stock pursuant to the ESPP. The percentage must be a whole number (from 1%, up to a maximum of 15%). Please ¨ -increase ¨ -decrease my contribution percentage. Note:  You may change your contribution percentage only once within an Offering Period to be effective during such Offering Period and such change can only be to decrease your contribution percentage. An increase in your contribution percentage can only take effect with the next Offering Period. Each change will become effective as soon as reasonably practicable after the form is received by the Company.
SECTION 5: DISCONTINUE CONTRIBUTIONS	¨      I hereby elect to stop my contributions under the ESPP, effective as soon as reasonably practicable after this form is received by the Company. Please ¨ -refund all contributions to me in cash, without interest OR ¨ -use my contributions to purchase shares on the next Purchase Date. I understand that I cannot resume participation until the start of the next Offering Period and must timely file a new enrollment form to do so.
SECTION 6: ACKNOWLEDGMENT  AND SIGNATURE	I acknowledge that I have received a copy of the ESPP and of the Prospectus (which summarizes the major features of the ESPP). I have read the Prospectus and my signature below (or my clicking on the Accept box if this is an electronic form) indicates that I hereby agree to be bound by the terms of the ESPP.
	Signature:		Date:

EX-10.05

EXHIBIT 10.05

AMYRIS, INC.
2010 EQUITY INCENTIVE PLAN
NOTICE OF PERFORMANCE STOCK OPTION GRANT

Unless otherwise defined herein, the terms defined in the 2010 Amyris, Inc. (the “Company”) Equity Incentive Plan (the “Plan”) shall have the same meanings in this Notice of Performance Stock Option Grant (the “Notice”).

Name: __John Melo_______________________________________________________

You (the “Participant”) have been granted an option to purchase shares of Common Stock of the Company (the “Option”) under the Plan subject to the terms and conditions of the Plan, this Notice and the Performance Stock Option Award Agreement (the Notice and Performance Stock Option Award Agreement together, the “Agreement”).

Date of Grant: _May 29, 2018_________________________________

Exercise Price per Share: _$5.08__________________________________

Total Number of Shares: 3,250,000

Type of Option: Non-Qualified Stock Option

Expiration Date: _May 29, 2028_________________________________

Vesting Schedule: As set forth below

I. Vesting Requirements

This Option is a performance-based stock option award and, subject to Participant continuing as the Chief Executive Officer of the Company (the “Chief Executive Officer”) through each vesting event, shall vest and be exercisable upon the vesting dates set forth below subject to the satisfaction of both EBITDA Milestones and Stock Price Milestones as described in more detail below.

Vesting. The Option is divided into four (4) vesting tranches (each a “Tranche”), with each Tranche representing a portion of the Option covering that number of Shares specified next to the applicable Tranche in the Milestone Table below. Each Tranche shall vest upon the vesting date specified as applicable to the Tranche in the Milestone Table (each, an “Earliest Vesting Date”) subject to all of the following: (a) the achievement of the EBITDA Milestone applicable to the Tranche in the Milestone Table during the EBITDA Measurement Period (as defined below) (each, an “EBITDA Milestone”), (b) the achievement of the Stock Price Milestone applicable to the Tranche in the Milestone Table during the Stock Price Measurement Period (as defined below) (each, a “Stock Price Milestone”) (the EBITDA Milestones and the Stock Price Milestones, collectively, the “Milestones”), (c) Participant continuing as the Chief Executive Officer through the Earliest Vesting Date applicable to the Tranche in the Milestone Table and (d) the Certification (as defined below) of the Milestones by the Board of Directors of the Company (the “Board”) or the Board’s Compensation Committee (the “Compensation Committee”). Any Milestone may be met before, at or after the applicable Earliest Vesting Date for that Tranche provided that the Milestone is met during its applicable Measurement Period.

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Milestone Table

Tranche	Number of Shares	EBITDA Milestone ($M)	Stock Price Milestone	Earliest Vesting Date
1 “Tranche One”	750,000 “Tranche One Shares”	$10	$15	July 1, 2019 “Tranche One Earliest Vesting Date”
2 “Tranche Two”	750,000 “Tranche Two Shares”	$60	$20	July 1, 2020 “Tranche Two Earliest Vesting Date”
3 “Tranche Three”	750,000 “Tranche Three Shares”	$80	$25	July 1, 2021 “Tranche Three Earliest Vesting Date”
4 “Tranche Four”	1,000,000 “Tranche Four Shares”	$100	$30	July 1, 2022 “Tranche Four Earliest Vesting Date”

In the event that either the EBITDA Milestone or the Stock Price Milestone is not yet achieved for a Tranche, no Shares attributable to such Tranche will be eligible to vest on such Tranche’s Earliest Vesting Date; provided, however, the EBITDA Milestones will remain eligible to be achieved during the remaining EBITDA Measurement Period and the Stock Price Milestones will remain eligible to be achieved during the remaining Stock Price Measurement Period (both as defined below).

Any portion of the Option that does not vest (i) on or prior to the end of the EBITDA Measurement Period and the Stock Price Measurement Period, as applicable, or (ii) prior to Participant’s termination as Chief Executive Officer (except in connection with a Change of Control (as defined below) as set forth in Section IV below) shall immediately terminate.

For clarity, as set forth above, upon the achievement of both the applicable EBITDA Milestone and Stock Price Milestone for a Tranche, the Shares attributable to such Tranche (the “Unvested Achieved Options”) may vest only if Participant remains the Chief Executive Officer on the applicable Earliest Vesting Date for such Tranche (except in connection with a Change of Control as set forth in Section IV below).

More than one Tranche may vest simultaneously provided that: the Earliest Vesting Date for each applicable Tranche has occurred, the requisite EBITDA Milestone and Stock Price Milestone for each applicable Tranche have been met and Participant continued as the Chief Executive Officer through the applicable date of vesting. For example, assume that (i) either or both of the Milestones for the First Tranche were not achieved on or prior to the Tranche One Earliest Vesting Date, (ii) all of the Milestones for Tranche One, Tranche Two and Tranche Three were achieved on or prior to the Tranche Two Earliest Vesting Date, then, (x) subject to Participant remaining the Chief Executive Officer through the Tranche Two Earliest Vesting Date, both Tranche One and Tranche Two will become vested on the Tranche Two Earliest Vesting Date and (y) subject to Participant remaining the Chief Executive Officer through the Tranche Three Earliest Vesting Date, Tranche Three will become vested on the Tranche Three Earliest Vesting Date.

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Certification. Achievement of the Milestones for each Tranche shall be determined, approved and certified by the Board or the Compensation Committee, in its sole, good faith discretion (a “Certification” and the date of such Certification, the “Certification Date”). Separate Certifications may occur on separate dates with respect to the achievement of each of EBITDA Milestone and Stock Price Milestone that are required for the vesting of any particular Tranche.

Term; Expiration. The maximum term of the Option shall be ten (10) years unless earlier terminated as set forth herein, and the Option shall expire automatically on the Expiration Date specified above (without regard to whether any or all of the Option vested or whether Participant exercised any vested part of the Option).

II. Determination of EBITDA Milestone

The EBITDA Milestone for a Tranche is achieved if the Company’s EBITDA (as defined below) equals or exceeds the EBITDA threshold amount set forth in the Milestone Table for such Tranche for any fiscal year during the EBITDA Measurement Period. The Committee will measure and certify the level of achievement of the EBITDA Milestones as of the end of each fiscal year within the EBITDA Measurement Period.

A. For purposes of this Option, “EBITDA” shall mean the Company’s net (loss) income attributable to common stockholders for the relevant year as determined in accordance with U.S. Generally Accepted Accounting Principles (“GAAP”) and as reported by the Company in its audited financial statements on the Form 10-K filed with the SEC, for the applicable fiscal year during the EBITDA Measurement Period plus interest expense (benefit), provision for income taxes, depreciation and amortization for the same year as reflected in the audited financial statements. For the avoidance of doubt, there will be no adjustment to the reported net (loss) for stock based compensation in determining EBITDA.

B. For purposes of this Option, “EBITDA Measurement Period” shall mean the period starting January 1, 2018 and ending December 31, 2021.

C. In the event of unusual non-recurring events such as acquisition activities or divestitures of significant assets or changes in applicable accounting rules, as a result of which the calculation of the Company’s EBITDA for any EBITDA Measurement Period is increased or decreased by 10% or more in determining the Company’s financial statements on Form 10-K filed with the SEC for the most recently completed fiscal year, the Board or, if the Board delegates authority to the Compensation Committee, the Compensation Committee may provide for one or more equitable adjustments to the EBITDA Milestones to preserve the original intent regarding the EBITDA Milestones at the time of the initial award grant.

III. Determination of Stock Price Milestone

The Stock Price Milestone for a Tranche is achieved if the both the 180-Day Average Stock Price (as defined below) and the 30-Day Average Stock Price (as defined below) equal or exceed the price set forth in the Milestone Table for such Tranche during the Stock Price Measurement Period. The Committee will measure and certify the level of achievement of the Stock Price Milestone during the Stock Price Measurement Period as described below.

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A. For purposes of this Option, “180-Day Average Stock Price” shall mean for each applicable Tranche, the average of the daily closing prices of the Company’s common stock on the Nasdaq Global Select Market for any one hundred and eighty (180)-consecutive day period (x) starting at any time after the last day of the fiscal year in which the applicable EBITDA Milestone was achieved and (y) ending on or prior to the final day of the Stock Price Measurement Period.

B. For purposes of this Option, “30-Day Average Stock Price” shall mean for each applicable Tranche, the average of the daily closing prices of the Company’s common stock on the Nasdaq Global Select Market for a thirty (30)-consecutive day period ending on the date on which the 180-Day Average Stock Price is achieved for the applicable Tranche, but in any event on or prior to final day of the Stock Price Measurement Period.

C. For purposes of this Option, “Stock Price Measurement Period” shall mean the period starting January 1, 2018 and ending December 31, 2022.

D. If the event of a stock dividend, recapitalization, stock split, reverse stock split, subdivision, combination, reclassification or similar change in the capital structure of the Company, without consideration, the Board or the Compensation Committee, in order to prevent diminution or enlargement of the benefits or potential benefits intended to be made available under the Option (and in a manner that will not provide Participant with any greater benefit or potential benefits than intended to be made available under the Option, other than as may be necessary solely to reflect changes resulting from any such aforementioned event), will adjust the Stock Price Milestones.

IV. Vesting Determination upon Change of Control of the Company

Calculation of Milestones upon Change of Control. Notwithstanding Sections I, II and III above, in the event of a Change of Control (as defined in the Company’s Executive Severance Plan, adopted November 6, 2013, and Participant’s related Participation Agreement thereunder (together, the “Severance Plan”)), for purposes of determining whether any Tranches are eligible to vest on or after the Change of Control, the EBITDA Milestones shall be disregarded and only the Stock Price Milestones shall be required to be met as determined pursuant to this Section IV.

In the event of a Change of Control, a Stock Price Milestone relating to any Tranche that has not yet vested pursuant to Section I above as of immediately before the closing of the Change of Control, shall be achieved if the per Share price (plus the per Share value of any other consideration) received by the Company’s stockholders in the Change of Control equals or exceeds the price set forth in the Milestone Table for the relevant Stock Price Milestone, and the Shares specified for any such Tranche will be eligible to vest pursuant to the time-based vesting schedule set forth below (the “COC Time-Based Options”). To the extent a Stock Price Milestone is not achieved as a result of the Change of Control pursuant to the preceding sentence, the corresponding Tranche of Shares will be forfeited automatically as of the immediately prior to closing of the Change of Control and never shall become vested.

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Vesting Requirements Upon Change of Control. Subject to Participant’s remaining the Chief Executive Officer, (i) the COC Time-Based Options for Tranche One, if any, will vest on the later of the Tranche One Earliest Vesting Date and the closing date of the Change of Control (the “Closing Date”); (ii) the COC Time-Based Options for Tranche Two, if any, will vest on the later of the Tranche Two Earliest Vesting Date and the Closing Date; (iii) the COC Time-Based Options for Tranche Three, if any, will vest on the later of the Tranche Three Earliest Vesting Date and the Closing Date and (iv) the COC Time-Based Options for Tranche Four, if any, will vest on the later of the Tranche Four Earliest Vesting Date and the Closing Date. Notwithstanding the foregoing, in the event the Participant’s employment as Chief Executive Officer terminates as a result of an Involuntary Termination (as defined in Participant’s Severance Plan) at any time within the period beginning three (3) months before a Change of Control and ending twelve (12) months after a Change of Control, the unvested Achieved Options and COC Time-Based Options shall be eligible for accelerated vesting as provided in the Participant’s Severance Plan subject to Participant’s satisfaction of all terms and conditions in the Severance Plan, including, but not limited to delivery of a release of claims. If the Participant’s employment as Chief Executive Officer terminates as a result of an Involuntary Termination prior to a Change of Control, any then-unvested portion of the Option that would otherwise forfeit upon such termination shall remain outstanding, but cease to continue vesting, for three (3) months following such termination (provided that in no event will the Option remain outstanding beyond the expiration of its maximum term) to permit the acceleration described above. In the event that a Change in Control is not completed during such three (3) month period, any unvested portion of the Option will be automatically and permanently forfeited without having vested effective three (3) months following such termination. For the avoidance of doubt, the accelerated vesting provisions of the Severance Plan apply only upon a Change of Control and apply only to the Unvested Achieved Options and COC Time-Based Options.

Non-Assumption upon Change of Control. Notwithstanding anything to the contrary, if the successor or acquiring corporation (if any) of the Company refuses to assume, convert, replace or substitute the Option in connection with a Change of Control, then notwithstanding any other provision in this Agreement, the Plan or the Severance Plan to the contrary, 100% of Participant’s COC Time-Based Options shall accelerate and become vested effective immediately prior to the Change of Control.

V. Termination as Chief Executive Officer

Notwithstanding anything to the contrary in this Agreement, the Severance Agreement Plan or any other agreement, upon Participant’s termination as the Chief Executive Officer (except in connection with a Change of Control as set forth in Section IV above), any then-unvested portion of the Option will automatically terminate.

If, upon Participant’s termination as the Chief Executive Officer, Participant continues as an Employee of the Company, and so long as Participant continues as an Employee of the Company, any vested and unexercised portion of the Option may be exercised until the Expiration Date of the Option.

If Participant ceases to be an Employee for any reason, this Option may, to the extent vested as of the date of Participant’s cessation as an Employee, be exercised during the time periods set forth in the Agreement, but in no event later than the Expiration Date of the Option.

VI. Award Subject to Company Clawback or Recoupment

In the event that the Company determines at any time between the Date of Grant set forth in the Notice and December 31, 2025 that it is required to prepare a material accounting restatement resulting from material noncompliance with financial reporting requirements under applicable law (a “financial restatement”), and any of the Milestones that were previously Certified as achieved are subsequently determined to have not been achieved as a result of a financial restatement, the Tranches of the Option that vested as a result of the Certification will be subject to recoupment. In such case, Participant will be required to forfeit, reimburse or repay any portion of the Option that vested based on the original financial statement as compared to the Option that would have vested based on the financial restatement. For purposes of this compensation recovery by the Company: (a) if the Option, or a portion of the Option, is held at the time of recovery, the recoverable amount shall be the number Shares subject to the Option that vested in in excess of the number that should have been vested based on the financial restatement; (b) if the Option, or a portion of the Option, has been exercised, but the underlying Shares have not been sold, the recoverable amount shall be the number of Shares underlying the Option in excess of the number of Shares that should have been vested and exercisable based on the financial restatement; and (c) if Shares have been sold, the recoverable amount shall be the sale proceeds received by Participant in respect of the excess number of Shares underlying the Option in excess of the number of Shares that should have been vested and exercisable based on the financial restatement. In all cases, the determination of amounts to be recovered shall be calculated net of any taxes paid.

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In addition to the Company’s right to repayment pursuant to the preceding paragraph, the Option shall also be subject to clawback or recoupment pursuant to any compensation clawback or recoupment policy adopted by the Board as required by law during the term of Participant’s employment or other Service that is applicable to Participant. In addition to any other remedies available under such policy, applicable law may require the cancellation of Participant’s Option (whether vested or unvested) and the recoupment of any gains realized with respect to Participant’s Option.

VII. Exercise Method; Holding Period

Notwithstanding anything to the contrary in this Notice, the Agreement or the Plan, payment of the aggregate exercise price and any tax withholding obligations, may be paid only by any of the following, or a combination thereof, unless the Board or the Compensation Committee determines otherwise: (i) cash; (ii) check or (iii) a “broker-assisted” or “same-day sale” (as described in Section 11(d) of the Plan).

Participant must retain and may not sell, transfer or dispose at least fifty percent (50%) of the Shares acquired upon exercise of the Option net of any shares sold in a same-day sale to pay the exercise price and any tax withholding obligations as described above until after the second (2^nd) year anniversary of the applicable date of exercise of such Shares; provided, however, that the Participant may conduct transactions that involve merely a change in the form in which Participant owns such Shares (e.g., transfer Shares to a revocable inter vivos trust for which Participant is the trustee and sole beneficiary during Participant’s lifetime) as permitted by the Board or the Compensation Committee consistent with the Company’s internal policies.

VIII. Acceptance of Option

By Participant’s acceptance of this Agreement either electronically through the electronic acceptance procedure established by the Company or through a written acceptance delivered to the Company in a form satisfactory to the Company, Participant agrees that this Option is granted under and governed by the terms and conditions of this Notice, Agreement and the Plan, all of which are made a part of this document. Participant confirms that he has reviewed this Agreement in its entirety, has had an opportunity to obtain the advice of counsel prior to executing this Agreement and fully understands all provisions of the Agreement. Participant understand that his employment or service with the Company is for an unspecified duration, can be terminated at any time (i.e., is “at-will”), and that nothing in this Notice, the Agreement or the Plan changes the at-will nature of that relationship. Participant hereby agrees to accept as binding, conclusive and final all decisions or interpretations of the Board or the Compensation Committee upon any questions relating to the Agreement. Participant further agrees to notify the Company upon any change in the residence address indicated on the Notice.

Amyris, INC.

By: /s/ Christine Ofori

Name: Christine Ofori

Title: Chief People Officer

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Agreed and Accepted By PARTICIPANT:

By: /s/ John Melo

Name: John Melo

Title: President and Chief Executive Officer

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AMYRIS, INC.

2010 EQUITY INCENTIVE PLAN

PERFORMANCE STOCK OPTION AWARD AGREEMENT

Unless otherwise defined in this Performance Stock Option Award Agreement (the “Agreement”), any capitalized terms used herein shall have the meaning ascribed to them in the Amyris, Inc. (the “Company”) 2010 Equity Incentive Plan (the “Plan”).

Participant has been granted an option to purchase Shares (the “Option”), subject to the terms and conditions of the Plan, the Notice of Stock Option Grant (the “Notice”) and this Agreement. The Agreement incorporates the terms of the Notice and any reference to Agreement will be deemed to also include the terms of the Notice. In the event of a conflict between the terms and conditions of the Plan and the terms and conditions of this Agreement, the terms and conditions of the Plan shall prevail.

1.       Vesting Rights. Subject to the applicable provisions of the Plan and this Agreement, this Option may be exercised, in whole or in part, in accordance with the schedule set forth in the Notice.

2.       Termination Period.

(a)       General Rule. Except as provided below, and subject to the Plan, this Option may be exercised for 3 months after termination of Participant’s employment with the Company. In no event shall this Option be exercised later than the Expiration Date set forth in the Notice.

(b)       Death; Disability. Unless provided otherwise in the Notice, upon the termination of Participant’s service to the Company by reason of his or her Disability or death, or if a Participant dies within three months of the Termination Date, this Option may be exercised for twelve months, provided that in no event shall this Option be exercised later than the Expiration Date set forth in the Notice.

(c)       Cause. Upon the termination of Participant’s employment by the Company for Cause, the Option shall expire on such date of Participant’s Termination Date. For purposes of this Agreement, “Cause” shall be defined in the Plan.

3.       Grant of Option. The Participant named in the Notice has been granted an Option for the number of Shares set forth in the Notice at the exercise price per Share set forth in the Notice (the “Exercise Price”). This Option shall be treated as a Nonqualified Stock Option (“NSO”).

4.       Exercise of Option.

(a)       Right to Exercise. This Option is exercisable during its term in accordance with the Vesting Schedule set forth in the Notice and the applicable provisions of the Plan and this Agreement. In the event of Participant’s death, Disability, Termination for Cause or other Termination, the exercisability of the Option is governed by the applicable provisions of the Plan, the Notice and this Agreement.

(b)       Method of Exercise. This Option is exercisable by delivery of an exercise notice (the “Exercise Notice”), which shall state the election to exercise the Option, the number of Shares in respect of which the Option is being exercised (the “Exercised Shares”), and such other representations and agreements as may be required by the Company pursuant to the provisions of the Plan. The Exercise Notice shall be delivered in person, by mail, via electronic mail or facsimile or by other authorized method to the Secretary of the Company or other person designated by the Company. The Exercise Notice shall be accompanied by payment of the aggregate Exercise Price as to all Exercised Shares. This Option shall be deemed to be exercised upon receipt by the Company of such fully executed Exercise Notice accompanied by such aggregate Exercise Price.

(c)       No Shares shall be issued pursuant to the exercise of this Option unless such issuance and exercise complies with all relevant provisions of law and the requirements of any stock exchange or quotation service upon which the Shares are then listed. Assuming such compliance, for income tax purposes the Exercised Shares shall be considered transferred to the Participant on the date the Option is exercised with respect to such Exercised Shares.

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5.       Method of Payment. Payment of the aggregate Exercise Price and any tax liability (as described in Section 8 below) shall be by the methods set forth in the Notice.

6.       Non-Transferability of Option. This Option may not be transferred in any manner other than by will or by the laws of descent or distribution or court order and may be exercised during the lifetime of Participant only by the Participant unless otherwise permitted by the Board or the Compensation Committee on a case-by-case basis. The terms of the Plan and this Agreement shall be binding upon the executors, administrators, heirs, successors and assigns of the Participant.

7.       Term of Option. This Option shall in any event expire on the expiration date set forth in the Notice, which date is 10 years after the Date of Grant.

8.       U.S. Tax Consequences. For Participants subject to U.S. income tax, some of the federal tax consequences relating to this Option, as of the date of this Option, are set forth below. All other Participants should consult a tax advisor for tax consequences relating to this Option in their respective jurisdiction. THIS SUMMARY IS NECESSARILY INCOMPLETE, AND THE TAX LAWS AND REGULATIONS ARE SUBJECT TO CHANGE. THE PARTICIPANT SHOULD CONSULT A TAX ADVISER BEFORE EXERCISING THIS OPTION OR DISPOSING OF THE SHARES.

(a)       Exercising the Option.

(i)       Nonqualified Stock Option. The Participant may incur federal ordinary income tax liability upon exercise of a NSO. The Participant will be treated as having received compensation income (taxable at ordinary income tax rates) equal to the excess, if any, of the Fair Market Value of the Exercised Shares on the date of exercise over their aggregate Exercise Price. If the Participant is an Employee or a former Employee, the Company will be required to withhold from his or her compensation an amount equal to the minimum amount the Company is required to withhold for income and employment taxes or collect from Participant and pay to the applicable taxing authorities an amount in cash equal to a percentage of this compensation income at the time of exercise, and may refuse to honor the exercise and refuse to deliver Shares if such withholding amounts are not delivered at the time of exercise.

(b)       Disposition of Shares.

(i)       NSO. If the Participant holds NSO Shares for at least one year, any gain realized on disposition of the Shares will be treated as long-term capital gain for federal income tax purposes.

9.       Acknowledgement. The Company and Participant agree that the Option is granted under and governed by the Notice, this Agreement and by the provisions of the Plan (incorporated herein by reference). Participant: (i) acknowledges receipt of a copy of the Plan and the Plan prospectus, (ii) represents that Participant has carefully read and is familiar with their provisions, and (iii) hereby accepts the Option subject to all of the terms and conditions set forth herein and those set forth in the Plan and the Notice.

10.       Entire Agreement; Enforcement of Rights. This Agreement, the Plan and the Notice constitute the entire agreement and understanding of the parties relating to the subject matter herein and supersede all prior discussions between them. Any prior agreements, commitments or negotiations concerning the purchase of the Shares hereunder are superseded. No modification of or amendment to this Agreement, nor any waiver of any rights under this Agreement, shall be effective unless in writing and signed by the parties to this Agreement. The failure by either party to enforce any rights under this Agreement shall not be construed as a waiver of any rights of such party.

9

11.       Compliance with Laws and Regulations. The issuance of Shares will be subject to and conditioned upon compliance by the Company and Participant with all applicable state and federal laws and regulations and with all applicable requirements of any stock exchange or automated quotation system on which the Company’s Common Stock may be listed or quoted at the time of such issuance or transfer.

12.       Governing Law; Severability. If one or more provisions of this Agreement are held to be unenforceable under applicable law, the parties agree to renegotiate such provision in good faith. In the event that the parties cannot reach a mutually agreeable and enforceable replacement for such provision, then (i) such provision shall be excluded from this Agreement, (ii) the balance of this Agreement shall be interpreted as if such provision were so excluded and (iii) the balance of this Agreement shall be enforceable in accordance with its terms. This Agreement and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of California, without giving effect to principles of conflicts of law.

13.       No Rights as Employee, Director or Consultant. Nothing in this Agreement shall affect in any manner whatsoever the right or power of the Company, or a Parent or Subsidiary of the Company, to terminate Participant’s service, for any reason, with or without cause.

10

EX-10.06

EXHIBIT 10.06

Amendment #1 to Participation Agreement

This Amendment #1 to Participation Agreement (this “Amendment”) is made as of May 30, 2018 by and between Amyris, Inc., a Delaware corporation (the “Company”), and John Melo (the “Employee”).

WHEREAS, the Company has selected the Employee to participate in the Amyris, Inc. Executive Severance Plan (the “Plan”; capitalized terms not otherwise defined herein shall have the meanings given to them in the Plan) and has previously executed a Participation Agreement, dated as of December 18, 2013 (the “Participation Agreement”), with the Employee setting forth the terms and conditions of such participation.

WHEREAS, the Company and the Employee desire to amend the Participation Agreement as set forth herein.

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereby agree as follows:

1.       Amendment. Section 2 of the Participation Agreement (“Waiver of Other Severance and Benefits”) is hereby deleted in its entirety and replaced with the following:

“2. Waiver of Other Severance and Benefits. By signing below, the Employee agrees to waive any rights the Employee may have in connection with any change of control or severance benefits that may be contained in the Company’s employment offer letter to the Employee, any equity agreement by and between the Company and the Employee and any other agreement that specifically relates to accelerated vesting of any Stock Awards, other than any such rights contained in that certain Performance Stock Option Award Agreement between the Company and the Employee relating to that certain stock option award granted to the Employee on May 29, 2018 (the “Option Award Agreement”). In the event of any conflict between this Participation Agreement or the Plan and the Option Award Agreement relating to accelerated vesting of Stock Awards, the terms of the Option Award Agreement shall govern and control.”

2.       Full Force and Effect. Except as expressly modified by this Amendment, the terms of the Participation Agreement shall remain in full force and effect.

3.       Entire Agreement. This Amendment, the Participation Agreement and the Plan constitute the entire agreement between the Employee and the Company with respect to the subject matter hereof and thereof and supersede all prior agreements, written or oral, relating hereto or thereto.

4.       Counterparts; Facsimile. This Amendment may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf), and delivery of any signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other party.

[remainder of this page intentionally left blank]

1

Amyris, Inc.

By: /s/ Christine Ofori

Title: Chief People Officer

Employee

Signature /s/ John Melo

John Melo

Printed Name

[signature page to Amendment #1 to Participation Agreement]

2

EX-31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John G. Melo, certify that:

1.       I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2.       Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.       Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.       The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a)       Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b)       Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c)       Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d)       Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5.       The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a)       All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b)       Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 14, 2018	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Kathleen Valiasek, certify that:

1.       I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2.       Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.       Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.       The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a)       Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b)       Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c)       Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d)       Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5.       The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a)       All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b)       Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 14, 2018	/s/ Kathleen Valiasek
	Kathleen Valiasek
	Chief Financial Officer

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2018, as filed with the Securities and Exchange Commission on the date hereof, I, John G. Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2018 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 14, 2018	/s/ John G. Melo
	John G. Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended June 30, 2018, as filed with the Securities and Exchange Commission on the date hereof, I, Kathleen Valiasek, Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended June 30, 2018 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: August 14, 2018	/s/ Kathleen Valiasek
	Kathleen Valiasek
	Chief Financial Officer
	(Principal Financial Officer)

XML

Document And Entity Information - shares	6 Months Ended
	Jun. 30, 2018	Aug. 10, 2018
Document Information [Line Items]
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Trading Symbol	amrs
Current Fiscal Year End Date	--12-31
Entity Filer Category	Smaller Reporting Company
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Well-known Seasoned Issuer	No
Entity Common Stock, Shares Outstanding (in shares)		50,368,507
Document Type	10-Q
Document Period End Date	Jun. 30, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	Q2
Amendment Flag	false

XML

Condensed Consolidated Balance Sheets (Current Period Unaudited) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 14,050	$ 57,059
Restricted cash	1,846	2,994
Short-term investments	130
Accounts receivable, net of allowance of $642 as of June 30, 2018 and December 31, 2017	26,814	24,281
Unbilled receivable, current	12,683	9,340
Inventories	6,632	5,408
Prepaid expenses and other current assets	4,687	5,525
Total current assets	66,842	104,607
Property, plant and equipment, net	15,300	13,892
Unbilled receivable, noncurrent	9,747	7,940
Restricted cash, noncurrent	959	959
Recoverable taxes from Brazilian government entities	1,057	1,445
Other assets	24,747	22,640
Total assets	118,652	151,483
Current liabilities:
Accounts payable	19,206	15,921
Accrued and other current liabilities	20,101	29,402
Deferred revenue, current	9,643	4,880
Debt, current portion	59,987	36,924
Related party debt, current portion	49,669	20,019
Total current liabilities	158,606	107,146
Long-term debt, net of current portion	43,642	61,893
Related party debt, net of current portion	18,104	46,541
Derivative liabilities	138,695	119,978
Other noncurrent liabilities	8,581	10,632
Total liabilities	367,628	346,190
Commitments and contingencies (Note 9)
Preferred stock - $0.0001 par value, 5,000,000 shares authorized as of June 30, 2018 and December 31, 2017, and 19,334 and 22,171 shares issued and outstanding as of June 30, 2018 and December 31, 2017, respectively
Common stock - $0.0001 par value, 250,000,000 shares authorized as of June 30, 2018 and December 31, 2017; 50,340,680 and 45,637,433 shares issued and outstanding as of June 30, 2018 and December 31, 2017, respectively	5	5
Additional paid-in capital	1,086,814	1,048,274
Accumulated other comprehensive loss	(42,818)	(42,156)
Accumulated deficit	(1,298,914)	(1,206,767)
Total Amyris, Inc. stockholders’ deficit	(254,913)	(200,644)
Noncontrolling interest	937	937
Total stockholders' deficit	(253,976)	(199,707)
Total liabilities, mezzanine equity and stockholders' deficit	118,652	151,483
Contingently Redeemable Common Stock [Member]
Current liabilities:
Mezzanine Equity	$ 5,000	$ 5,000

XML

Condensed Consolidated Balance Sheets (Current Period Unaudited) (Parentheticals) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Accounts receivable, allowance	$ 642	$ 642
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	19,334	22,171
Preferred stock, shares outstanding (in shares)	19,334	22,171
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	250,000,000	250,000,000
Common stock, shares issued (in shares)	50,340,680	45,637,433
Common stock, shares outstanding (in shares)	50,340,680	45,637,433

XML

Condensed Consolidated Statements of Operations (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Revenue:
Revenues	$ 23,194	$ 25,679	$ 46,192	$ 38,660
Cost and operating expenses:
Cost of products sold	5,984	17,279	11,299	30,047
Research and development	15,287	14,249	34,100	28,956
Sales, general and administrative	20,189	15,949	38,946	28,799
Total cost and operating expenses	41,460	47,477	84,345	87,802
Loss from operations	(18,266)	(21,798)	(38,153)	(49,142)
Other income (expense):
Interest expense	(8,824)	(9,303)	(17,029)	(21,486)
Gain (loss) from change in fair value of derivative instruments	24,365	35,775	(39,548)	38,114
Gain upon extinguishment of derivative liability	1,857		1,857
Loss upon extinguishment of debt	(26)	(3,624)	(26)	(3,528)
Other income (expense), net	2,427	(120)	2,936	(440)
Total other income (expense), net	19,799	22,728	(51,810)	12,660
Income (loss) before income taxes	1,533	930	(89,963)	(36,482)
Provision for income taxes		(310)		(269)
Net income (loss) attributable to Amyris, Inc.	1,533	620	(89,963)	(36,751)
Less deemed dividend on capital distribution to related parties		(8,648)		(8,648)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		(562)		(562)
Less cumulative dividends on Series A and B preferred stock	(399)	(1,675)	(794)	(1,675)
Less earnings allocated to participating securities	(67)
Net income (loss) attributable to Amyris, Inc. common stockholders	$ 1,067	$ (10,265)	$ (90,757)	$ (47,636)
Net income (loss) per share attributable to common stockholders, basic (in dollars per share)	$ 0.02	$ (0.44)	$ (1.71)	$ (2.24)
Net loss per share attributable to common stockholders, diluted (in dollars per share)	$ (0.29)	$ (0.44)	$ (1.71)	$ (2.24)
Weighted-average shares of common stock outstanding used in computing net income (loss) per share of common stock, basic (in shares)	54,932,411	23,155,874	53,076,975	21,226,013
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, diluted (in shares)	60,729,736	23,155,874	53,076,975	21,226,013
Product [Member]
Revenue:
Revenues	$ 6,633	$ 9,892	$ 11,828	$ 17,929
Licenses and Royalties [Member]
Revenue:
Revenues	6,887	5,497	18,324	5,752
Grants and Collaborations [Member]
Revenue:
Revenues	$ 9,674	$ 10,290	$ 16,040	$ 14,979

XML

Condensed Consolidated Statements of Operations (Unaudited) (Parentheticals) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Product [Member]
Revenues, related party	$ 144	$ 0	$ 295	$ 0

XML

Condensed Consolidated Statements of Comprehensive Loss (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Comprehensive income (loss):
Net income (loss) attributable to Amyris, Inc.	$ 1,533	$ 620	$ (89,963)	$ (36,751)
Foreign currency translation adjustment, net of tax	(525)	(1,422)	(662)	(1,099)
Total comprehensive income (loss) attributable to Amyris, Inc.	$ 1,008	$ (802)	$ (90,625)	$ (37,850)

XML

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017
Cash flows from operating activities
Net loss	$ (89,963)	$ (36,751)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss (gain) from change in fair value of derivative liabilities	39,548	(38,115)
Amortization of debt discount	6,587	7,637
Stock-based compensation	3,178	2,684
Depreciation and amortization	2,944	5,550
Loss (gain) on disposal of property, plant and equipment	942	(161)
Loss on foreign currency exchange rates	271	63
Loss upon extinguishment of debt	26	3,528
Gain on extinguishment of derivative liability	(1,857)
Gain on change in fair value of equity investment	(1,717)
Receipt of equity in connection with collaboration arrangements revenue		(2,660)
Changes in assets and liabilities:
Accounts receivable	(2,027)	(3,509)
Unbilled receivables	(5,150)
Inventories	(1,313)	409
Prepaid expenses and other assets	(1,072)	(4,220)
Accounts payable	2,681	(1,739)
Accrued and other liabilities	(10,031)	7,943
Increase (Decrease) in Contract with Customer, Liability	3,959	(838)
Net cash used in operating activities	(52,994)	(60,179)
Cash flows from investing activities
Purchases of property, plant and equipment	(4,207)	(264)
Increase in short-term investments	(157)	(85)
Net cash used in investing activities	(4,364)	(349)
Cash flows from financing activities
Proceeds from issuance of debt	34,611	12,455
Proceeds from issuance of common stock upon exercise of warrants	14,549
Proceeds from issuance of common stock in private placement	1,416
Proceeds from exercises of ESPP purchases	270
Proceeds from exercises of common stock options	248	69
Principal payments on debt	(37,037)	(24,372)
Principal payments on capital leases	(593)	(764)
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units	(185)	(110)
Proceeds from issuance of convertible preferred stock		50,661
Net cash provided by financing activities	13,279	37,939
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(78)	7
Net decrease in cash, cash equivalents and restricted cash	(44,157)	(22,582)
Cash, cash equivalents and restricted cash at beginning of period	61,012	32,433
Cash, cash equivalents and restricted cash at end of the period	16,855	9,851
Reconciliation of cash, cash equivalents and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	14,050	5,078
Restricted cash, current	1,846	3,815
Restricted cash, noncurrent	959	958
Cash, cash equivalents and restricted cash at end of the period	16,855	9,851
Supplemental disclosures of cash flow information:
Cash paid for interest	8,035	4,526
Supplemental disclosures of non-cash investing and financing activities:
Settlement of derivative liability into equity	9,536
Accrued interest added to debt principal	1,894	1,745
Acquisition of property, plant and equipment under accounts payable, accrued liabilities and notes payable	744	1,189
Financing of equipment	642	138
Issuance of convertible preferred stock upon conversion of debt		40,204
Issuance of common stock upon conversion of debt		28,702
Issuance of common stock for settlement of debt principal and interest payments		3,233
Financing of insurance premium under notes payable		$ 191

XML

Note 1 - Basis of Presentation and Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Significant Accounting Policies [Text Block]

1.

Basis of Presentation and Summary of Significant Accounting Policies

Amyris, Inc. (Amyris or the Company) is a leading industrial biotechnology company that applies its technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness, Clean Beauty, and Flavors & Fragrances markets. The Company's proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company's biotechnology platform and industrial fermentation process replace existing complex and expensive manufacturing processes. The Company has successfully used its technology to develop and produce

six

distinct molecules at commercial volumes.

The accompanying unaudited condensed consolidated financial statements of Amyris, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the

10

-K, from which the condensed consolidated balance sheet as of

December 

31,

2017

is derived. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (U.S. GAAP), for interim financial information and with the instructions to Form

10

-Q and Article

10

of Regulation S-

X.

Accordingly, since they are interim statements, the accompanying condensed consolidated financial statements do

not

include all of the information and notes required by U.S. GAAP for complete financial statements. The accompanying condensed consolidated financial statements reflect all adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary to a fair statement of the results for the interim periods presented. Interim results are

not

necessarily indicative of results for a full year.

Liquidity

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations for at least the next

12

months following the issuance of these financial statements. As of

June 

30,

2018,

the Company had negative working capital of

$105.9

million, excluding cash and cash equivalents and short-term investments (compared to negative working capital of

$59.6

million as of

December 

31,

2017

), and an accumulated deficit of

$1.3

billion.

As of

June 

30,

2018,

the Company's debt (including related party debt), net of deferred discount and issuance costs of

$25.5

million, totaled

$171.4

million, of which

$109.7

million is classified as current and

$23.2

million is mandatorily convertible into equity and within the control of the Company. The Company's debt service obligations through

August 31, 2019

are

$114.5

million, including

$15.8

million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness and cross-default clauses. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of the Company's outstanding indebtedness.

Cash and cash equivalents of

$14.1

million as of

June 

30,

2018

are

not

sufficient to fund expected future negative cash flows from operations and cash debt service obligations through

one

year following the issuance of these financial statements. These factors raise substantial doubt about the Company’s ability to continue as a going concern within

one

year after the date that these financial statements are issued. The financial statements do

not

include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to extend existing debt maturities by restructuring a majority of its convertible debt, which is uncertain and outside the control of the Company, in addition to the mandatory conversion of certain debt obligations into equity, which conversion is within the control of the Company. Further, the Company's operating plan for the next

12

months from the date of issuance of these financial statements contemplates a significant reduction in its net operating cash outflows as compared to the previous

12

months, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) significantly increased royalty revenues (previously referred to as value share revenues), (iii) reduced cost of products sold as a percentage of renewable products revenue due to anticipated procurement and production efficiencies, and (iv) cash inflows from grants and collaborations. Finally, during the

second

half of

2018,

the Company plans to obtain project financing for the construction of a new specialty ingredients manufacturing facility in Brazil. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it

may

be forced to liquidate its assets or obtain additional equity or debt financing, which

may

not

occur timely or on reasonable terms, if at all.

Significant Accounting Policies

Note

1,

"Basis of Presentation and Summary of Significant Accounting Policies", to the audited consolidated financial statements in the

10

-K includes a discussion of the significant accounting policies and estimates used in the preparation of the Company’s consolidated financial statements. Except as noted below for the adoption of Accounting Standards Codification (“ASC”) Topic

606

(“ASC

606”

),

Revenue from Contracts with Customers

, and Accounting Standards Update (“ASU”)

2016

-

01,

 

Financial Instruments-Overall (Subtopic

825

-

10

): Recognition and Measurement of Financial Assets and Financial Liabilities

, there have been

no

material changes to the Company's significant accounting policies and estimates during the

three

and

six

months ended

June 

30,

2018.

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer and recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does

not

incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators among others when determining whether it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does

not

meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note

10,

"Significant Revenue Agreements" in Part II, Item

8

of the

10

-K.

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. The Company’s renewable products are delivered to customers from the Company’s facilities with shipping terms typically specifying F.O.B. shipping point.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts

may

contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the

first

transportation carrier. The Company, on occasion,

may

recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does

not

have the ability to direct the product to a different customer. It is at this point that we have right to payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do

not

include rights of return. Returns are accepted only if the product does

not

meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a

two

-year assurance-type warranty to replace squalane products that do

not

meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property:

When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property:

The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception and revenue is estimated and recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends.

When the Company’s intellectual property license is

not

the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will

not

occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services:

The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaborators with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include

one

or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will

not

occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will

not

occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment.

The Company generally invoices its collaborators on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Deferred revenue arises from amounts received in advance of performing the research and development activities and is recognized as revenue in future periods as the performance obligations are satisfied.

Grants:

The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will

not

occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

For descriptions of the Company's other significant accounting policies, see the Company's Annual Report on Form

10

-K for the year ended

December 

31,

2017.

Recent Accounting Pronouncements

(a) Recent Accounting Standards, Pronouncements or Updates Recently Adopted

In the

six

months ended

June 

30,

2018,

the Company adopted these new accounting standards or updates:

Revenue Recognition

The Company adopted ASC

606

with a date of initial application of

January 1, 2018.

As a result, the Company has changed its accounting policy for revenue recognition as detailed above in “Significant Accounting Policies”. The Company applied ASC

606

using the modified retrospective approach by recognizing the cumulative effect of initially applying ASC

606

to all contracts

not

completed as of the date of adoption as an adjustment to the opening balance of accumulated deficit at

January 1, 2018.

Therefore, the comparative information has

not

been adjusted and continues to be reported under the legacy revenue recognition guidance of ASC

605,

"Revenue Recognition".

The Company applied ASC

606

using a practical expedient for contracts that were modified before the application date, which allowed us to determine an aggregate effect of all modifications that occurred before

January 1, 2018,

when determining the satisfied and unsatisfied performance obligations, the transaction price, and allocating that transaction price to the performance obligations instead of retrospectively restating the contracts for such contract modifications.

The cumulative effect of initially applying ASC

606

resulted in an increase to accumulated deficit at

January 1, 2018

of approximately

$0.8

million. The increase in accumulated deficit arose primarily from a

$0.8

million increase of deferred revenue related to the effects of measuring and allocating the transaction price to the performance obligations under ASC

606

compared to the legacy guidance of ASC

605.

The most significant change in accounting policy is the Company now estimates royalty revenues from licenses of the Company’s intellectual property and recognizes estimated royalty revenues at a point in time when the Company sells its renewable products to its customers (if the sales-based royalty exception does

not

apply) or when the licensee sells its products to its customer (if the sales-based royalty exception does apply). Also, the transaction price for royalty revenues is reduced for variable incentive payments that

may

be payable by the Company to customers.

The following table presents the amounts by which revenue is affected in the current reporting period by the application of ASC

606

as compared with the legacy guidance that was in effect before the accounting change.

No

other consolidated statements of operations financial statement line items were impacted by the adoption of ASC

606.

	Three Months Ended June 30, 2018							Six Months Ended June 30, 2018
(In thousands)	As Reported		Adjustments			Amounts Without the Adoption of ASC 606		As Reported		Adjustments			Amounts Without the Adoption of ASC 606
Renewable products	$	6,633	$	—		$	6,633	$	11,828	$	—		$	11,828
Licenses and royalties		6,887		(4,980	)		1,907		18,324		(15,747	)		2,577
Grants and collaborations		9,674		(2,039	)		7,635		16,040		(2,265	)		13,775
Total revenue from all customers	$	23,194	$	(7,019	)	$	16,175	$	46,192	$	(18,012	)	$	28,180

Financial Instruments

In

January 2016,

the Financial Accounting Standards Board (FASB) issued ASU

2016

-

01,

 

Financial Instruments-Overall (Subtopic

825

-

10

): Recognition and Measurement of Financial Assets and Financial Liabilities

, which changes the accounting for equity investments, financial liabilities under the fair value option, and the presentation and disclosure requirements for financial instruments. The Company adopted ASU

2016

-

01

on

January 1, 2018

and, as a result, has changed its accounting policy to account for investments in equity securities (other than those accounted for using the equity method of accounting) at fair value with changes in fair value recognized in net income. The Company applied the modified retrospective approach by recognizing a

$1.4

million cumulative effect adjustment as an increase to the opening balance of accumulated deficit at

January 1, 2018

representing an unrealized loss measured as the difference between the fair value and the cost basis of the Company’s equity investments as of

January 1, 2018

previously accounted for using the cost method of accounting.

Classification of Cash Flow Elements

In

August 2016,

the FASB issued ASU

2016

-

15,

 

Statement of Cash Flows (Topic

230

): Classification of Certain Cash Receipts and Cash Payments,

 which affects the classification of certain cash receipts and cash payments on the statement of cash flows. ASU

2016

-

15

resulted in a change in cash flow classification of debt prepayment or extinguishment costs. Prior to the adoption of ASU

2016

-

15,

the Company classified gains or losses upon extinguishment of debt as an operating activity in the statements of cash flows. ASU

2016

-

15

became effective

January 1, 2018

on a retrospective basis. Upon the Company's adoption of ASU

2016

-

15,

such gains or losses are now classified in statements of cash flows as a financing activity.

Restricted Cash in Statement of Cash Flows

In

November 2016,

the FASB issued ASU

2016

-

18,

 

Statement of Cash Flows (Topic

230

): Restricted Cash,

 which requires that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The accounting standard update became effective

January 1, 2018

using a retrospective transition method for each period presented. Upon adoption, ASU

2016

-

18

has resulted in a change in the presentation of restricted cash in the statement of cash flows for current and prior periods presented.

Derecognition of Nonfinancial Assets

In

February 2017,

the FASB issued ASU

2017

-

05,

 

Other Income—Gains and Losses from the Derecognition of Nonfinancial Assets (Subtopic

610

-

20

): Clarifying the Scope of Asset Derecognition Guidance and Accounting for Partial Sales of Nonfinancial Assets

, which requires entities to apply certain recognition and measurement principles in ASC

606

when they derecognize nonfinancial assets, and in substance, nonfinancial assets, and the counterparty is

not

a customer. The guidance applies to: (

1

) contracts to transfer to a noncustomer a nonfinancial asset or group of nonfinancial assets, or an ownership interest in a consolidated subsidiary that does

not

meet the definition of a business and is

not

a

not

-for-profit activity; and (

2

) contributions of nonfinancial assets that are

not

a business to a joint venture or other noncontrolled investee. The accounting standard update became effective

January 1, 2018

on a modified retrospective basis. Adoption of this ASU did

not

 impact the Company's consolidated financial position, results of operations or cash flows.

Staff Accounting Bulletin

No

118

- Tax Cuts and Jobs Act of

2017

On

December 22, 2017,

the Tax Cuts and Jobs Act of

2017

(the Act) was signed into law, making significant changes to the Internal Revenue Code. Changes include, but are

not

limited to, a corporate tax rate decrease from

35%

to

21%

,

the transition of U.S. international taxation from a worldwide tax system to a territorial system, and a

one

-time transition tax on the mandatory deemed repatriation of cumulative foreign earnings as of

December 31, 2017.

Based on the Company’s current operations it is anticipated that the only significant current impact of the Act for the Company will be the reduction in the U.S. corporate tax rate. The Act reduces the corporate tax rate to

21

percent, effective

January 1, 2018.

In

December 2017,

Staff Accounting Bulletin

No.

118

(SAB

118

) was issued to address the application of U.S. GAAP in situations when a registrant does

not

have the necessary information available, prepared, or analyzed in reasonable detail to complete the accounting for certain income tax effects of the Tax Act. As of

June 

30,

2018,

due to the complexities of the new law, the Company has

not

yet completed its accounting for all the tax effects of the Tax Act, but has made a reasonable estimate of the effects on the Company's existing deferred tax balances. In all cases, the Company will continue to make and refine its calculations as additional analysis is completed. In addition, the Company's provisional estimate of the effects on its existing deferred tax balances

may

also be adjusted as the Company gains a more thorough understanding of the tax law during the

one

-year measurement period allowed under SAB

118.

Additionally, the Act created a new requirement that certain income, referred to as "Global Intangible Low-Taxed Income" (GILTI) earned by controlled foreign corporations (CFCs) must be included currently in the gross income of the CFCs’ U.S. shareholder. The Company’s selection of an accounting policy with respect to the new GILTI tax rules will depend, in part, on analyzing its global income to determine whether it expects to have future U.S. inclusions in taxable income related to GILTI and, if so, what the impact is expected to be. As of

June 

30,

2018,

the Company has

not

made a policy decision regarding whether to record deferred taxes on GILTI.

(b) Recent Accounting Standards Pronouncements or Updates

Not

Yet Effective as of Period End

Leases

In

February 2016,

the FASB issued ASU

2016

-

02,

 

Leases (Topic

842

),

 with fundamental changes as to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach, which requires lessees and lessors to recognize and measure leases at the beginning of the earliest period presented. The Company is in the initial stages of evaluating the impact of the new standard on its accounting policies, processes and system requirements. The Company anticipates that the standard

may

have a material impact on the Company’s condensed consolidated balance sheets due to the requirement to recognize leased right-of-use assets and corresponding liabilities related to leases on the Company’s condensed consolidated balance sheets, but is still evaluating whether the standard might have a material impact on the Company’s other condensed consolidated financial statements.

Financial Instruments with "Down Round" Features

In

July 2017,

the FASB issued ASU

2017

-

11,

 

Earnings Per Share (Topic

260

); Distinguishing Liabilities from Equity (Topic

480

); Derivatives and Hedging (Topic

815

): Accounting for Certain Financial Instruments with Down Round Features

. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature

no

longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach. The Company is in the initial stages of evaluating the impact of the new standard on its consolidated financial statements.

Non-employee Stock-based Compensation

In

June 2018,

the FASB issued ASU

2018

-

07,

Improvements to Nonemployee Share-Based Payment Accounting,

which more closely aligns the accounting for employee and nonemployee stock-based compensation. Under the new standard, companies will

no

longer be required to value non-employee awards differently from employee awards. This accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach. The Company anticipates that the new standard will

not

materially impact the Company's consolidated financial statements.

Use of Estimates

The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the periods presented. Actual results could differ from these estimates, and such differences

may

be material to the financial statements.

Reclassifications

Certain prior period amounts have been reclassified to conform to the current period presentation in the Company’s condensed consolidated financial statements and the accompanying notes to the condensed consolidated financial statements. The condensed consolidated statements of operations previously presented license fee revenue in combination with grants and collaborations revenue, and royalties (formerly referred to as “value share”) were previously presented in combination with renewable products revenue. Licenses and royalties revenue is presented as a separate line within the condensed consolidated statements of operations. The reclassifications reflect the growth in the Company’s business model of licensing its technology and earning royalties from customers utilizing the Company’s technology in the products it produces and sells. The reclassifications had

no

impact on total revenue.

In the statements of cash flows, the prior period has been restated to reflect accounting standards changes for reporting (i) restricted cash, and (ii) debt extinguishment costs, in statements of cash flows.

XML

Note 2 - Balance Sheet Details

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Supplemental Balance Sheet Disclosures [Text Block]

2.

Balance Sheet Details

Accounts Receivable, Net

Accounts receivable, net is comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable	$	9,567	$	18,953
Related party accounts receivable		17,247		5,328
	$	26,814	$	24,281

Inventories

Inventories are stated at the lower of cost or net realizable value and are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Raw materials	$	823	$	819
Work-in-process		1,147		364
Finished goods		4,662		4,225
Inventories	$	6,632	$	5,408

Property, Plant and Equipment, Net

Property, plant and equipment, net is comprised of the following:

(In thousands)	June 30, 2018			December 31, 2017
Machinery and equipment	$	46,755		$	49,277
Leasehold improvements		40,571			40,036
Computers and software		10,497			9,555
Furniture and office equipment, vehicles and land		3,463			3,415
Construction in progress		18,583			17,438
		119,869			119,721
Less: accumulated depreciation and amortization		(104,569	)		(105,829	)
Property, plant and equipment, net	$	15,300		$	13,892

Property, plant and equipment, net includes

$4.8

million and

$4.2

million of machinery and equipment under capital leases as of

June 

30,

2018

and

December 

31,

2017,

respectively. Accumulated amortization of assets under capital leases totaled

$1.9

million and

$1.6

million as of

June 

30,

2018

and

December 

31,

2017,

respectively.

During the

three

and

six

months ended

June 30, 2018,

the Company capitalized

$1.2

million and

$1.6

million, respectively, of internal labor costs required to automate, integrate and ready certain laboratory and plant equipment for its intended use.

Depreciation and amortization expense, including amortization of assets under capital leases, was

$1.4

million and

$2.7

million for the

three

months ended

June 

30,

2018

and

2017,

respectively, and

$2.9

million and

$5.6

million for the

six

months ended

June 

30,

2018

and

2017,

respectively.

Other Assets

Other assets are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Contingent consideration	$	8,151	$	8,151
Prepaid royalty		7,285		7,409
Deposits		3,662		2,462
Equity investment in SweeGen		3,570		3,233
Goodwill		560		560
Other		1,519		825
Other assets	$	24,747	$	22,640

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Payroll and related expenses	$	7,074	$	7,238
Accrued interest		2,325		8,213
SMA relocation accrual		3,417		3,587
Tax-related liabilities		2,305		5,837
Professional services		1,400		1,894
Other		3,580		2,633
Total accrued and other current liabilities	$	20,101	$	29,402

XML

Note 3 - Fair Value Measurement

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Financial Instruments Disclosure [Text Block]

3.

Fair Value Measurement

Assets and Liabilities Measured and Recorded at Fair Value on a Recurring Basis

The following tables summarize assets and liabilities measured at fair value, and the respective fair value by input classification level within the fair value hierarchy:

(In thousands)	June 30, 2018								December 31, 2017
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Money market funds	$	—	$	—	$	—	$	—	$	53,199	$	—	$	—	$	53,199
Certificates of deposit		130		—		—		130		7,813		—		—		7,813
Equity investment in SweeGen		—		3,570		—		3,570		—		—		—		—
Total assets measured and recorded at fair value	$	130	$	3,570	$	—	$	3,700	$	61,012	$	—	$	—	$	61,012
Liabilities
Embedded derivatives in connection with the issuance of debt and equity instruments	$	—	$	—	$	6,560	$	6,560	$	—	$	—	$	4,203	$	4,203
Freestanding derivative instruments in connection with the issuance of equity instruments		—		—		132,135		132,135		—		—		115,775		115,775
Total liabilities measured and recorded at fair value	$	—	$	—	$	138,695	$	138,695	$	—	$	—	$	119,978	$	119,978

There were

no

transfers between levels during the periods presented.

Equity Investment in SweeGen

The Company holds

850,115

unregistered shares of SweeGen, Inc. common stock received as payment in connection with a

December 2016

revenue agreement between the Company and Phyto Tech Corp. (d/b/a Blue California). At

June 

30,

2018,

the fair value of the shares was

$3.6

million, determined based on the over-the-counter market (OTCMKTS) trading price of the SweeGen shares (Level

2

). For the

three

and

six

months ended

June 

30,

2018,

the Company recorded unrealized gains of

$1.4

million and

$1.7

million, respectively, for changes in fair value of the shares. The Company adopted ASU

2016

-

01

on

January 1, 2018

and now accounts for its equity investment in SweeGen at fair value, with changes in fair value recognized in net income; see "Recent Accounting Pronouncements" in Note

1,

“Basis of Presentation and Summary of Significant Accounting Policies” above. The fair value of the SweeGen shares is included in Other Assets in the condensed consolidated balance sheets.

Derivative Liabilities Recognized in Connection with the Issuance of Debt and Equity Instruments

The following table provides a reconciliation of the beginning and ending balances for the Company's derivative liabilities recognized in connection with the issuance of debt and equity instruments, measured at fair value using significant unobservable inputs (Level

3

):

(In thousands)	Equity-related Derivative Liability			Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2017	$	112,368		$	7,610	$	119,978
Loss from change in fair value of derivative liabilities		34,650			6,709		41,359
Derecognition upon extinguishment of derivative liabilities		(22,642	)		—		(22,642	)
Balance at June 30, 2018	$	124,376		$	14,319	$	138,695

The derivative liabilities recognized in connection with the issuance of equity and debt instruments represent the fair value of the make-whole provisions of the Series A and B Preferred Stock as well as the cash and anti-dilution warrants issued concurrently with the Series A, B and D Preferred Stock (see Note

6,

“Stockholders’ Deficit” in Part II, Item

8

of the

10

-K), and conversion options, conversion price adjustment features and down round provisions associated with the R&D Note, Temasek Funding Warrant, Tranche Notes,

2014

144A

Notes and

2015

144A

Notes (see Note

4,

“Debt” and Note

6,

"Stockholders' Deficit" in Part II, Item

8

of the

10

-K).

The market-based assumptions and estimates used in applying a Monte Carlo simulation approach and Black-Scholes-Merton option value approach for valuing the derivative liabilities in connection with debt and equity instruments include amounts in the following ranges and amounts:

	June 30, 2018			June 30, 2017
Risk-free interest rate	1.97%	-	2.85%	1.68%	-	2.40%
Risk-adjusted yields	15.10%	-	25.23%	18.40%	-	28.53%
Stock price volatility	45%	-	75%	45%	-	80%
Probability of change in control	0%	-	5%		5%
Stock price		$6.39			$3.75
Credit spread	12.96%	-	22.98%	16.63%	-	26.70%
Estimated conversion dates	2018	-	2025	2018	-	2025

The valuation of the embedded derivatives in connection with the issuance of debt and equity instruments and freestanding derivative instruments in connection with the issuance of equity instruments can be significantly affected by changes in valuation assumptions. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. A

third

-party valuation specialist assisted in determining estimates of fair value.

See Note

6,

"Stockholders' Deficit", for more information about the derecognition upon extinguishment of derivative liabilities in connection with the

April 2018

warrants exercise.

Changes in Fair Value

Changes in the fair value of assets or liabilities measured at fair value on a recurring basis are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. Loans payable, credit facilities and convertible notes are recorded at carrying value, which is representative of fair value at the date of acquisition. The Company estimates the fair value of loans payable and credit facilities using observable market-based inputs (Level

2

) and estimates the fair value of convertible notes based on rates currently offered for instruments with similar maturities and terms (Level

3

). The fair values and carrying values of the Company's debt were as follows:

(In thousands)	June 30, 2018				December 31, 2017
	Fair Value		Carrying Value		Fair Value		Carrying Value
Total debt	$	165,844	$	171,402	$	156,900	$	165,377

XML

Note 4 - Debt

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Debt Disclosure [Text Block]

4.

Debt

Net carrying amounts of debt are as follows:

	June 30, 2018								December 31, 2017
(In thousands)	Principal		Unamortized Debt Discount			Net Balance			Principal		Unamortized Debt Discount			Net Balance
Nonrelated Party
Convertible notes
2015 Rule 144A convertible notes	$	37,887	$	(4,576	)	$	33,311		$	37,887	$	(6,872	)	$	31,015
2014 Rule 144A convertible notes		24,004		(2,023	)		21,981			24,004		(3,170	)		20,834
December 2017 convertible note		—		—			—			5,000		(25	)		4,975
August 2013 financing convertible notes		4,416		(2,541	)		1,875			4,009		(2,918	)		1,091
		66,307		(9,140	)		57,167			70,900		(12,985	)		57,915
Loans payable and credit facilities
GACP term loan facility		36,000		(1,596	)		34,404			—		—			—
Senior secured loan facility		—		—			—			28,566		(253	)		28,313
Ginkgo notes		12,000		(4,599	)		7,401			12,000		(4,983	)		7,017
Other loans payable		5,696		(1,234	)		4,462			6,463		(1,277	)		5,186
Other credit facilities		195		—			195			381		—			381
		53,891		(7,429	)		46,462			47,410		(6,513	)		40,897
Subtotal nonrelated party		120,198		(16,569	)		103,629			118,310		(19,498	)		98,812
Related Party
Related party convertible notes
August 2013 financing convertible notes		23,199		432			23,631			21,711		897			22,608
2014 Rule 144A convertible notes		24,705		(2,423	)		22,282			24,705		(3,784	)		20,921
R&D note		3,700		—			3,700			3,700		(18	)		3,682
		51,604		(1,991	)		49,613			50,116		(2,905	)		47,211
Related party loans payable
DSM note		25,000		(6,896	)		18,104			25,000		(8,039	)		16,961
Other DSM loan		56		—			56			393		—			393
February 2016 private placement		—		—			—			2,000		—			2,000
		25,056		(6,896	)		18,160			27,393		(8,039	)		19,354
Subtotal related party		76,660		(8,887	)		67,773			77,509		(10,944	)		66,565
Total debt		196,858		(25,456	)		171,402			195,819		(30,442	)		165,377
Less: current portion							(109,656	)							(56,943	)
Long-term debt, net of current portion						$	61,746							$	108,434

During the

six

months ended

June 

30,

2018,

aside from debt payments (including payments-in-kind), the following debt transactions occurred:

• Senior Secured Loan Facility Repayment: On June 29, 2018, the Company repaid in full the $27.3 million outstanding principal balance owed under the Senior Secured Loan Facility.

• GACP Term Loan Facility: On June 29, 2018, the Company, certain of the Company’s subsidiaries and GACP Finance Co., LLC (GACP) entered into a Loan and Security Agreement (the LSA) to borrow $36.0 million (the GACP Term Loan Facility). The LSA also provides for an incremental secured term loan facility in an aggregate principal amount of up to $35.0 million (the Incremental GACP Term Loan Facility and, together with the GACP Term Loan Facility, the GACP Term Loan Facilities), subject to certain conditions and approvals, to fund the construction of a custom-built manufacturing facility in Brazil. The majority of the net proceeds from the GACP Term Loan Facility were used to repay all amounts outstanding under the Senior Secured Loan Facility between the Company and Stegodon. The remaining net proceeds were used on July 2, 2018 to repay amounts outstanding under the R&D Note at maturity.   Loans under the GACP Term Loan Facilities have a maturity date of July 1, 2021; provided, that if the Company has not (i) met certain financial conditions on or prior to January 7, 2019 or (ii) refinanced the 2015 144A Notes and 2014 144A Notes with indebtedness that has a maturity date which is later than July 1, 2021 or converted such notes into equity prior to January 12, 2019, then the maturity date will be January 12, 2019. The GACP Term Loan Facilities will amortize beginning on July 1, 2019 in quarterly installments equal to 2.5% of the original loan amounts, with the remaining principal balance payable on the maturity date. Loans under the GACP Term Loan Facilities will accrue interest at a rate per annum equal to the sum of (i) the greater of (A) the U.S. prime rate as reported in the Wall Street Journal and (B) 4.0%, plus (ii) 6.25%, payable monthly. The GACP Term Loan Facilities are guaranteed by the subsidiaries of the Company party to the LSA and collateralized by first -priority liens on substantially all the Company’s and such subsidiaries’ assets, including intellectual property, subject to certain exceptions. The LSA includes customary terms, covenants and restrictions, including mandatory prepayments upon the occurrence of certain events, including asset sales, casualty events, incurrence of additional indebtedness and borrowing base deficiencies, subject to certain exceptions and reinvestment rights. The LSA contains three financial covenants: minimum revenue, liquidity and asset coverage ratio.   The Company paid origination fees at closing equal to 4%, or $1.4 million, of the funded amount of the GACP Term Loan Facility and other closing costs totaling $0.2 million, plus an agency fee of $25,000 per quarter during the term of the GACP Term Loan Facilities. The $1.6 million of issuance costs will be amortized using the effective interest method over the expected 3 -year loan term.

Future Minimum Payments

Future minimum payments under the Company's debt agreements as of

June 

30,

2018

are as follows:

Years ending December 31 (In thousands)	Convertible Notes			Loans Payable			Credit Facilities			Related Party Convertible Notes			Related Party Loans Payable			Total
2018 (remaining six months)	$	2,580		$	3,323		$	1,878		$	4,503		$	1,306		$	13,590
2019		69,334			1,627			5,912			25,508			2,500			104,881
2020		—			1,626			7,289			—			2,500			11,415
2021		—			1,627			32,551			—			27,500			61,678
2022		—			13,417			—			—			—			13,417
Thereafter		—			2,528			—			—			—			2,528
Total future minimum payments		71,914			24,148			47,630			30,011			33,806			207,509
Less: amount representing interest		(5,160	)		(6,453	)		(11,434	)		(1,606	)		(8,750	)		(33,403	)
Add: amount mandatorily convertible into common stock upon maturity		—			—			—			24,802			—			24,802
Less: future interest accruals to be converted to principal		(447	)		—			—			(1,603	)		—			(2,050	)
Present value of minimum debt payments		66,307			17,695			36,196			51,604			25,056			196,858
Less: current portion of debt principal		(66,307	)		(2,714	)		(196	)		(51,604	)		(56	)		(120,877	)
Noncurrent portion of debt principal	$	—		$	14,981		$	36,000		$	—		$	25,000		$	75,981

XML

Note 5 - Mezzanine Equity

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Mezzanine Equity Disclosure [Text Block]

5.

Mezzanine Equity

Mezzanine equity is comprised of the following:

(In thousands)	June 30, 2018		December 31, 2017
Contingently redeemable common stock	$	5,000	$	5,000

Mezzanine equity at

June 

30,

2018

and

December 

31,

2017

is comprised of proceeds from shares of common stock sold on

May 10, 2016

to the Bill & Melinda Gates Foundation (Gates Foundation). In connection with the stock sale, the Company and the Gates Foundation entered into an agreement under which the Company agreed to expend an aggregate amount

not

less than the proceeds from the stock sale to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria. If the Company defaults in its obligation to use the proceeds from the stock sale as set forth above or defaults under certain other commitments in the agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a

third

party, the shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, or (ii) an amount equal to

$17.10

plus a compounded annual return of

10%.

XML

Note 6 - Stockholders' Deficit

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Stockholders' Equity Note Disclosure [Text Block]

6.

Stockholders' Deficit

Warrants

In connection with various debt and equity transactions (see Note

4,

"Debt" and Note

6,

“Stockholders’ Deficit” in Part II, Item

8

of the

10

-K), the Company has issued warrants exercisable for shares of common stock. The following table summarizes warrant activity for the

six

months ended

June 

30,

2018:

Transaction	Number Outstanding as of December 31, 2017		Additional Warrants Issued		Exercises			Number Outstanding as of June 30, 2018
July 2015 private placement		81,197		—		—			81,197
July 2015 related party debt exchange		2,082,010		—		—			2,082,010
February 2016 related party private placement		171,429		—		—			171,429
May 2017 warrants (Series A and B preferred stock)		18,042,568		—		(3,801,330	)		14,241,238
August 2017 DSM offering (Series B preferred stock)		3,968,116		—		—			3,968,116
August 2017 Vivo offering (Series D preferred stock)		5,575,118		—		—			5,575,118
Tranche 1 new cash warrants		—		3,616,174		—			3,616,174
Other		1,406		—		—			1,406
		29,921,844		3,616,174		(3,801,330	)		29,736,688

For the

six

months ended

June 

30,

2018,

net proceeds were

$14.5

million from the issuance of common stock upon exercise of

3,801,330

warrants.

Warrants Exercises and New Warrant Issuance

On

April 12, 2018,

certain holders of the

May 2017

Warrants (see Note

6,

“Stockholders’ Deficit” in Part II, Item

8

of the

10

-K) exercised their

May 2017

Cash Warrants to purchase

3,616,174

shares of common stock for net proceeds to the Company of

$14.5

million and surrendered their

May 2017

Dilution Warrants. Upon exercise of such

May 2017

Cash Warrants and surrender of such

May 2017

Dilution Warrants, certain derivative liabilities representing certain anti-dilution rights embedded in the

May 2017

Warrants were effectively settled. Concurrent with the exercise of the

May 2017

Cash Warrants and surrender of such

May 2017

Dilution Warrants, the Company issued new warrants to these same holders to purchase

3,616,174

shares of common stock, exercisable at a price of

$7.00

per share. The new warrants were fully exercisable upon issuance, with an expiration date of

July 12, 2019.

The new warrants do

not

provide the holders with anti-dilution protection. Consequently, the new warrants were treated as additional consideration to the

May 2017

Warrant holders in exchange for their anti-dilution rights embedded in the original

May 2017

Warrants. The Company used the Black-Scholes-Merton option pricing model to determine the fair value of the new warrants, which resulted in a fair value of

$9.4

million. Black-Scholes-Merton input assumptions were as follows: volatility of

90%,

risk-free rate of

2.16%,

expected term of

1.25

years, expected dividend yield of

$0,

exercise price of

$7.00,

and Company stock price on issue date of

$6.80.

As a result of this exchange transaction, the Company recorded a

$1.9

million net gain on the extinguishment of the related derivative liability during the

three

months ended

June 30, 2018.

This net gain was comprised of an

$11.3

million gain on derecognition of the derivative liability and a

$9.4

million loss on issuance of the new warrant.

At

Market Issuance Sales

Agreement

On

March 8, 2016,

the Company entered into an At Market Issuance Sales Agreement (the ATM Sales Agreement) with FBR Capital Markets & Co. and MLV & Co. LLC (the Agents) under which the Company

may

issue and sell shares of its common stock having an aggregate offering price of up to

$50.0

million (the ATM Shares) from time to time through the Agents, acting as its sales agents, under the Company's Registration Statement on Form S-

3

(File

No.

333

-

203216

), effective

April 15, 2015.

Sales of the ATM Shares through the Agents

may

be made by any method that is deemed an "at the market offering" as defined in Rule

415

under the Securities Act of

1933,

as amended, including by means of ordinary brokers' transactions at market prices, in block transactions, or as otherwise agreed by the Company and the Agents. The Company will pay the applicable Agent a commission rate of up to

3.0%

of the gross proceeds from the sale of any ATM Shares sold through such Agent under the ATM Sales Agreement. The ATM Sales Agreement includes

no

commitment by other parties to purchase ATM Shares the Company offers for sale.

During the 

three

and

six

months ended

June 

30,

2018,

the Company issued and sold 

191,639

and

205,168

shares of common stock under the ATM Sales Agreement, at average prices of 

$6.91

and

$6.90

per share, respectively, resulting in total net proceeds to the Company of

$1.4

million. The ATM Sales Agreement expired on

April 15, 2018,

and as a result,

zero

remained available for issuance under the ATM Sales Agreement as of

June 

30,

2018.

XML

Note 7 - Variable-interest Entities and Unconsolidated Investments

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Variable Interest Entity Disclosure [Text Block]

7.

Variable-interest Entities and Unconsolidated Investments

Consolidated Variable-interest Entity

The table below reflects the carrying value of the Aprinnova JV's (see Note

7,

“Variable-interest Entities and Unconsolidated Investments” in Part II, Item

8

of the

10

-K) assets and liabilities, for which the Company is the primary beneficiary at

June 

30,

2018:

(In thousands)	June 30, 2018		December 31, 2017
Assets	$	37,133	$	36,781
Liabilities	$	1,873	$	3,187

The Aprinnova JV's creditors have recourse only to the assets of the Aprinnova JV.

During the

three

and

six

months ended

June 

30,

2018

and

2017,

there was

no

activity in noncontrolling interest.

Unconsolidated Investments

The Company's unconsolidated investments are summarized as follows:

				Carrying Value of Investment on Condensed Consolidated Balance Sheets
(Amounts in thousands)	Amyris Equity Ownership %			June 30, 2018		December 31, 2017
Equity-method investments:
Novvi LLC		20	%	$	—	$	—
Total Amyris BioSolutions B.V.		25	%	$	—	$	—
Other unconsolidated equity investment:
SweeGen, Inc.		3	%	$	3,570	$	3,233

XML

Note 8 - Net Loss Per Share Attributable to Common Stockholders

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Earnings Per Share [Text Block]

8.

Net Loss per Share Attributable to Common Stockholders

For the

three

months ended

June 

30,

2017

and the

six

months ended

June 

30,

2018

and

June 

30,

2017,

basic net loss per share attributable to common stockholders was the same as diluted net loss per share attributable to common stockholders because the inclusion of all potentially dilutive securities outstanding was antidilutive. For the

three

months ended

June 30, 2018,

income was allocated to participating Series B and Series D preferred shares, as they participate in profits. As the adjustments to net income due to the presumed conversion of dilutive securities created a net loss position for the

three

months ended

June 30, 2018

on a diluted basis, there was

no

allocation to participating securities for diluted EPS, as the participating securities do

not

participate in losses.

The following table presents the calculation of basic and diluted net loss per share attributable to common stockholders:

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2018			2017			2018			2017
Numerator:
Net income (loss) attributable to Amyris, Inc.	$	1,533		$	620		$	(89,963	)	$	(36,751	)
Less deemed dividend on capital distribution to related parties		—			(8,648	)		—			(8,648	)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		—			(562	)		—			(562	)
Less cumulative dividends on Series A and B preferred stock		(399	)		(1,675	)		(794	)		(1,675	)
Less earnings allocated to participating securities		(67	)		—			—			—
Net income (loss) attributable to Amyris, Inc. common stockholders, basic		1,067			(10,265	)		(90,757	)		(47,636	)
Earnings allocated to participating securities		67			—			—			—
Gain from change in fair value of dilutive common stock warrants		(13,421	)		—			—			—
Interest on dilutive convertible debt		357			—			—			—
Accretion of debt discount		(99	)		—			—			—
Gain from change in fair value of derivative instruments		(5,765	)		—			—			—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(17,794	)	$	(10,265	)	$	(90,757	)	$	(47,636	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic		54,932,411			23,155,874			53,076,975			21,226,013
Basic income (loss) per share	$	0.02		$	(0.44	)	$	(1.71	)	$	(2.24	)
Weighted-average shares of common stock outstanding		54,932,411			23,155,874			53,076,975			21,226,013
Effect of dilutive convertible debt		2,709,323			—			—			—
Effect of dilutive common stock warrants		3,088,002			—			—			—
Weighted-average common stock equivalents used in computing net loss per share of common stock, diluted		60,729,736			23,155,874			53,076,975			21,226,013
Diluted loss per share	$	(0.29	)	$	(0.44	)	$	(1.71	)	$	(2.24	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been antidilutive:

	Three Months Ended June 30,				Six Months Ended June 30,
	2018		2017		2018		2017
Period-end stock options to purchase common stock		5,424,330		997,275		5,424,330		997,275
Convertible promissory notes (1)		5,695,615		6,270,734		8,390,819		6,270,734
Period-end common stock warrants		18,177,362		16,871,700		24,341,772		16,871,700
Period-end restricted stock units		5,211,584		666,336		5,211,584		666,336
Period-end preferred stock		4,053,905		-		4,053,905		-
Total potentially dilutive securities excluded from computation of diluted net loss per share		38,562,796		24,806,045		47,422,410		24,806,045

______________

( 1 ) The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

XML

Note 9 - Commitments and Contingencies

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Contingencies Disclosure [Text Block]

9.

Commitments and Contingencies

Commitments

Future

minimum payments under the Company's lease obligations as of

June 

30,

2018

are as follows (in thousands):

Years ending December 31: (In thousands )	Capital Leases			Operating Leases		Total Lease Obligations
2018 (remaining six months)	$	424		$	4,941	$	5,365
2019		451			8,755		9,206
2020		125			7,017		7,142
2021		—			7,241		7,241
2022		—			7,414		7,414
Thereafter		—			3,281		3,281
Total future minimum payments	$	1,000		$	38,649	$	39,649
Less: amount representing interest		(49	)
Present value of minimum lease payments		951
Less: current portion		(583	)
Long-term portion	$	368

Guarantor Arrangements

In

November 2010,

the Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel; see Note

4,

"Debt" in Part II, Item

8

of the

10

-K. The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee as of

June 

30,

2018

and

December 

31,

2017

was

R$6.0

million (

US$1.6

million and

US$1.8

million, respectively) based on exchange rates at each date.

Contingencies

The Company has levied indirect taxes on sugarcane-based biodiesel sales that took place several years ago by Amyris Brasil Ltda. (see Note

13,

“Divestiture” in Part II, Item

8

of the

10

-K) to customers in Brazil, based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate the Company levied.

The Company and a number of the Company’s current officers and directors are parties to

four

separate purported shareholder derivative complaints based on allegedly misleading statements and/or omissions made in connection with the Company’s securities filings (the Derivative Complaints). The Derivative Complaints seek to recover, on the Company's behalf, unspecified damages purportedly sustained by the Company and also seek a series of changes to the Company’s corporate governance policies, restitution to the Company from the individual defendants, and an award of attorneys’ fees. Two of the Derivative Complaints were filed in the U.S. District Court for the Northern District of California (together, the Federal Derivative Cases). On

December 21, 2017,

the defendants filed a motion to dismiss the Federal Derivative Cases, which was granted on

March 9, 2018.

On

March 29, 2018,

the plaintiffs filed an amended complaint, and on

May 4, 2018

the defendants filed a motion to dismiss the amended complaint. On

July 23, 2018,

the court granted defendants’ motion to dismiss the amended complaint with prejudice and entered judgment in favor of the defendants. The remaining

two

Derivative Complaints were filed in the Superior Court for the State of California and are in the initial pleadings stage. The Company believes the Derivative Complaints lack merit and intends to continue to defend itself vigorously. Given the early stage of these proceedings, it is

not

yet possible to reliably determine any potential liability that could result from this matter. See Part II, Item

1,

“Legal Proceedings” in this Quarterly Report on Form

10

-Q for more details.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have

not

resulted in legal proceedings or have

not

been fully adjudicated. Such matters that

may

arise in the ordinary course of business are subject to many uncertainties and outcomes are

not

predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if

one

or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management's expectations, the Company's consolidated financial statements for the relevant reporting period could be materially adversely affected.

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Note 10 - Revenue Recognition and Contract Assets and Liabilities

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Collaborative Arrangement Disclosure [Text Block]

10.

Revenue Recognition and Contract Assets and Liabilities

Disaggregation of Revenue

The following table presents revenue by major product and service, as well as by primary geographical market, based on the location of the customer:

	Three Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	2,339	$	—	$	4,624	$	6,963	$	1,902	$	2,663	$	7,379	$	11,944
Europe		2,987		6,887		4,314		14,188		749		202		2,786		3,737
Asia		1,113		—		—		1,113		7,161		2,632		125		9,918
South America		194		—		736		930		80		—		—		80
Other		—		—		—		—		—		—		—		—
	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892	$	5,497	$	10,290	$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	4,301	$	—	$	5,832	$	10,133	$	2,998	$	2,673	$	9,369	$	15,040
Europe		5,421		18,324		7,815		31,560		3,307		446		5,359		9,112
Asia		1,791		—		1,000		2,791		11,468		2,633		251		14,352
South America		215		—		1,393		1,608		144		—		—		144
Other		100		—		—		100		12		—		—		12
	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Significant Revenue Agreements

In

connection with significant revenue agreements (also see Note

10,

“

Significant Revenue Agreements” in Part II, Item

8

of the

10

-K), the Company recognized the following revenues for the

three

and

six

months ended

June 

30,

2018

and

2017

:

	Three Months Ended June 30,
(In thousands)	2018									2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total			Renewable Products			Licenses and Royalties			Grants and Collaborations			Total
DSM - related party	$	—	$	6,887	$	1,737	$	8,624		$	—		$	—		$	149		$	149
Givaudan		2,109		—		1,358		3,467			—			—			1,500			1,500
Firmenich		—		—		1,219		1,219			—			202			2,137			2,339
Nenter		—		—		—		—			4,016			2,633			—			6,649
DARPA		—		—		4,191		4,191			—			—			4,671			4,671
Subtotal revenue from significant revenue agreements		2,109		6,887		8,505		17,501			4,016			2,835			8,457			15,308
Revenue from all other customers		4,524		—		1,169		5,693			5,876			2,662			1,833			10,371
Total revenue from all customers	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892		$	5,497		$	10,290		$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	—	$	18,287	$	3,127	$	21,414	$	—	$	—	$	149	$	149
Givaudan		3,184		—		2,859		6,043		619		—		3,000		3,619
Firmenich		207		37		2,486		2,730		998		446		3,211		4,655
Nenter		—		—		1,000		1,000		6,324		2,633		—		8,957
DARPA		—		—		5,038		5,038		—		—		5,642		5,642
Subtotal revenue from significant revenue agreements		3,391		18,324		14,510		36,225		7,941		3,079		12,002		23,022
Revenue from all other customers		8,437		—		1,530		9,967		9,988		2,673		2,977		15,638
Total revenue from all customers	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Contract Assets and Liabilities

When a contract results in revenue being recognized in excess of the amount the Company has invoiced or has the right to invoice to the customer, a contract asset is recognized. Contract assets are transferred to accounts receivable, net when the rights to the consideration become unconditional. Contract assets are presented as Unbilled Receivables on the consolidated balance sheets.

Contract liabilities consist of payments received from customers, or such consideration that is contractually due, in advance of providing the product or performing services such that control has

not

passed to the customer. Contract liabilities are presented as deferred revenue on the consolidated balance sheets.

Trade receivables related to revenue from contracts with customers are included in accounts receivable on the consolidated balance sheets, net of the allowance for doubtful accounts. Trade accounts receivable are recorded at the point of renewable product sale or in accordance with the contractual payment terms for licenses and royalties, and grants and collaborative research and development services for the amount payable by the customer to the Company for sale of goods or the performance of services.

Contract Balances

The following table provides information about unbilled receivables, deferred revenue, and accounts receivable from contracts with customers:

(In thousands)	June 30, 2018			December 31, 2017
Unbilled receivable, current	$	12,683		$	9,340
Unbilled receivable, noncurrent	$	9,747		$	7,940
Deferred revenue, current	$	9,643		$	4,880
Deferred revenue, noncurrent	$	383	(1)	$	383	(1)
Accounts receivable, net	$	26,814		$	24,281

(

1

)    

As of

June 

30,

2018

and

December 

31,

2017,

deferred revenue, noncurrent is presented in Other Noncurrent Liabilities in the consolidated balance sheets because of its insignificance.

Unbilled receivables, current, as of

June 30, 2018

relate to satisfied performance obligations that the Company has

not

invoiced to the customer and, as of

December 31, 2017,

primarily relate to the Company’s right to consideration from DSM for minimum future royalties which the Company received cash of

$9,250,000

during the

three

months ended

June 30, 2018.

Unbilled receivables, noncurrent, relate to the Company’s right to consideration from DSM for minimum future royalties. The Company’s right to cash receipt for these minimum royalty amounts occurs on or before

December 31, 2019.

Deferred revenue, current increased by

$4.8

million at

June 

30,

2018

resulting from a

$0.8

million increase upon adoption of ASC

606

on

January 1, 2018

plus the net amount of collaboration and royalty revenues invoiced in excess of amounts recognized as revenue, less

$3.3

million of revenue recognized during the

six

months ended

June 

30,

2018

that was included in deferred revenue at the beginning of the period.

Remaining Performance Obligations

The following table provides information regarding the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied (or partially unsatisfied) based on the Company's existing agreements with customers as of

June 

30,

2018.

(In thousands)	June 30, 2018
Remaining 2018	$	4,032
2019		6,338
2020		6,338
2021 and thereafter		572
Total from all customers	$	17,280

In accordance with the disclosure provisions of ASC

606,

the table above excludes estimated future revenues for performance obligations that are part of a contract that has an original expected duration of

one

year or less or a performance obligation with variable consideration that is recognized using the sales-based royalty exception for licenses of intellectual property. Additionally, approximately

$12.4

million of estimated future revenue is excluded from the table above, as that amount represents constrained variable consideration.

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Note 11 - Related Party Transactions

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Related Party Transactions Disclosure [Text Block]

11.

Related Party Transactions

Related Party Debt

See

Note

4.

Debt, for related party debt balances

as of

June 

30,

2018

and

December 

31,

2017.

Related Party Accounts Receivable and Unbilled Receivables

Related party accounts receivable and unbilled receivables as of

June 

30,

2018

and

December 

31,

2017

were as follows:

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable, net:
DSM	$	15,829	$	3,483
Novvi		472		1,607
Total		384		238
	$	16,685	$	5,328
Unbilled receivable, current:
DSM	$	12,683	$	9,340
Unbilled receivable, noncurrent:
DSM	$	9,747	$	7,940

Related Party Joint Ventures

See Note

7,

"Variable-interest Entities and Unconsolidated Investments" above and in Part II, Item

8

of the

10

-K for information about the Company's:

• Aprinnova joint venture with Nikko, and

• TAB joint venture with Total

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Note 12 - Stock-based Compensation

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Disclosure of Compensation Related Costs, Share-based Payments [Text Block]

12.

Stock-based Compensation

The Company’s stock option activity and related information for the

six

months ended

June 

30,

2018

was as follows:

	Quantity of Stock Options			Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years		Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2017		1,338,367		$	33.40		7.7	$	97
Granted		4,192,476		$	5.12
Exercised		(43,055	)	$	3.68
Forfeited or expired		(63,458	)	$	29.29
Outstanding - June 30, 2018		5,424,330		$	11.83		9.2	$	8,541
Vested or expected to vest after June 30, 2018		4,981,859		$	12.42		9.2	$	7,790
Exercisable at June 30, 2018		949,237		$	42.07		6.7	$	1,119

The Company’s restricted stock units (RSUs) activity and related information for the

six

months ended

June 

30,

2018

was as follows:

	Quantity of Restricted Stock Units			Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2017		683,554		$	8.62		1.40
Awarded		4,712,787		$	5.27
RSUs released		(144,572	)	$	11.18
RSUs forfeited		(37,879	)	$	7.01
Outstanding - June 30, 2018		5,213,890		$	5.53		2.03
Vested or expected to vest after June 30, 2018		4,927,426		$	5.54		2.00

Stock-based compensation expense related to options and RSUs granted to employees and non-employees during the

three

and

six

months ended

June 

30,

2018

and

2017

was allocated to research and development expense and sales, general and administrative expense as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Research and development	$	333	$	441	$	696	$	925
Sales, general and administrative		1,567		597		2,482		1,759
Total stock-based compensation expense	$	1,900	$	1,038	$	3,178	$	2,684

As of

June 

30,

2018,

there was unrecognized compensation expense of

$36.0

million related to stock options and RSUs. The Company expects to recognize this expense over a weighted-average period of

3.7

years.

The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended June 30,						Six Months Ended June 30,
	2018			2017			2018			2017
Expected dividend yield		—	%		—	%		—	%		—	%
Risk-free interest rate		2.7	%		1.8	%		2.7	%		1.8	%
Expected term (in years)		6.86			5.38			6.85			5.38
Expected volatility		79.6	%		85.7	%		79.7	%		85.7	%

In

May 2018,

shareholders approved amendments to the Company's

2010

Equity Incentive Plan (EIP) to (i) increase the number of shares of common stock available for grant and issuance thereunder by

9

million shares and (ii) increase the annual per-participant award limit thereunder to

4

million shares.

Also in

May 2018,

shareholders approved an amendment to the Company's

2010

Employee Stock Purchase Plan (ESPP) to increase the maximum number of shares of common stock that

may

be issued over the term of the ESPP by

1

million shares.

In

May 2018,

the Company granted its chief executive officer performance-based stock options (PSOs) to purchase

3,250,000

shares. PSOs are equity awards with the final number of PSOs that

may

vest determined based on the Company’s performance against pre-established EBITDA milestones and Amyris stock price milestones. The EBITDA milestones are measured from the grant date through

December 31, 2021,

and the stock price milestones are measured from the grant date through

December 31, 2022.

The PSOs vest in

four

tranches contingent upon the achievement of both the EBITDA milestones and stock price milestones for each respective tranche, and the chief executive officer’s continued employment with the Company. Over the measurement periods, the number of PSOs that

may

be issued and the related stock-based compensation expense that is recognized is adjusted upward or downward based upon the probability of achieving the EBITDA milestones. Depending on the probability of achieving the EBITDA milestones and stock price milestones and certification of achievement of those milestones for each vesting tranche by the Company’s Board of Directors or Compensation Committee, the PSOs issued could be from

zero

to

3,250,000

stock options, with an exercise price of

$5.08

per share.

Stock-based compensation expense for this award will be recognized using a graded-vesting approach over the service period beginning at the grant date thru

December 31, 2022,

as the Company’s management has determined that certain EBITDA milestones are probable of achievement as of

June 30, 2018,

The Company utilized a Monte Carlo simulation model to estimate the grant date fair value of each tranche of the award which totaled

$5.1

million. Approximately,

$0.1

million of compensation expense was recognized for this award for the

three

and

six

months ended

June 30, 2018.

The assumptions used to estimate the fair value of this award with performance and market vesting conditions were as follows:

Stock Option Award with Performance and Market Vesting Conditions
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility		70	%
Risk-free interest rate		2.75	%
Dividend yield		0.0	%

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Note 13 - Subsequent Events

6 Months Ended

Jun. 30, 2018

Notes to Financial Statements

Subsequent Events [Text Block]

13.

Subsequent Events

R&D Note Repayment

On

July 2, 2018,

the Company repaid the R&D Note (see Note

4,

"Debt" above and Note

4,

"Debt" and Note

18,

“Subsequent Events” in Part II, Item

8

of the

10

-K) in full at maturity. The principal amount was

$3.7

million.

XML

Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2018

Accounting Policies [Abstract]

Liquidity [Policy Text Block]

Liquidity

The Company has incurred significant operating losses since its inception and expects to continue to incur losses and negative cash flows from operations for at least the next

12

months following the issuance of these financial statements. As of

June 

30,

2018,

the Company had negative working capital of

$105.9

million, excluding cash and cash equivalents and short-term investments (compared to negative working capital of

$59.6

million as of

December 

31,

2017

), and an accumulated deficit of

$1.3

billion.

As of

June 

30,

2018,

the Company's debt (including related party debt), net of deferred discount and issuance costs of

$25.5

million, totaled

$171.4

million, of which

$109.7

million is classified as current and

$23.2

million is mandatorily convertible into equity and within the control of the Company. The Company's debt service obligations through

August 31, 2019

are

$114.5

million, including

$15.8

million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as restrictions on additional indebtedness and cross-default clauses. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required, would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of a substantial portion of the Company's outstanding indebtedness.

Cash and cash equivalents of

$14.1

million as of

June 

30,

2018

are

not

sufficient to fund expected future negative cash flows from operations and cash debt service obligations through

one

year following the issuance of these financial statements. These factors raise substantial doubt about the Company’s ability to continue as a going concern within

one

year after the date that these financial statements are issued. The financial statements do

not

include any adjustments that might result from the outcome of this uncertainty. The Company's ability to continue as a going concern will depend, in large part, on its ability to extend existing debt maturities by restructuring a majority of its convertible debt, which is uncertain and outside the control of the Company, in addition to the mandatory conversion of certain debt obligations into equity, which conversion is within the control of the Company. Further, the Company's operating plan for the next

12

months from the date of issuance of these financial statements contemplates a significant reduction in its net operating cash outflows as compared to the previous

12

months, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) significantly increased royalty revenues (previously referred to as value share revenues), (iii) reduced cost of products sold as a percentage of renewable products revenue due to anticipated procurement and production efficiencies, and (iv) cash inflows from grants and collaborations. Finally, during the

second

half of

2018,

the Company plans to obtain project financing for the construction of a new specialty ingredients manufacturing facility in Brazil. If the Company is unable to complete these actions, it expects to be unable to meet its operating cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it

may

be forced to liquidate its assets or obtain additional equity or debt financing, which

may

not

occur timely or on reasonable terms, if at all.

Revenue from Contract with Customer [Policy Text Block]

Revenue Recognition

The Company recognizes revenue from the sale of renewable products, licenses of and royalties from intellectual property, and grants and collaborative research and development services. Revenue is measured based on the consideration specified in a contract with a customer and recognized when, or as, the Company satisfies a performance obligation by transferring control over a product or service to a customer. The Company generally does

not

incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both parties, the rights of the parties are identified, payment terms are established, the contract has commercial substance and collectability of the consideration is probable. Changes to contracts are assessed for whether they represent a modification or should be accounted for as a new contract. The Company considers the following indicators among others when determining whether it is acting as a principal in the transaction and recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to provide the specified goods or service, (ii) the Company has inventory risk before the specified good or service has been transferred to a customer or after transfer of control to the customer and (iii) the Company has discretion in establishing the price for the specified good or service. If a transaction does

not

meet the Company's indicators of being a principal in the transaction, then the Company is acting as an agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in Note

10,

"Significant Revenue Agreements" in Part II, Item

8

of the

10

-K.

The Company recognizes revenue when control has passed to the customer. The following indicators are evaluated in determining when control has passed to the customer: (i) the Company has a right to payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company has transferred physical possession of the product to the customer, (iv) the customer has the significant risk and rewards of ownership of the product and (v) the customer has accepted the product. The Company’s renewable products are delivered to customers from the Company’s facilities with shipping terms typically specifying F.O.B. shipping point.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized as revenue when, or as, the performance obligation is satisfied. The Company's contracts

may

contain multiple performance obligations if a promise to transfer the individual goods or services is separately identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with multiple performance obligations, the Company determines the standalone selling price of each performance obligation and allocates the total transaction price using the relative selling price basis.

The following is a description of the principal goods and services from which the Company generates revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross basis as the Company is acting as a principal in these transactions, with the selling price to the customer recorded net of discounts and allowances. Revenues are recognized at a point in time when control has passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with the

first

transportation carrier. The Company, on occasion,

may

recognize revenue under a bill and hold arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later date. Under these arrangements, control transfers to the customer when the product is ready for delivery, which occurs when the product is identified separately as belonging to the customer, the product is ready for shipment to the customer in its current form, and the Company does

not

have the ability to direct the product to a different customer. It is at this point that we have right to payment, the customer obtains legal title, and the customer has the significant risks and rewards of ownership. The Company’s renewable product sales do

not

include rights of return. Returns are accepted only if the product does

not

meet product specifications and such nonconformity is communicated to the Company within a set number of days of delivery. The Company offers a

two

-year assurance-type warranty to replace squalane products that do

not

meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to replace the squalane products sold is made based on a historical rate of experience and recognized as a liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property:

When the Company’s intellectual property licenses are determined to be distinct from the other performance obligations identified in the arrangement, revenue is recognized from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses that are combined with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property:

The Company earns royalties from the licensing of its intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the predominant performance obligation in arrangements with multiple performance obligations, the Company applies the sales-based royalty exception and revenue is estimated and recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty revenues are made using the most likely outcome method, which is the single amount in a range of possible amounts derived from the licensee’s historical sales volumes and sales prices of its products and recent commodity market pricing data and trends.

When the Company’s intellectual property license is

not

the predominant performance obligation in arrangements with multiple performance obligations, the royalty represents variable consideration and is allocated to the transaction price of the predominant performance obligation which generally is the supply of renewable products to the Company's customers. Revenue is estimated and recognized at a point in time when the renewable products are delivered to the customer. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts determined based on the cost to produce the renewable product plus a reasonable margin for the profit share. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will

not

occur when the uncertainty associated with the variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services:

The Company earns revenues from collaboration agreements with customers to perform research and development services to develop new molecules using the Company’s technology and to scale production of the molecules for commercialization and use in the collaborator’s products. The collaboration agreements generally include providing the Company's collaborators with research and development services and with licenses to the Company’s intellectual property to use the technology underlying the development of the molecules and to sell its products that incorporate the technology. The terms of the Company's collaboration agreements typically include

one

or more of the following: advance payments for the research and development services that will be performed, nonrefundable upfront license payments, milestone payments to be received upon the achievement of the milestone events defined in the agreements, and royalty payments upon the commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property licenses represent distinct performance obligations separate from the research and development services. If the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from the license while the research and development service fees are recognized over time as the performance obligations are satisfied. The research and development service fees represent variable consideration. Estimates of the amount of variable consideration to include in the transaction price are made using the expected value method, which is the sum of probability-weighted amounts in a range of possible amounts. The Company only includes an amount of variable consideration in the transaction price to the extent it is probable that a significant reversal in the cumulative revenue recognized will

not

occur when the uncertainty associated with the variable consideration is subsequently resolved. Revenue is recognized over time using either an input-based measure of labor hours expended or a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

Collaboration agreements that include milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will

not

occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment.

The Company generally invoices its collaborators on a monthly or quarterly basis, or upon the completion of the effort or achievement of a milestone, based on the terms of each agreement. Deferred revenue arises from amounts received in advance of performing the research and development activities and is recognized as revenue in future periods as the performance obligations are satisfied.

Grants:

The Company earns revenues from grants with government agencies to, among other things, provide research and development services to develop molecules using the Company’s technology, and create research and development tools to improve the timeline and predictability for scaling molecules from proof of concept to market by reducing time and costs. Grants typically consist of research and development milestone payments to be received upon the achievement of the milestone events defined in the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are considered probable of achievement and estimates are made of the amount of the milestone payments to include in the transaction price using the most likely amount method which is the single amount in a range of possible amounts. If it is probable that a significant revenue reversal will

not

occur, the estimated milestone payment amount is included in the transaction price. Each reporting period, the Company re-evaluates the probability of achievement of the milestone events and any related constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of adjustment. Revenue is recognized over time using a time-based measure of progress towards the satisfaction of the performance obligations. The measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

For descriptions of the Company's other significant accounting policies, see the Company's Annual Report on Form

10

-K for the year ended

December 

31,

2017.

New Accounting Pronouncements, Policy [Policy Text Block]

Recent Accounting Pronouncements

(a) Recent Accounting Standards, Pronouncements or Updates Recently Adopted

In the

six

months ended

June 

30,

2018,

the Company adopted these new accounting standards or updates:

Revenue Recognition

The Company adopted ASC

606

with a date of initial application of

January 1, 2018.

As a result, the Company has changed its accounting policy for revenue recognition as detailed above in “Significant Accounting Policies”. The Company applied ASC

606

using the modified retrospective approach by recognizing the cumulative effect of initially applying ASC

606

to all contracts

not

completed as of the date of adoption as an adjustment to the opening balance of accumulated deficit at

January 1, 2018.

Therefore, the comparative information has

not

been adjusted and continues to be reported under the legacy revenue recognition guidance of ASC

605,

"Revenue Recognition".

The Company applied ASC

606

using a practical expedient for contracts that were modified before the application date, which allowed us to determine an aggregate effect of all modifications that occurred before

January 1, 2018,

when determining the satisfied and unsatisfied performance obligations, the transaction price, and allocating that transaction price to the performance obligations instead of retrospectively restating the contracts for such contract modifications.

The cumulative effect of initially applying ASC

606

resulted in an increase to accumulated deficit at

January 1, 2018

of approximately

$0.8

million. The increase in accumulated deficit arose primarily from a

$0.8

million increase of deferred revenue related to the effects of measuring and allocating the transaction price to the performance obligations under ASC

606

compared to the legacy guidance of ASC

605.

The most significant change in accounting policy is the Company now estimates royalty revenues from licenses of the Company’s intellectual property and recognizes estimated royalty revenues at a point in time when the Company sells its renewable products to its customers (if the sales-based royalty exception does

not

apply) or when the licensee sells its products to its customer (if the sales-based royalty exception does apply). Also, the transaction price for royalty revenues is reduced for variable incentive payments that

may

be payable by the Company to customers.

The following table presents the amounts by which revenue is affected in the current reporting period by the application of ASC

606

as compared with the legacy guidance that was in effect before the accounting change.

No

other consolidated statements of operations financial statement line items were impacted by the adoption of ASC

606.

	Three Months Ended June 30, 2018							Six Months Ended June 30, 2018
(In thousands)	As Reported		Adjustments			Amounts Without the Adoption of ASC 606		As Reported		Adjustments			Amounts Without the Adoption of ASC 606
Renewable products	$	6,633	$	—		$	6,633	$	11,828	$	—		$	11,828
Licenses and royalties		6,887		(4,980	)		1,907		18,324		(15,747	)		2,577
Grants and collaborations		9,674		(2,039	)		7,635		16,040		(2,265	)		13,775
Total revenue from all customers	$	23,194	$	(7,019	)	$	16,175	$	46,192	$	(18,012	)	$	28,180

Financial Instruments

In

January 2016,

the Financial Accounting Standards Board (FASB) issued ASU

2016

-

01,

 

Financial Instruments-Overall (Subtopic

825

-

10

): Recognition and Measurement of Financial Assets and Financial Liabilities

, which changes the accounting for equity investments, financial liabilities under the fair value option, and the presentation and disclosure requirements for financial instruments. The Company adopted ASU

2016

-

01

on

January 1, 2018

and, as a result, has changed its accounting policy to account for investments in equity securities (other than those accounted for using the equity method of accounting) at fair value with changes in fair value recognized in net income. The Company applied the modified retrospective approach by recognizing a

$1.4

million cumulative effect adjustment as an increase to the opening balance of accumulated deficit at

January 1, 2018

representing an unrealized loss measured as the difference between the fair value and the cost basis of the Company’s equity investments as of

January 1, 2018

previously accounted for using the cost method of accounting.

Classification of Cash Flow Elements

In

August 2016,

the FASB issued ASU

2016

-

15,

 

Statement of Cash Flows (Topic

230

): Classification of Certain Cash Receipts and Cash Payments,

 which affects the classification of certain cash receipts and cash payments on the statement of cash flows. ASU

2016

-

15

resulted in a change in cash flow classification of debt prepayment or extinguishment costs. Prior to the adoption of ASU

2016

-

15,

the Company classified gains or losses upon extinguishment of debt as an operating activity in the statements of cash flows. ASU

2016

-

15

became effective

January 1, 2018

on a retrospective basis. Upon the Company's adoption of ASU

2016

-

15,

such gains or losses are now classified in statements of cash flows as a financing activity.

Restricted Cash in Statement of Cash Flows

In

November 2016,

the FASB issued ASU

2016

-

18,

 

Statement of Cash Flows (Topic

230

): Restricted Cash,

 which requires that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The accounting standard update became effective

January 1, 2018

using a retrospective transition method for each period presented. Upon adoption, ASU

2016

-

18

has resulted in a change in the presentation of restricted cash in the statement of cash flows for current and prior periods presented.

Derecognition of Nonfinancial Assets

In

February 2017,

the FASB issued ASU

2017

-

05,

 

Other Income—Gains and Losses from the Derecognition of Nonfinancial Assets (Subtopic

610

-

20

): Clarifying the Scope of Asset Derecognition Guidance and Accounting for Partial Sales of Nonfinancial Assets

, which requires entities to apply certain recognition and measurement principles in ASC

606

when they derecognize nonfinancial assets, and in substance, nonfinancial assets, and the counterparty is

not

a customer. The guidance applies to: (

1

) contracts to transfer to a noncustomer a nonfinancial asset or group of nonfinancial assets, or an ownership interest in a consolidated subsidiary that does

not

meet the definition of a business and is

not

a

not

-for-profit activity; and (

2

) contributions of nonfinancial assets that are

not

a business to a joint venture or other noncontrolled investee. The accounting standard update became effective

January 1, 2018

on a modified retrospective basis. Adoption of this ASU did

not

 impact the Company's consolidated financial position, results of operations or cash flows.

Staff Accounting Bulletin

No

118

- Tax Cuts and Jobs Act of

2017

On

December 22, 2017,

the Tax Cuts and Jobs Act of

2017

(the Act) was signed into law, making significant changes to the Internal Revenue Code. Changes include, but are

not

limited to, a corporate tax rate decrease from

35%

to

21%

,

the transition of U.S. international taxation from a worldwide tax system to a territorial system, and a

one

-time transition tax on the mandatory deemed repatriation of cumulative foreign earnings as of

December 31, 2017.

Based on the Company’s current operations it is anticipated that the only significant current impact of the Act for the Company will be the reduction in the U.S. corporate tax rate. The Act reduces the corporate tax rate to

21

percent, effective

January 1, 2018.

In

December 2017,

Staff Accounting Bulletin

No.

118

(SAB

118

) was issued to address the application of U.S. GAAP in situations when a registrant does

not

have the necessary information available, prepared, or analyzed in reasonable detail to complete the accounting for certain income tax effects of the Tax Act. As of

June 

30,

2018,

due to the complexities of the new law, the Company has

not

yet completed its accounting for all the tax effects of the Tax Act, but has made a reasonable estimate of the effects on the Company's existing deferred tax balances. In all cases, the Company will continue to make and refine its calculations as additional analysis is completed. In addition, the Company's provisional estimate of the effects on its existing deferred tax balances

may

also be adjusted as the Company gains a more thorough understanding of the tax law during the

one

-year measurement period allowed under SAB

118.

Additionally, the Act created a new requirement that certain income, referred to as "Global Intangible Low-Taxed Income" (GILTI) earned by controlled foreign corporations (CFCs) must be included currently in the gross income of the CFCs’ U.S. shareholder. The Company’s selection of an accounting policy with respect to the new GILTI tax rules will depend, in part, on analyzing its global income to determine whether it expects to have future U.S. inclusions in taxable income related to GILTI and, if so, what the impact is expected to be. As of

June 

30,

2018,

the Company has

not

made a policy decision regarding whether to record deferred taxes on GILTI.

(b) Recent Accounting Standards Pronouncements or Updates

Not

Yet Effective as of Period End

Leases

In

February 2016,

the FASB issued ASU

2016

-

02,

 

Leases (Topic

842

),

 with fundamental changes as to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach, which requires lessees and lessors to recognize and measure leases at the beginning of the earliest period presented. The Company is in the initial stages of evaluating the impact of the new standard on its accounting policies, processes and system requirements. The Company anticipates that the standard

may

have a material impact on the Company’s condensed consolidated balance sheets due to the requirement to recognize leased right-of-use assets and corresponding liabilities related to leases on the Company’s condensed consolidated balance sheets, but is still evaluating whether the standard might have a material impact on the Company’s other condensed consolidated financial statements.

Financial Instruments with "Down Round" Features

In

July 2017,

the FASB issued ASU

2017

-

11,

 

Earnings Per Share (Topic

260

); Distinguishing Liabilities from Equity (Topic

480

); Derivatives and Hedging (Topic

815

): Accounting for Certain Financial Instruments with Down Round Features

. The amendments of this ASU update the classification analysis of certain equity-linked financial instruments, or embedded features, with down round features, as well as clarify existing disclosure requirements for equity-classified instruments. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature

no

longer precludes equity classification when assessing whether the instrument is indexed to an entity’s own stock. The accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach. The Company is in the initial stages of evaluating the impact of the new standard on its consolidated financial statements.

Non-employee Stock-based Compensation

In

June 2018,

the FASB issued ASU

2018

-

07,

Improvements to Nonemployee Share-Based Payment Accounting,

which more closely aligns the accounting for employee and nonemployee stock-based compensation. Under the new standard, companies will

no

longer be required to value non-employee awards differently from employee awards. This accounting standard update will be effective beginning in the

first

quarter of fiscal

2019

using a modified retrospective approach. The Company anticipates that the new standard will

not

materially impact the Company's consolidated financial statements.

Use of Estimates, Policy [Policy Text Block]

Use of Estimates

The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the periods presented. Actual results could differ from these estimates, and such differences

may

be material to the financial statements.

Reclassification, Policy [Policy Text Block]

Reclassifications

Certain prior period amounts have been reclassified to conform to the current period presentation in the Company’s condensed consolidated financial statements and the accompanying notes to the condensed consolidated financial statements. The condensed consolidated statements of operations previously presented license fee revenue in combination with grants and collaborations revenue, and royalties (formerly referred to as “value share”) were previously presented in combination with renewable products revenue. Licenses and royalties revenue is presented as a separate line within the condensed consolidated statements of operations. The reclassifications reflect the growth in the Company’s business model of licensing its technology and earning royalties from customers utilizing the Company’s technology in the products it produces and sells. The reclassifications had

no

impact on total revenue.

In the statements of cash flows, the prior period has been restated to reflect accounting standards changes for reporting (i) restricted cash, and (ii) debt extinguishment costs, in statements of cash flows.

XML

Note 1 - Basis of Presentation and Summary of Significant Accounting Policies (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of New Accounting Pronouncements and Changes in Accounting Principles [Table Text Block]

	Three Months Ended June 30, 2018							Six Months Ended June 30, 2018
(In thousands)	As Reported		Adjustments			Amounts Without the Adoption of ASC 606		As Reported		Adjustments			Amounts Without the Adoption of ASC 606
Renewable products	$	6,633	$	—		$	6,633	$	11,828	$	—		$	11,828
Licenses and royalties		6,887		(4,980	)		1,907		18,324		(15,747	)		2,577
Grants and collaborations		9,674		(2,039	)		7,635		16,040		(2,265	)		13,775
Total revenue from all customers	$	23,194	$	(7,019	)	$	16,175	$	46,192	$	(18,012	)	$	28,180

XML

Note 2 - Balance Sheet Details (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Accounts, Notes, Loans and Financing Receivable [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable	$	9,567	$	18,953
Related party accounts receivable		17,247		5,328
	$	26,814	$	24,281

Schedule of Inventory, Current [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Raw materials	$	823	$	819
Work-in-process		1,147		364
Finished goods		4,662		4,225
Inventories	$	6,632	$	5,408

Property, Plant and Equipment [Table Text Block]

(In thousands)	June 30, 2018			December 31, 2017
Machinery and equipment	$	46,755		$	49,277
Leasehold improvements		40,571			40,036
Computers and software		10,497			9,555
Furniture and office equipment, vehicles and land		3,463			3,415
Construction in progress		18,583			17,438
		119,869			119,721
Less: accumulated depreciation and amortization		(104,569	)		(105,829	)
Property, plant and equipment, net	$	15,300		$	13,892

Schedule of Other Assets, Noncurrent [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Contingent consideration	$	8,151	$	8,151
Prepaid royalty		7,285		7,409
Deposits		3,662		2,462
Equity investment in SweeGen		3,570		3,233
Goodwill		560		560
Other		1,519		825
Other assets	$	24,747	$	22,640

Schedule of Accrued and Other Current Liabilities [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Payroll and related expenses	$	7,074	$	7,238
Accrued interest		2,325		8,213
SMA relocation accrual		3,417		3,587
Tax-related liabilities		2,305		5,837
Professional services		1,400		1,894
Other		3,580		2,633
Total accrued and other current liabilities	$	20,101	$	29,402

XML

Note 3 - Fair Value Measurement (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis [Table Text Block]

(In thousands)	June 30, 2018								December 31, 2017
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Money market funds	$	—	$	—	$	—	$	—	$	53,199	$	—	$	—	$	53,199
Certificates of deposit		130		—		—		130		7,813		—		—		7,813
Equity investment in SweeGen		—		3,570		—		3,570		—		—		—		—
Total assets measured and recorded at fair value	$	130	$	3,570	$	—	$	3,700	$	61,012	$	—	$	—	$	61,012
Liabilities
Embedded derivatives in connection with the issuance of debt and equity instruments	$	—	$	—	$	6,560	$	6,560	$	—	$	—	$	4,203	$	4,203
Freestanding derivative instruments in connection with the issuance of equity instruments		—		—		132,135		132,135		—		—		115,775		115,775
Total liabilities measured and recorded at fair value	$	—	$	—	$	138,695	$	138,695	$	—	$	—	$	119,978	$	119,978

Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]

(In thousands)	Equity-related Derivative Liability			Debt-related Derivative Liability		Total Derivative Liability
Balance at December 31, 2017	$	112,368		$	7,610	$	119,978
Loss from change in fair value of derivative liabilities		34,650			6,709		41,359
Derecognition upon extinguishment of derivative liabilities		(22,642	)		—		(22,642	)
Balance at June 30, 2018	$	124,376		$	14,319	$	138,695

Fair Value Measurement Inputs and Valuation Techniques [Table Text Block]

	June 30, 2018			June 30, 2017
Risk-free interest rate	1.97%	-	2.85%	1.68%	-	2.40%
Risk-adjusted yields	15.10%	-	25.23%	18.40%	-	28.53%
Stock price volatility	45%	-	75%	45%	-	80%
Probability of change in control	0%	-	5%		5%
Stock price		$6.39			$3.75
Credit spread	12.96%	-	22.98%	16.63%	-	26.70%
Estimated conversion dates	2018	-	2025	2018	-	2025

Fair Value, by Balance Sheet Grouping [Table Text Block]

(In thousands)	June 30, 2018				December 31, 2017
	Fair Value		Carrying Value		Fair Value		Carrying Value
Total debt	$	165,844	$	171,402	$	156,900	$	165,377

XML

Note 4 - Debt (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Debt [Table Text Block]

	June 30, 2018								December 31, 2017
(In thousands)	Principal		Unamortized Debt Discount			Net Balance			Principal		Unamortized Debt Discount			Net Balance
Nonrelated Party
Convertible notes
2015 Rule 144A convertible notes	$	37,887	$	(4,576	)	$	33,311		$	37,887	$	(6,872	)	$	31,015
2014 Rule 144A convertible notes		24,004		(2,023	)		21,981			24,004		(3,170	)		20,834
December 2017 convertible note		—		—			—			5,000		(25	)		4,975
August 2013 financing convertible notes		4,416		(2,541	)		1,875			4,009		(2,918	)		1,091
		66,307		(9,140	)		57,167			70,900		(12,985	)		57,915
Loans payable and credit facilities
GACP term loan facility		36,000		(1,596	)		34,404			—		—			—
Senior secured loan facility		—		—			—			28,566		(253	)		28,313
Ginkgo notes		12,000		(4,599	)		7,401			12,000		(4,983	)		7,017
Other loans payable		5,696		(1,234	)		4,462			6,463		(1,277	)		5,186
Other credit facilities		195		—			195			381		—			381
		53,891		(7,429	)		46,462			47,410		(6,513	)		40,897
Subtotal nonrelated party		120,198		(16,569	)		103,629			118,310		(19,498	)		98,812
Related Party
Related party convertible notes
August 2013 financing convertible notes		23,199		432			23,631			21,711		897			22,608
2014 Rule 144A convertible notes		24,705		(2,423	)		22,282			24,705		(3,784	)		20,921
R&D note		3,700		—			3,700			3,700		(18	)		3,682
		51,604		(1,991	)		49,613			50,116		(2,905	)		47,211
Related party loans payable
DSM note		25,000		(6,896	)		18,104			25,000		(8,039	)		16,961
Other DSM loan		56		—			56			393		—			393
February 2016 private placement		—		—			—			2,000		—			2,000
		25,056		(6,896	)		18,160			27,393		(8,039	)		19,354
Subtotal related party		76,660		(8,887	)		67,773			77,509		(10,944	)		66,565
Total debt		196,858		(25,456	)		171,402			195,819		(30,442	)		165,377
Less: current portion							(109,656	)							(56,943	)
Long-term debt, net of current portion						$	61,746							$	108,434

Schedule of Long-term Debt Instruments [Table Text Block]

Years ending December 31 (In thousands)	Convertible Notes			Loans Payable			Credit Facilities			Related Party Convertible Notes			Related Party Loans Payable			Total
2018 (remaining six months)	$	2,580		$	3,323		$	1,878		$	4,503		$	1,306		$	13,590
2019		69,334			1,627			5,912			25,508			2,500			104,881
2020		—			1,626			7,289			—			2,500			11,415
2021		—			1,627			32,551			—			27,500			61,678
2022		—			13,417			—			—			—			13,417
Thereafter		—			2,528			—			—			—			2,528
Total future minimum payments		71,914			24,148			47,630			30,011			33,806			207,509
Less: amount representing interest		(5,160	)		(6,453	)		(11,434	)		(1,606	)		(8,750	)		(33,403	)
Add: amount mandatorily convertible into common stock upon maturity		—			—			—			24,802			—			24,802
Less: future interest accruals to be converted to principal		(447	)		—			—			(1,603	)		—			(2,050	)
Present value of minimum debt payments		66,307			17,695			36,196			51,604			25,056			196,858
Less: current portion of debt principal		(66,307	)		(2,714	)		(196	)		(51,604	)		(56	)		(120,877	)
Noncurrent portion of debt principal	$	—		$	14,981		$	36,000		$	—		$	25,000		$	75,981

XML

Note 5 - Mezzanine Equity (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Mezzanine Equity Table [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Contingently redeemable common stock	$	5,000	$	5,000

XML

Note 6 - Stockholders' Deficit (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Stockholders' Equity Note, Warrants or Rights [Table Text Block]

Transaction	Number Outstanding as of December 31, 2017		Additional Warrants Issued		Exercises			Number Outstanding as of June 30, 2018
July 2015 private placement		81,197		—		—			81,197
July 2015 related party debt exchange		2,082,010		—		—			2,082,010
February 2016 related party private placement		171,429		—		—			171,429
May 2017 warrants (Series A and B preferred stock)		18,042,568		—		(3,801,330	)		14,241,238
August 2017 DSM offering (Series B preferred stock)		3,968,116		—		—			3,968,116
August 2017 Vivo offering (Series D preferred stock)		5,575,118		—		—			5,575,118
Tranche 1 new cash warrants		—		3,616,174		—			3,616,174
Other		1,406		—		—			1,406
		29,921,844		3,616,174		(3,801,330	)		29,736,688

XML

Note 7 - Variable-interest Entities and Unconsolidated Investments (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Variable Interest Entities [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Assets	$	37,133	$	36,781
Liabilities	$	1,873	$	3,187

Unconsolidated Investments [Table Text Block]

				Carrying Value of Investment on Condensed Consolidated Balance Sheets
(Amounts in thousands)	Amyris Equity Ownership %			June 30, 2018		December 31, 2017
Equity-method investments:
Novvi LLC		20	%	$	—	$	—
Total Amyris BioSolutions B.V.		25	%	$	—	$	—
Other unconsolidated equity investment:
SweeGen, Inc.		3	%	$	3,570	$	3,233

XML

Note 8 - Net Loss Per Share Attributable to Common Stockholders (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Earnings Per Share, Basic and Diluted [Table Text Block]

	Three Months Ended June 30,						Six Months Ended June 30,
(In thousands, except shares and per share amounts)	2018			2017			2018			2017
Numerator:
Net income (loss) attributable to Amyris, Inc.	$	1,533		$	620		$	(89,963	)	$	(36,751	)
Less deemed dividend on capital distribution to related parties		—			(8,648	)		—			(8,648	)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		—			(562	)		—			(562	)
Less cumulative dividends on Series A and B preferred stock		(399	)		(1,675	)		(794	)		(1,675	)
Less earnings allocated to participating securities		(67	)		—			—			—
Net income (loss) attributable to Amyris, Inc. common stockholders, basic		1,067			(10,265	)		(90,757	)		(47,636	)
Earnings allocated to participating securities		67			—			—			—
Gain from change in fair value of dilutive common stock warrants		(13,421	)		—			—			—
Interest on dilutive convertible debt		357			—			—			—
Accretion of debt discount		(99	)		—			—			—
Gain from change in fair value of derivative instruments		(5,765	)		—			—			—
Net loss attributable to Amyris, Inc. common stockholders, diluted	$	(17,794	)	$	(10,265	)	$	(90,757	)	$	(47,636	)
Denominator:
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock, basic		54,932,411			23,155,874			53,076,975			21,226,013
Basic income (loss) per share	$	0.02		$	(0.44	)	$	(1.71	)	$	(2.24	)
Weighted-average shares of common stock outstanding		54,932,411			23,155,874			53,076,975			21,226,013
Effect of dilutive convertible debt		2,709,323			—			—			—
Effect of dilutive common stock warrants		3,088,002			—			—			—
Weighted-average common stock equivalents used in computing net loss per share of common stock, diluted		60,729,736			23,155,874			53,076,975			21,226,013
Diluted loss per share	$	(0.29	)	$	(0.44	)	$	(1.71	)	$	(2.24	)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block]

	Three Months Ended June 30,				Six Months Ended June 30,
	2018		2017		2018		2017
Period-end stock options to purchase common stock		5,424,330		997,275		5,424,330		997,275
Convertible promissory notes (1)		5,695,615		6,270,734		8,390,819		6,270,734
Period-end common stock warrants		18,177,362		16,871,700		24,341,772		16,871,700
Period-end restricted stock units		5,211,584		666,336		5,211,584		666,336
Period-end preferred stock		4,053,905		-		4,053,905		-
Total potentially dilutive securities excluded from computation of diluted net loss per share		38,562,796		24,806,045		47,422,410		24,806,045

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Note 9 - Commitments and Contingencies (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule Of Future Minimum Payments For Lease Obligations [Table Text Block]

Years ending December 31: (In thousands )	Capital Leases			Operating Leases		Total Lease Obligations
2018 (remaining six months)	$	424		$	4,941	$	5,365
2019		451			8,755		9,206
2020		125			7,017		7,142
2021		—			7,241		7,241
2022		—			7,414		7,414
Thereafter		—			3,281		3,281
Total future minimum payments	$	1,000		$	38,649	$	39,649
Less: amount representing interest		(49	)
Present value of minimum lease payments		951
Less: current portion		(583	)
Long-term portion	$	368

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Note 10 - Revenue Recognition and Contract Assets and Liabilities (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Disaggregation of Revenue [Table Text Block]

	Three Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	2,339	$	—	$	4,624	$	6,963	$	1,902	$	2,663	$	7,379	$	11,944
Europe		2,987		6,887		4,314		14,188		749		202		2,786		3,737
Asia		1,113		—		—		1,113		7,161		2,632		125		9,918
South America		194		—		736		930		80		—		—		80
Other		—		—		—		—		—		—		—		—
	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892	$	5,497	$	10,290	$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
United States	$	4,301	$	—	$	5,832	$	10,133	$	2,998	$	2,673	$	9,369	$	15,040
Europe		5,421		18,324		7,815		31,560		3,307		446		5,359		9,112
Asia		1,791		—		1,000		2,791		11,468		2,633		251		14,352
South America		215		—		1,393		1,608		144		—		—		144
Other		100		—		—		100		12		—		—		12
	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Revenue in Connection with Significant Revenue Agreement [Table Text Block]

	Three Months Ended June 30,
(In thousands)	2018									2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total			Renewable Products			Licenses and Royalties			Grants and Collaborations			Total
DSM - related party	$	—	$	6,887	$	1,737	$	8,624		$	—		$	—		$	149		$	149
Givaudan		2,109		—		1,358		3,467			—			—			1,500			1,500
Firmenich		—		—		1,219		1,219			—			202			2,137			2,339
Nenter		—		—		—		—			4,016			2,633			—			6,649
DARPA		—		—		4,191		4,191			—			—			4,671			4,671
Subtotal revenue from significant revenue agreements		2,109		6,887		8,505		17,501			4,016			2,835			8,457			15,308
Revenue from all other customers		4,524		—		1,169		5,693			5,876			2,662			1,833			10,371
Total revenue from all customers	$	6,633	$	6,887	$	9,674	$	23,194	$	9,892		$	5,497		$	10,290		$	25,679

	Six Months Ended June 30,
(In thousands)	2018								2017
	Renewable Products		Licenses and Royalties		Grants and Collaborations		Total		Renewable Products		Licenses and Royalties		Grants and Collaborations		Total
DSM - related party	$	—	$	18,287	$	3,127	$	21,414	$	—	$	—	$	149	$	149
Givaudan		3,184		—		2,859		6,043		619		—		3,000		3,619
Firmenich		207		37		2,486		2,730		998		446		3,211		4,655
Nenter		—		—		1,000		1,000		6,324		2,633		—		8,957
DARPA		—		—		5,038		5,038		—		—		5,642		5,642
Subtotal revenue from significant revenue agreements		3,391		18,324		14,510		36,225		7,941		3,079		12,002		23,022
Revenue from all other customers		8,437		—		1,530		9,967		9,988		2,673		2,977		15,638
Total revenue from all customers	$	11,828	$	18,324	$	16,040	$	46,192	$	17,929	$	5,752	$	14,979	$	38,660

Contract with Customer, Asset and Liability [Table Text Block]

(In thousands)	June 30, 2018			December 31, 2017
Unbilled receivable, current	$	12,683		$	9,340
Unbilled receivable, noncurrent	$	9,747		$	7,940
Deferred revenue, current	$	9,643		$	4,880
Deferred revenue, noncurrent	$	383	(1)	$	383	(1)
Accounts receivable, net	$	26,814		$	24,281

Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Table Text Block]

(In thousands)	June 30, 2018
Remaining 2018	$	4,032
2019		6,338
2020		6,338
2021 and thereafter		572
Total from all customers	$	17,280

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Note 11 - Related Party Transactions (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Related Party Accounts Receivables [Table Text Block]

(In thousands)	June 30, 2018		December 31, 2017
Accounts receivable, net:
DSM	$	15,829	$	3,483
Novvi		472		1,607
Total		384		238
	$	16,685	$	5,328
Unbilled receivable, current:
DSM	$	12,683	$	9,340
Unbilled receivable, noncurrent:
DSM	$	9,747	$	7,940

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Note 12 - Stock-based Compensation (Tables)

6 Months Ended

Jun. 30, 2018

Notes Tables

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Table Text Block]

	Quantity of Stock Options			Weighted- average Exercise Price		Weighted-average Remaining Contractual Life, in Years		Aggregate Intrinsic Value, in Thousands
Outstanding - December 31, 2017		1,338,367		$	33.40		7.7	$	97
Granted		4,192,476		$	5.12
Exercised		(43,055	)	$	3.68
Forfeited or expired		(63,458	)	$	29.29
Outstanding - June 30, 2018		5,424,330		$	11.83		9.2	$	8,541
Vested or expected to vest after June 30, 2018		4,981,859		$	12.42		9.2	$	7,790
Exercisable at June 30, 2018		949,237		$	42.07		6.7	$	1,119

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Table Text Block]

	Quantity of Restricted Stock Units			Weighted-average Grant-date Fair Value		Weighted-average Remaining Contractual Life, in Years
Outstanding - December 31, 2017		683,554		$	8.62		1.40
Awarded		4,712,787		$	5.27
RSUs released		(144,572	)	$	11.18
RSUs forfeited		(37,879	)	$	7.01
Outstanding - June 30, 2018		5,213,890		$	5.53		2.03
Vested or expected to vest after June 30, 2018		4,927,426		$	5.54		2.00

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]

	Three Months Ended June 30,				Six Months Ended June 30,
(In thousands)	2018		2017		2018		2017
Research and development	$	333	$	441	$	696	$	925
Sales, general and administrative		1,567		597		2,482		1,759
Total stock-based compensation expense	$	1,900	$	1,038	$	3,178	$	2,684

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

	Three Months Ended June 30,						Six Months Ended June 30,
	2018			2017			2018			2017
Expected dividend yield		—	%		—	%		—	%		—	%
Risk-free interest rate		2.7	%		1.8	%		2.7	%		1.8	%
Expected term (in years)		6.86			5.38			6.85			5.38
Expected volatility		79.6	%		85.7	%		79.7	%		85.7	%

Performance-based Stock Options [Member]

Notes Tables

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

Stock Option Award with Performance and Market Vesting Conditions
Fair value of the Company’s common stock on grant date	$	5.08
Expected volatility		70	%
Risk-free interest rate		2.75	%
Dividend yield		0.0	%

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Note 1 - Basis of Presentation and Summary of Significant Accounting Policies (Details Textual) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Jun. 30, 2018	Jan. 01, 2018
Working Capital		$ (59,600)	$ (105,900)
Retained Earnings (Accumulated Deficit), Ending Balance		(1,206,767)	(1,298,914)
Debt Instrument, Unamortized Discount (Premium) and Debt Issuance Costs, Net, Total			25,500
Long-term Debt, Total		165,377	171,402
Long-term Debt, Current Maturities, Including Due to Related Parties		$ 56,943	109,656
Convertible Debt, Total			23,200
Long-term Debt, Maturities, Repayments of Principal and Interest in Next 15 Months			114,500
Long-term Debt, Maturities, Repayments of Interest in Next 15 Months			15,800
Cash, Cash Equivalents, and Short-term Investments, Total			$ 14,100
Effective Income Tax Rate Reconciliation, at Federal Statutory Income Tax Rate, Percent		35.00%
Scenario, Forecast [Member]
Effective Income Tax Rate Reconciliation, at Federal Statutory Income Tax Rate, Percent	21.00%
Accounting Standards Update 2014-09 [Member]
Retained Earnings (Accumulated Deficit), Ending Balance				$ (800)
Accounting Standards Update 2016-01 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption				$ (1,400)

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Note 1 - Basis of Presentation and Summary of Significant Accounting Policies - Adoption of ASC 606 (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Revenues	$ 23,194	$ 25,679	$ 46,192	$ 38,660
Difference between Revenue Guidance in Effect before and after Topic 606 [Member] | Accounting Standards Update 2014-09 [Member]
Revenues	(7,019)		(18,012)
Calculated under Revenue Guidance in Effect before Topic 606 [Member]
Revenues	16,175		28,180
Product [Member]
Revenues	6,633	9,892	11,828	17,929
Product [Member] | Difference between Revenue Guidance in Effect before and after Topic 606 [Member] | Accounting Standards Update 2014-09 [Member]
Revenues
Product [Member] | Calculated under Revenue Guidance in Effect before Topic 606 [Member]
Revenues	6,633		11,828
Licenses and Royalties [Member]
Revenues	6,887	5,497	18,324	5,752
Licenses and Royalties [Member] | Difference between Revenue Guidance in Effect before and after Topic 606 [Member] | Accounting Standards Update 2014-09 [Member]
Revenues	(4,980)		(15,747)
Licenses and Royalties [Member] | Calculated under Revenue Guidance in Effect before Topic 606 [Member]
Revenues	1,907		2,577
Grants and Collaborations [Member]
Revenues	9,674	$ 10,290	16,040	$ 14,979
Grants and Collaborations [Member] | Difference between Revenue Guidance in Effect before and after Topic 606 [Member] | Accounting Standards Update 2014-09 [Member]
Revenues	(2,039)		(2,265)
Grants and Collaborations [Member] | Calculated under Revenue Guidance in Effect before Topic 606 [Member]
Revenues	$ 7,635		$ 13,775

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Note 2 - Balance Sheet Details (Details Textual) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Property, Plant and Equipment, Net, Ending Balance	$ 15,300		$ 15,300		$ 13,892
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment, Ending Balance	104,569		104,569		105,829
Capitalized Computer Software, Additions	1,200		1,600
Depreciation, Depletion and Amortization, Total			2,944	$ 5,550
Property, Plant and Equipment, Including Capital Leases [Member]
Depreciation, Depletion and Amortization, Total	1,400	$ 2,700	2,900	$ 5,600
Capital Lease Obligations [Member]
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment, Ending Balance	1,900		1,900		1,600
Capital Lease Obligations [Member] | Machinery and Equipment, Furniture and Office Equipment Under Capital Lease [Member]
Property, Plant and Equipment, Net, Ending Balance	$ 4,800		$ 4,800		$ 4,200

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Note 2 - Balance Sheet Details - Accounts Receivable (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Accounts receivable	$ 9,567	$ 18,953
Related party accounts receivable	17,247	5,328
	$ 26,814	$ 24,281

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Note 2 - Balance Sheet Details - Inventory, Current (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Raw materials	$ 823	$ 819
Work-in-process	1,147	364
Finished goods	4,662	4,225
Inventories	$ 6,632	$ 5,408

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Note 2 - Balance Sheet Details - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Property, plant and equipment	$ 119,869	$ 119,721
Less: accumulated depreciation and amortization	(104,569)	(105,829)
Property, plant and equipment, net	15,300	13,892
Machinery and Equipment [Member]
Property, plant and equipment	46,755	49,277
Leasehold Improvements [Member]
Property, plant and equipment	40,571	40,036
Computer Equipment and Software [Member]
Property, plant and equipment	10,497	9,555
Furniture and Office Equipment, Vehicles and Land [Member]
Property, plant and equipment	3,463	3,415
Construction in Progress [Member]
Property, plant and equipment	$ 18,583	$ 17,438

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Note 2 - Balance Sheet Details - Other Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Contingent consideration	$ 8,151	$ 8,151
Prepaid royalty	7,285	7,409
Deposits	3,662	2,462
Equity investment in SweeGen	3,570	3,233
Goodwill	560	560
Other	1,519	825
Other assets	$ 24,747	$ 22,640

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Note 2 - Balance Sheet Details - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Payroll and related expenses	$ 7,074	$ 7,238
Accrued interest	2,325	8,213
SMA relocation accrual	3,417	3,587
Tax-related liabilities	2,305	5,837
Professional services	1,400	1,894
Other	3,580	2,633
Total accrued and other current liabilities	$ 20,101	$ 29,402

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Note 3 - Fair Value Measurement (Details Textual) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Equity Securities, FV-NI	$ 3,570	$ 3,570		$ 3,233
Equity Securities, FV-NI, Unrealized Gain		$ 1,717
SweeGen Common Stock [Member]
Equity Securities, Number of Unregistered Shares Hold	850,115	850,115
Equity Securities, FV-NI, Unrealized Gain	$ 1,400	$ 1,700
SweeGen Common Stock [Member] | Other Noncurrent Assets [Member]
Equity Securities, FV-NI	$ 3,600	$ 3,600

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Note 3 - Fair Value Measurement - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Equity investment in SweeGen	$ 3,570	$ 3,233
Fair Value, Measurements, Recurring [Member]
Money market funds		53,199
Certificates of deposit	130	7,813
Equity investment in SweeGen	3,570
Total assets measured and recorded at fair value	3,700	61,012
Embedded derivatives in connection with the issuance of debt and equity instruments	6,560	4,203
Freestanding derivative instruments in connection with the issuance of equity instruments	132,135	115,775
Total liabilities measured and recorded at fair value	138,695	119,978
Fair Value, Inputs, Level 1 [Member] | Fair Value, Measurements, Recurring [Member]
Money market funds		53,199
Certificates of deposit	130	7,813
Equity investment in SweeGen
Total assets measured and recorded at fair value	130	61,012
Embedded derivatives in connection with the issuance of debt and equity instruments
Freestanding derivative instruments in connection with the issuance of equity instruments
Total liabilities measured and recorded at fair value
Fair Value, Inputs, Level 2 [Member] | Fair Value, Measurements, Recurring [Member]
Money market funds
Certificates of deposit
Equity investment in SweeGen	3,570
Total assets measured and recorded at fair value	3,570
Embedded derivatives in connection with the issuance of debt and equity instruments
Freestanding derivative instruments in connection with the issuance of equity instruments
Total liabilities measured and recorded at fair value
Fair Value, Inputs, Level 3 [Member] | Fair Value, Measurements, Recurring [Member]
Money market funds
Certificates of deposit
Equity investment in SweeGen
Total assets measured and recorded at fair value
Embedded derivatives in connection with the issuance of debt and equity instruments	6,560	4,203
Freestanding derivative instruments in connection with the issuance of equity instruments	132,135	115,775
Total liabilities measured and recorded at fair value	$ 138,695	$ 119,978

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Note 3 - Fair Value Measurement - Reconciliation for Compound Embedded Derivative Liability (Details) - Fair Value, Inputs, Level 3 [Member] $ in Thousands	6 Months Ended
	Jun. 30, 2018 USD ($)
Derivative Liability, Equity-related [Member]
Balance, compound embedded derivative liabilities	$ 112,368
Loss from change in fair value of derivative liabilities	34,650
Derecognition upon extinguishment of derivative liabilities	(22,642)
Balance, compound embedded derivative liabilities	124,376
Derivative Liability, Debt-related [Member]
Balance, compound embedded derivative liabilities	7,610
Loss from change in fair value of derivative liabilities	6,709
Derecognition upon extinguishment of derivative liabilities
Balance, compound embedded derivative liabilities	14,319
Derivative Financial Instruments, Liabilities [Member]
Balance, compound embedded derivative liabilities	119,978
Loss from change in fair value of derivative liabilities	41,359
Derecognition upon extinguishment of derivative liabilities	(22,642)
Balance, compound embedded derivative liabilities	$ 138,695

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Note 3 - Fair Value Measurement - Market-based Assumption and Estimates for Compound Embedded Derivative Liabilities Valuation (Details)	6 Months Ended
	Jun. 30, 2018 $ / shares	Jun. 30, 2017 $ / shares
Share Price	$ 6.39	$ 3.75
Estimated conversion dates
Measurement Input, Risk Free Interest Rate [Member]
Risk-free interest rate
Measurement Input, Risk-adjusted Yields [Member]
Risk-free interest rate
Measurement Input, Probability of Change in Control [Member]
Risk-free interest rate		0.05
Measurement Input, Credit Spread [Member]
Risk-free interest rate
Minimum [Member]
Estimated conversion dates	2018	2018
Minimum [Member] | Measurement Input, Risk Free Interest Rate [Member]
Risk-free interest rate	0.0197	0.0168
Minimum [Member] | Measurement Input, Risk-adjusted Yields [Member]
Risk-free interest rate	0.151	0.184
Minimum [Member] | Measurement Input, Price Volatility [Member]
Risk-free interest rate	0.45	0.45
Minimum [Member] | Measurement Input, Probability of Change in Control [Member]
Risk-free interest rate	0
Minimum [Member] | Measurement Input, Credit Spread [Member]
Risk-free interest rate	0.1296	0.1663
Maximum [Member]
Estimated conversion dates	2025	2025
Maximum [Member] | Measurement Input, Risk Free Interest Rate [Member]
Risk-free interest rate	0.0285	0.024
Maximum [Member] | Measurement Input, Risk-adjusted Yields [Member]
Risk-free interest rate	0.2523	0.2853
Maximum [Member] | Measurement Input, Price Volatility [Member]
Risk-free interest rate	0.75	0.8
Maximum [Member] | Measurement Input, Probability of Change in Control [Member]
Risk-free interest rate	0.05
Maximum [Member] | Measurement Input, Credit Spread [Member]
Risk-free interest rate	0.2298	0.267

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Note 3 - Fair Value Measurement - Financial Assets and Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Total debt	$ 165,844	$ 156,900
Reported Value Measurement [Member]
Total debt	$ 171,402	$ 165,377

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Note 4 - Debt (Details Textual) - USD ($)		3 Months Ended	6 Months Ended
	Jun. 29, 2018	Jun. 30, 2018	Jun. 30, 2018	Jun. 30, 2017
Repayments of Long-term Debt, Total			$ 37,037,000	$ 24,372,000
Loan Annual Amortization Percentage of Loan Accounts Outstanding	2.50%
Debt Instrument, Facility Charge, Percentage		4.00%	4.00%
Debt Instrument, Origination Fee Amount		$ 1,400,000	$ 1,400,000
Debt Instrument, Funded Amount and Other Closing Costs		200,000	200,000
Debt Instrument, Agency Fee Amount Per Quarter		25,000	25,000
Unamortized Debt Issuance Expense		1,600,000	1,600,000
Proceeds from Issuance of Debt			$ 34,611,000	$ 12,455,000
Debt Conversion, Original Debt, Amount		$ 0
Minimum [Member] | Prime Rate [Member]
Debt Instrument, Basis Spread on Variable Rate	4.00%
Maximum [Member] | Prime Rate [Member]
Debt Instrument, Basis Spread on Variable Rate	6.25%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Loan and Security Agreement [Member]
Repayments of Long-term Debt, Total	$ 27,300,000
Great American Capital Partners, LLC [Member] | Loan and Security Agreement [Member]
Debt Instrument, Face Amount	36,000,000
Line of Credit Facility, Maximum Borrowing Capacity	35,000,000
Proceeds from Issuance of Debt	$ 36,000,000

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Note 4 - Debt - Debt Components (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Debt, principal	$ 196,858	$ 195,819
Unamortized Debt Discount	(25,456)	(30,442)
Debt	171,402	165,377
Debt, current	109,656	56,943
Debt, noncurrent	61,746	108,434
Convertible Debt [Member]
Debt, principal	66,307	70,900
Unamortized Debt Discount	(9,140)	(12,985)
Debt	57,167	57,915
Convertible Debt [Member] | The 2015 144A Notes [Member]
Debt, principal	37,887	37,887
Unamortized Debt Discount	(4,576)	(6,872)
Debt	33,311	31,015
Convertible Debt [Member] | The 2014 144A Notes [Member]
Debt, principal	24,004	24,004
Unamortized Debt Discount	(2,023)	(3,170)
Debt	21,981	20,834
Convertible Debt [Member] | December 2017 Convertible Note [Member]
Debt, principal		5,000
Unamortized Debt Discount		(25)
Debt		4,975
Convertible Debt [Member] | August 2013 Convertible Notes [Member]
Debt, principal	4,416	4,009
Unamortized Debt Discount	(2,541)	(2,918)
Debt	1,875	1,091
Loans Payable [Member]
Debt, principal	53,891	47,410
Unamortized Debt Discount	(7,429)	(6,513)
Debt	46,462	40,897
Loans Payable [Member] | Great American Capital Partners, LLC Term Loan Facility [Member]
Debt, principal	36,000
Unamortized Debt Discount	(1,596)
Debt	34,404
Loans Payable [Member] | Senior Secured Convertible Note [Member]
Debt, principal		28,566
Unamortized Debt Discount		(253)
Debt		28,313
Loans Payable [Member] | Ginkgo Collaboration Note [Member]
Debt, principal	12,000	12,000
Unamortized Debt Discount	(4,599)	(4,983)
Debt	7,401	7,017
Loans Payable [Member] | Other Loans Payable [Member]
Debt, principal	5,696	6,463
Unamortized Debt Discount	(1,234)	(1,277)
Debt	4,462	5,186
Loans Payable [Member] | Other Credit Facilities [Member]
Debt, principal	195	381
Unamortized Debt Discount
Debt	195	381
Nonrelated Party Debt [Member]
Debt, principal	120,198	118,310
Unamortized Debt Discount	(16,569)	(19,498)
Debt	103,629	98,812
Related Party Convertible Notes [Member]
Debt, principal	51,604	50,116
Unamortized Debt Discount	(1,991)	(2,905)
Debt	49,613	47,211
Related Party Convertible Notes [Member] | The 2014 144A Notes [Member]
Debt, principal	24,705	24,705
Unamortized Debt Discount	(2,423)	(3,784)
Debt	22,282	20,921
Related Party Convertible Notes [Member] | August 2013 Convertible Notes [Member]
Debt, principal	23,199	21,711
Unamortized Debt Discount	432	897
Debt	23,631	22,608
Related Party Convertible Notes [Member] | Secured R&D Notes [Member]
Debt, principal	3,700	3,700
Unamortized Debt Discount		(18)
Debt	3,700	3,682
Related Party Loan Payable [Member]
Debt, principal	25,056	27,393
Unamortized Debt Discount	(6,896)	(8,039)
Debt	18,160	19,354
Related Party Loan Payable [Member] | Other Loans Payable [Member]
Debt, principal	56	393
Unamortized Debt Discount
Debt	56	393
Related Party Loan Payable [Member] | DSM Note [Member]
Debt, principal	25,000	25,000
Unamortized Debt Discount	(6,896)	(8,039)
Debt	18,104	16,961
Related Party Loan Payable [Member] | Private Placement February 2016 [Member]
Debt, principal		2,000
Unamortized Debt Discount
Debt		2,000
Related Party Debt [Member]
Debt, principal	76,660	77,509
Unamortized Debt Discount	(8,887)	(10,944)
Debt	$ 67,773	$ 66,565

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Note 4 - Debt - Long-term Debt Instruments (Details) $ in Thousands	Jun. 30, 2018 USD ($)
2018 (remaining six months)	$ 13,590
2019	104,881
2020	11,415
2021	61,678
2022	13,417
Thereafter	2,528
Total future minimum payments	207,509
Less: amount representing interest	(33,403)
Add: amount mandatorily convertible into common stock upon maturity	(24,802)
Less: future interest accruals to be converted to principal	(2,050)
Present value of minimum debt payments	196,858
Less: current portion of debt principal	(120,877)
Noncurrent portion of debt principal	75,981
Related Party Convertible Notes [Member]
2018 (remaining six months)	2,580
2019	69,334
2020
2021
2022	13,417
Thereafter
Total future minimum payments	71,914
Less: amount representing interest	(5,160)
Add: amount mandatorily convertible into common stock upon maturity
Less: future interest accruals to be converted to principal	(447)
Present value of minimum debt payments	66,307
Less: current portion of debt principal	(66,307)
Noncurrent portion of debt principal
Convertible Debt [Member]
2018 (remaining six months)	3,323
2019	1,627
2020	1,626
2021	1,627
2022
Thereafter	2,528
Total future minimum payments	24,148
Less: amount representing interest	(6,453)
Add: amount mandatorily convertible into common stock upon maturity
Less: future interest accruals to be converted to principal
Present value of minimum debt payments	17,695
Less: current portion of debt principal	(2,714)
Noncurrent portion of debt principal	14,981
Loans Payable [Member]
2018 (remaining six months)	1,878
2019	5,912
2020	7,289
2021	32,551
2022
Thereafter
Total future minimum payments	47,630
Less: amount representing interest	(11,434)
Add: amount mandatorily convertible into common stock upon maturity
Less: future interest accruals to be converted to principal
Present value of minimum debt payments	36,196
Less: current portion of debt principal	(196)
Noncurrent portion of debt principal	36,000
Related Party Loan Payable [Member]
2018 (remaining six months)	4,503
2019	25,508
2020
2021
2022
Thereafter
Total future minimum payments	30,011
Less: amount representing interest	(1,606)
Add: amount mandatorily convertible into common stock upon maturity	(24,802)
Less: future interest accruals to be converted to principal	(1,603)
Present value of minimum debt payments	51,604
Less: current portion of debt principal	(51,604)
Noncurrent portion of debt principal
Credit Facility [Member]
2018 (remaining six months)	1,306
2019	2,500
2020	2,500
2021	27,500
2022
Thereafter
Total future minimum payments	33,806
Less: amount representing interest	(8,750)
Add: amount mandatorily convertible into common stock upon maturity
Less: future interest accruals to be converted to principal
Present value of minimum debt payments	25,056
Less: current portion of debt principal	(56)
Noncurrent portion of debt principal	$ 25,000

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Note 5 - Mezzanine Equity (Details Textual) - $ / shares	Apr. 08, 2016	Jun. 30, 2018	Jun. 30, 2017
Share Price		$ 6.39	$ 3.75
Gates Foundation Purchase Agreement [Member]
Share Price	$ 17.10
Compound Annual Return	10.00%

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Note 5 - Mezzanine Equity - Mezzanine Equity (Details) - USD ($) $ in Millions	Jun. 30, 2018	Dec. 31, 2017
Contingently Redeemable Common Stock [Member]
Mezzanine Equity	$ 5	$ 5

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Note 6 - Stockholders' Deficit (Details Textual)			3 Months Ended		6 Months Ended
	Apr. 12, 2018 USD ($) yr $ / shares shares	Mar. 08, 2016 USD ($)	Jun. 30, 2018 USD ($) $ / shares	Jun. 30, 2017 USD ($)	Jun. 30, 2018 USD ($) $ / shares shares	Jun. 30, 2017 USD ($)
Proceeds from Warrant Exercises					$ 14,549,000
Stock Issued During Period, Shares, Warrants Exercised | shares	3,801,330				3,801,330
Class of Warrants or Right, Issued in Period | shares					3,616,174
Gain on Extinguishment of Derivative Liability			$ 1,857,000		$ 1,857,000
At the Market Offering [Member]
Common Stock, Value, Subscriptions		$ 50,000,000	0		0
Commission Rate		3.00%
Stock Issued During Period, Value, New Issues			$ 191,639		205,168
Proceeds from Issuance of Common Stock					$ 1,400,000
At the Market Offering, Three Months Ended [Member]
Shares Issued, Price Per Share | $ / shares			$ 6.91		$ 6.91
At The Market Offering, Six Months Ended [Member]
Shares Issued, Price Per Share | $ / shares			$ 6.90		$ 6.90
May 2017 Warrants [Member]
Proceeds from Warrant Exercises	$ 8,000,000
Stock Issued During Period, Shares, Warrants Exercised | shares	6
Class of Warrants or Right, Issued in Period | shares	3,616,174
Class of Warrant or Right, Term	1 year 75 days
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares	$ 7
Warrants and Rights Outstanding	$ 9,400,000
Loss on Extinguishment of Derivative Liability			$ 9,400,000
May 2017 Warrants [Member] | Measurement Input, Price Volatility [Member]
Warrants and Rights Outstanding, Measurement Input	0.009
May 2017 Warrants [Member] | Measurement Input, Risk Free Interest Rate [Member]
Warrants and Rights Outstanding, Measurement Input	0.0216
May 2017 Warrants [Member] | Measurement Input, Expected Term [Member]
Warrants and Rights Outstanding, Measurement Input | yr	1.25
May 2017 Warrants [Member] | Measurement Input, Expected Dividend Payment [Member]
Warrants and Rights Outstanding, Measurement Input	0
May 2017 Warrants [Member] | Measurement Input, Exercise Price [Member]
Warrants and Rights Outstanding, Measurement Input	7
May 2017 Warrants [Member] | Measurement Input, Share Price [Member]
Warrants and Rights Outstanding, Measurement Input	6.8

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Note 6 - Stockholders' Deficit - Warrant Activity (Details) - shares		6 Months Ended
	Apr. 12, 2018	Jun. 30, 2018
Number outstanding, beginning balance (in shares)		29,921,844
Additional Warrants Issued (in shares)		3,616,174
Exercises (in shares)	(3,801,330)	(3,801,330)
Number outstanding, ending balance (in shares)		29,736,688
Warrant 1 [Member]
Number outstanding, beginning balance (in shares)		81,197
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		81,197
Warrant 2 [Member]
Number outstanding, beginning balance (in shares)		2,082,010
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		2,082,010
Warrant 3 [Member]
Number outstanding, beginning balance (in shares)		171,429
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		171,429
Warrant 4 [Member]
Number outstanding, beginning balance (in shares)		18,042,568
Additional Warrants Issued (in shares)
Exercises (in shares)		(3,801,330)
Number outstanding, ending balance (in shares)		14,241,238
Warrant 5 [Member]
Number outstanding, beginning balance (in shares)		3,968,116
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		3,968,116
Warrant 6 [Member]
Number outstanding, beginning balance (in shares)		5,575,118
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		5,575,118
Warrant 7 [Member]
Number outstanding, beginning balance (in shares)
Additional Warrants Issued (in shares)		3,616,174
Exercises (in shares)
Number outstanding, ending balance (in shares)		3,616,174
Warrant 8 [Member]
Number outstanding, beginning balance (in shares)		1,406
Additional Warrants Issued (in shares)
Exercises (in shares)
Number outstanding, ending balance (in shares)		1,406

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Note 7 - Variable-interest Entities and Unconsolidated Investments - Variable Interest Entities (Details) - Variable Interest Entity, Primary Beneficiary [Member] - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Assets	$ 37,133	$ 36,781
Liabilities	$ 1,873	$ 3,187

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Note 7 - Variable-interest Entities and Unconsolidated Investments - Unconsolidated Investments (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Equity investment in SweeGen	$ 3,570	$ 3,233
Novvi LLC [Member]
Equity-method investment, percentage	20.00%
Equity-method investment
Total Amyris Biosolutions B.V. [Member]
Equity-method investment, percentage	25.00%
Equity-method investment
SweeGen, Inc. [Member]
SweeGen, Inc.	3.00%
Equity investment in SweeGen	$ 3,570	$ 3,233

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Note 8 - Net Loss Per Share Attributable to Common Stockholders - Calculation of Basic and Diluted Net Loss Per Share of Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Net income (loss) attributable to Amyris, Inc.	$ 1,533	$ 620	$ (89,963)	$ (36,751)
Less deemed dividend on capital distribution to related parties		(8,648)		(8,648)
Less deemed dividend related to beneficial conversion feature on Series A preferred stock		(562)		(562)
Less cumulative dividends on Series A and B preferred stock	(399)	(1,675)	(794)	(1,675)
Less earnings allocated to participating securities	(67)
Net income (loss) attributable to Amyris, Inc. common stockholders, basic	1,067	(10,265)	(90,757)	(47,636)
Earnings allocated to participating securities	67
Gain from change in fair value of dilutive common stock warrants	(13,421)
Interest on dilutive convertible debt	357
Accretion of debt discount	(99)
Gain from change in fair value of derivative instruments	(5,765)
Net loss attributable to Amyris, Inc. common stockholders, diluted	$ (17,794)	$ (10,265)	$ (90,757)	$ (47,636)
Weighted-average shares of common stock outstanding used in computing net income (loss) per share of common stock, basic (in shares)	54,932,411	23,155,874	53,076,975	21,226,013
Net income (loss) per share attributable to common stockholders, basic (in dollars per share)	$ 0.02	$ (0.44)	$ (1.71)	$ (2.24)
Effect of dilutive convertible debt (in shares)	2,709,323
Effect of dilutive common stock warrants (in shares)	3,088,002
Weighted-average common stock equivalents used in computing net loss per share of common stock, diluted (in shares)	60,729,736	23,155,874	53,076,975	21,226,013
Net loss per share attributable to common stockholders, diluted (in dollars per share)	$ (0.29)	$ (0.44)	$ (1.71)	$ (2.24)

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Note 8 - Net Loss Per Share Attributable to Common Stockholders - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares		3 Months Ended		6 Months Ended
		Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Antidilutive securities (in shares)		38,562,796	24,806,045	47,422,410	24,806,045
Stock Options to Purchase Common Stock [Member]
Antidilutive securities (in shares)		5,424,330	997,275	5,424,330	997,275
Convertible Promissory Notes [Member]
Antidilutive securities (in shares)	[1]	5,695,615	6,270,734	8,390,819	6,270,734
Period-end Common Stock Warrants [Member]
Antidilutive securities (in shares)		18,177,362	16,871,700	24,341,772	16,871,700
Restricted Stock Units (RSUs) [Member]
Antidilutive securities (in shares)		5,211,584	666,336	5,211,584	666,336
Period-end Preferred Stock [Member]
Antidilutive securities (in shares)		4,053,905		4,053,905

[1] The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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Note 9 - Commitments and Contingencies (Details Textual) R$ in Millions, $ in Millions	6 Months Ended		12 Months Ended
	Jun. 30, 2018 USD ($)	Jun. 30, 2018 BRL (R$)	Dec. 31, 2017 USD ($)	Dec. 31, 2017 BRL (R$)
FINEP Credit Facility [Member] | Chattel Mortgage [Member]
Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired	$ 1.6	R$ 6	$ 1.8	R$ 6

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Note 9 - Commitments and Contingencies - Future Minimum Payments for Lease Obligations (Details) $ in Thousands	Jun. 30, 2018 USD ($)
2018 (remaining six months)	$ 424
2018 (remaining six months)	4,941
2018 (remaining six months)	5,365
Capital leases 2019	451
Operating leases 2019	8,755
Total lease obligations 2019	9,206
Capital leases 2020	125
Operating leases 2020	7,017
Total lease obligations 2020	7,142
Capital leases 2021
Operating leases 2021	7,241
Total lease obligations 2021	7,241
Capital leases 2022
Operating leases 2022	7,414
Total lease obligations 2022	7,414
Capital leases thereafter
Operating leases thereafter	3,281
Total lease obligations thereafter	3,281
Total future minimum capital lease payments	1,000
Total future minimum operating lease payments	38,649
Total future minimum lease payments	39,649
Less: amount representing interest	(49)
Present value of minimum lease payments	951
Less: current portion	(583)
Long-term portion	$ 368

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Note 10 - Revenue Recognition and Contract Assets and Liabilities (Details Textual) - USD ($) $ in Thousands	6 Months Ended		24 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Dec. 31, 2017	Jun. 30, 2016
Increase (Decrease) in Contract with Customer, Liability	$ 3,959	$ (838)
Contract with Customer, Liability, Current	9,643		$ 9,643	$ 4,880
Givaudan International, SA [Member] | Collaborative Arrangement [Member]
Receivable from Collaborators					$ 12,000
Proceeds from Collaborators			0
Royalty [Member]
Contract with Customer, Liability, Revenue Recognized	3,300
Accounting Standards Update 2014-09 [Member]
Increase (Decrease) in Contract with Customer, Liability	4,800
Contract with Customer, Liability, Current	$ 800		$ 800

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Note 10 - Revenue Recognition and Contract Assets and Liabilities - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Revenues	$ 23,194	$ 25,679	$ 46,192	$ 38,660
Product [Member]
Revenues	6,633	9,892	11,828	17,929
Licenses and Royalties [Member]
Revenues	6,887	5,497	18,324	5,752
Grants and Collaborations [Member]
Revenues	9,674	10,290	16,040	14,979
UNITED STATES
Revenues	6,963	11,944	10,133	15,040
UNITED STATES | Product [Member]
Revenues	2,339	1,902	4,301	2,998
UNITED STATES | Licenses and Royalties [Member]
Revenues		2,663		2,673
UNITED STATES | Grants and Collaborations [Member]
Revenues	4,624	7,379	5,832	9,369
Europe [Member]
Revenues	14,188	3,737	31,560	9,112
Europe [Member] | Product [Member]
Revenues	2,987	749	5,421	3,307
Europe [Member] | Licenses and Royalties [Member]
Revenues	6,887	202	18,324	446
Europe [Member] | Grants and Collaborations [Member]
Revenues	4,314	2,786	7,815	5,359
Asia [Member]
Revenues	1,113	9,918	2,791	14,352
Asia [Member] | Product [Member]
Revenues	1,113	7,161	1,791	11,468
Asia [Member] | Licenses and Royalties [Member]
Revenues		2,632		2,633
Asia [Member] | Grants and Collaborations [Member]
Revenues		125	1,000	251
South America [Member]
Revenues	930	80	1,608	144
South America [Member] | Product [Member]
Revenues	194	80	215	144
South America [Member] | Licenses and Royalties [Member]
Revenues
South America [Member] | Grants and Collaborations [Member]
Revenues	736		1,393
Other Area [Member]
Revenues			100	12
Other Area [Member] | Product [Member]
Revenues			100	12
Other Area [Member] | Licenses and Royalties [Member]
Revenues
Other Area [Member] | Grants and Collaborations [Member]
Revenues

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Note 10 - Revenue Recognition and Contract Assets and Liabilities - Revenue in Connection With Significant Revenue Agreement (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Revenues	$ 23,194	$ 25,679	$ 46,192	$ 38,660
Significant Revenue Agreement [Member]
Revenues	17,501	15,308	36,225	23,022
DSM International B.V. [Member] | Significant Revenue Agreement [Member]
Revenues	8,624	149	21,414	149
Givaudan International, SA [Member] | Significant Revenue Agreement [Member]
Revenues	3,467	1,500	6,043	3,619
Firmenich [Member] | Significant Revenue Agreement [Member]
Revenues	1,219	2,339	2,730	4,655
Nenter & Co., Inc. [Member] | Significant Revenue Agreement [Member]
Revenues		6,649	1,000	8,957
DARPA [Member] | Significant Revenue Agreement [Member]
Revenues	4,191	4,671	5,038	5,642
All Other Customers [Member]
Revenues	5,693	10,371	9,967	15,638
Renewable Products [Member]
Revenues	6,633	9,892	11,828	17,929
Renewable Products [Member] | Significant Revenue Agreement [Member]
Revenues	2,109	4,016	3,391	7,941
Renewable Products [Member] | DSM International B.V. [Member] | Significant Revenue Agreement [Member]
Revenues
Renewable Products [Member] | Givaudan International, SA [Member] | Significant Revenue Agreement [Member]
Revenues	2,109		3,184	619
Renewable Products [Member] | Firmenich [Member] | Significant Revenue Agreement [Member]
Revenues			207	998
Renewable Products [Member] | Nenter & Co., Inc. [Member] | Significant Revenue Agreement [Member]
Revenues		4,016		6,324
Renewable Products [Member] | DARPA [Member] | Significant Revenue Agreement [Member]
Revenues
Renewable Products [Member] | All Other Customers [Member]
Revenues	4,524	5,876	8,437	9,988
Licenses and Royalties [Member]
Revenues	6,887	5,497	18,324	5,752
Licenses and Royalties [Member] | Significant Revenue Agreement [Member]
Revenues	6,887	2,835	18,324	3,079
Licenses and Royalties [Member] | DSM International B.V. [Member] | Significant Revenue Agreement [Member]
Revenues	6,887		18,287
Licenses and Royalties [Member] | Givaudan International, SA [Member] | Significant Revenue Agreement [Member]
Revenues
Licenses and Royalties [Member] | Firmenich [Member] | Significant Revenue Agreement [Member]
Revenues		202	37	446
Licenses and Royalties [Member] | Nenter & Co., Inc. [Member] | Significant Revenue Agreement [Member]
Revenues		2,633		2,633
Licenses and Royalties [Member] | DARPA [Member] | Significant Revenue Agreement [Member]
Revenues
Licenses and Royalties [Member] | All Other Customers [Member]
Revenues		2,662		2,673
Grants and Collaborations [Member]
Revenues	9,674	10,290	16,040	14,979
Grants and Collaborations [Member] | Significant Revenue Agreement [Member]
Revenues	8,505	8,457	14,510	12,002
Grants and Collaborations [Member] | DSM International B.V. [Member] | Significant Revenue Agreement [Member]
Revenues	1,737	149	3,127	149
Grants and Collaborations [Member] | Givaudan International, SA [Member] | Significant Revenue Agreement [Member]
Revenues	1,358	1,500	2,859	3,000
Grants and Collaborations [Member] | Firmenich [Member] | Significant Revenue Agreement [Member]
Revenues	1,219	2,137	2,486	3,211
Grants and Collaborations [Member] | Nenter & Co., Inc. [Member] | Significant Revenue Agreement [Member]
Revenues			1,000
Grants and Collaborations [Member] | DARPA [Member] | Significant Revenue Agreement [Member]
Revenues	4,191	4,671	5,038	5,642
Grants and Collaborations [Member] | All Other Customers [Member]
Revenues	$ 1,169	$ 1,833	$ 1,530	$ 2,977

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Note 10 - Revenue Recognition and Contract Assets and Liabilities - Contract Balances (Details) - USD ($) $ in Thousands		Jun. 30, 2018	Dec. 31, 2017
Unbilled receivable, current		$ 12,683	$ 9,340
Unbilled receivable, noncurrent		9,747	7,940
Deferred revenue, current		9,643	4,880
Deferred revenue, noncurrent	[1]	383	383
Accounts receivable, net		$ 26,814	$ 24,281

[1] As of June 30, 2018 and December 31, 2017, deferred revenue, noncurrent is presented in Other Noncurrent Liabilities in the consolidated balance sheets because of its insignificance.

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Note 10 - Revenue Recognition and Contract Assets and Liabilities - Remaining Performance Obligations (Details) $ in Thousands	Jun. 30, 2018 USD ($)
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-07-01
Remaining performance obligation	$ 4,032
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-01-01
Remaining performance obligation	6,338
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Remaining performance obligation	6,338
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Remaining performance obligation	572
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Remaining performance obligation	$ 17,280

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Note 11 - Related Party Transactions - Related Party Accounts Receivable (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Accounts receivable, net	$ 16,685	$ 5,328
Unbilled receivable, current	12,683	9,340
Unbilled receivable, noncurrent	9,747	7,940
DSM International B.V. [Member]
Accounts receivable, net	15,829	3,483
Unbilled receivable, current	12,683	9,340
Unbilled receivable, noncurrent	9,747	7,940
Novvi LLC [Member]
Accounts receivable, net	472	1,607
Total [Member]
Accounts receivable, net	$ 384	$ 238

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Note 12 - Stock-based Compensation (Details Textual) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		6 Months Ended
	May 31, 2018	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Performance-based Stock Options, Grant Date Fair Value		$ 5,100		$ 5,100
Allocated Share-based Compensation Expense, Total		$ 1,900	$ 1,038	$ 3,178	$ 2,684
Chief Executive Officer [Member]
Purchasable Shares Under Performance Based Options		3,250,000		3,250,000
Performance-Based Stock Options, Exercise Price		$ 5.08
Chief Executive Officer [Member] | Minimum [Member]
Performance-Based Stock Options Contingently Available for Issuance		0		0
Chief Executive Officer [Member] | Maximum [Member]
Performance-Based Stock Options Contingently Available for Issuance		3,250,000		3,250,000
Equity Incentive Plan, 2010 [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized	9,000,000
Share-based Compensation Arrangement by Share-based Payment Award, Maximum Number of Shares Per Employee	4,000,000
Employee Stock Purchase Plan, 2010 [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized	1,000,000
Employee Stock Option [Member]
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Total		$ 36,000		$ 36,000
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition				3 years 255 days
Performance-based Stock Options [Member]
Performance-Based Stock Options, Exercise Price				$ 5.08
Allocated Share-based Compensation Expense, Total		$ 100		$ 100

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Note 12 - Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Outstanding (in shares)	1,338,367
Outstanding, weighted average exercise price (in dollars per share)	$ 33.40
Outstanding, weighted average remaining contractual life (Year)	9 years 73 days	7 years 255 days
Outstanding, aggregate intrinsic value	$ 8,541	$ 97
Granted (in shares)	4,192,476
Granted, weighted average exercise price (in dollars per share)	$ 5.12
Exercised (in shares)	(43,055)
Exercised, weighted average exercise price (in dollars per share)	$ 3.68
Forfeited or expired (in shares)	(63,458)
Forfeited or expired, weighted average exercise price (in dollars per share)	$ 29.29
Outstanding (in shares)	5,424,330	1,338,367
Outstanding, weighted average exercise price (in dollars per share)	$ 11.83	$ 33.40
Vested or expected to vest after June 30, 2018 (in shares)	4,981,859
Vested and expected to vest after June 30, 2018, weighted average exercise price (in dollars per share)	$ 12.42
Vested and expected to vest after June 30, 2018, weighted average remaining contractual life (Year)	9 years 73 days
Vested and expected to vest after June 30, 2018, aggregate intrinsic value	$ 7,790
Exercisable at June 30, 2018 (in shares)	949,237
Exercisable at June 30, 2018, weighted average exercise price (in dollars per share)	$ 42.07
Exercisable at June 30, 2018, weighted average remaining contractual life (Year)	6 years 255 days
Exercisable at June 30, 2018, aggregate intrinsic value	$ 1,119

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Note 12 - Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Restricted Stock Units (RSUs) [Member] - $ / shares	6 Months Ended	12 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Outstanding, RSUs (in shares)	683,554
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 8.62
Outstanding, weighted average remaining contractual life (Year)	2 years 10 days	1 year 146 days
Awarded (in shares)	4,712,787
Awarded (in dollars per share)	$ 5.27
RSUs released (in shares)	(144,572)
RSUs released (in dollars per share)	$ 11.18
RSUs forfeited (in shares)	(37,879)
RSUs forfeited (in dollars per share)	$ 7.01
Outstanding, RSUs (in shares)	5,213,890	683,554
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 5.53	$ 8.62
Vested or expected to vest after June 30, 2018 (in shares)	4,927,426
Vested or expected to vest after June 30, 2018 (in dollars per share)	$ 5.54
Vested or expected to vest after June 30, 2018 (Year)	2 years

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Note 12 - Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Allocated share-based compensation expense	$ 1,900	$ 1,038	$ 3,178	$ 2,684
Research and Development Expense [Member]
Allocated share-based compensation expense	333	441	696	925
Selling, General and Administrative Expenses [Member]
Allocated share-based compensation expense	$ 1,567	$ 597	$ 2,482	$ 1,759

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Note 12 - Stock-based Compensation - Share-based Payment Award, Stock Options, Valuation Assumptions (Details) - Employee Stock Option [Member]	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Expected dividend yield
Risk-free interest rate	2.70%	1.80%	2.70%	1.80%
Expected term (in years) (Year)	6 years 313 days	5 years 138 days	6 years 310 days	5 years 138 days
Expected volatility	79.60%	85.70%	79.70%	85.70%

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Note 12 - Stock-based Compensation - Share-based Payment Award, Stock Options with Performance, Valuation Assumptions (Details) - Performance-based Stock Options [Member]	6 Months Ended
	Jun. 30, 2018 $ / shares
Fair value of the Company’s common stock on grant date (in dollars per share)	$ 5.08
Expected volatility	70.00%
Risk-free interest rate	2.75%
Dividend yield	0.00%

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Note 13 - Subsequent Events (Details Textual) - USD ($) $ in Thousands		6 Months Ended
	Jul. 02, 2018	Jun. 30, 2018	Jun. 30, 2017
Repayments of Long-term Debt, Total		$ 37,037	$ 24,372
Secured R&D Notes [Member] | Subsequent Event [Member] | Related Party Convertible Notes [Member]
Repayments of Long-term Debt, Total	$ 3,700