10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

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

For the quarterly period ended September 30, 2014

OR

¨ 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: 000-23930

AMPLIPHI BIOSCIENCES CORPORATION
(Exact name of registrant as specified in its charter)

Washington (State or other jurisdiction of incorporation or organization)	91-1549568 I.R.S. Employer Identification Number)
4870 Sadler Road, Suite 300 Glen Allen, Virginia	23060 (Zip Code)
(Address of principal executive offices)

Registrant’s telephone number, including area code: (804) 205-5069

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    ¨

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 pursuant 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    ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company as defined in Rule 12b-2 of the Exchange Act. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer  ¨	Accelerated filer  ¨
Non-accelerated filer ¨ (Do not check if a small reporting company)	Smaller reporting company  x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).

Yes ¨    No x

The number of shares of the Registrant’s Public Common Stock outstanding at October 20, 2014 was 187,159,093.

TABLE OF CONTENTS

		Page
PART I - FINANCIAL INFORMATION
Consolidated Balance Sheets		3
Consolidated Statements of Operations and Comprehensive Income (Loss)		4
Consolidated Statements of Stockholders’ Equity (Deficit)		5
Consolidated Statements of Cash Flows		6
Condensed Notes to Consolidated Financial Statements		7
Item 2.	Management's Discussion and Analysis of Financial Condition and Results of Operations	15
PART II.  OTHER INFORMATION		19
Item 1.	Legal Proceedings	19
Item 1A.	Risk Factors	19
Item 1A.	Unregistered Sales of Equity Securities and Use of Proceeds	19
Item 3.	Defaults upon Senior Securities	19
Item 4.	Mine Safety Disclosures	19
Item 5.	Other Information	19
Item 6.	Exhibits	19
Signatures		21

2

AMPLIPHI BIOSCIENCES CORPORATION
CONSOLIDATED BALANCE SHEETS

	September 30, 2014			December 31, 2013
	(Unaudited)			(Restated)
Assets
Current assets
Cash and cash equivalents	$	9,786,000		$	20,355,000
Accounts receivable		27,000			8,000
Prepaid expenses and other current assets		279,000			171,000
Total current assets		10,092,000			20,534,000
Property and equipment, net of accumulated depreciation of $559,000 and $473,000 as of September 30, 2014 and December 31, 2013, respectively		1,175,000			145,000
Intangible assets
In process research and development		12,446,000			12,446,000
Patents, net of accumulated amortization of $116,000 and $93,000 as of September 30, 2014 and December 31, 2013, respectively		377,000			400,000
Goodwill		4,329,000			4,329,000
Total intangible assets		17,152,000			17,175,000
Total assets	$	28,419,000		$	37,854,000
Liabilities and Stockholders’ Equity (Deficit)
Current liabilities
Accounts payable and accrued expenses	$	1,840,000		$	2,147,000
Accrued severance		659,000			—
Total current liabilities		2,499,000			2,147,000
Long term liabilities
Derivative preferred shares conversion liability		7,633,000			34,443,000
Derivative warrants liability		6,949,000			16,664,000
Total long term liabilities		14,582,000			51,107,000
Total liabilities		17,081,000			53,254,000
Stockholders’ equity (deficit)
Preferred stock, $0.01 par value, 10,000,000 shares authorized; 8,671,040 shares issued and outstanding at September 30, 2014 and 8,859,978 shares issued and outstanding at December 31, 2013		87,000			89,000
Common stock, $0.01 par value, 445,000,000 shares authorized, 187,159,093 shares issued and outstanding at September 30, 2014 and 182,535,562 shares issued and outstanding at December 31, 2013		1,872,000			1,825,000
Additional paid-in capital		363,032,000			358,988,000
Paid-in-capital – contingent shares		1,837,000			1,837,000
Accumulated other comprehensive loss		(178,000	)		(65,000	)
Accumulated deficit		(355,312,000	)		(378,074,000	)
Total stockholders’ equity (deficit)		11,338,000			(15,400,000	)
Total liabilities and stockholders’ equity (deficit)	$	28,419,000		$	37,854,000

See accompanying condensed notes to consolidated financial statements.

3

AMPLIPHI BIOSCIENCES CORPORATION

CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS)

	Three Months Ended September 30,						Nine Months Ended September 30,
	2014			2013			2014			2013
	(Unaudited)			(Unaudited)			(Unaudited)			(Unaudited)
Revenue	$	—		$	(3,000	)	$	310,000		$	333,000
Operating expenses
Research and development		1,804,000			1,106,000			4,687,000			5,378,000
General and administrative		1,632,000			1,211,000			5,377,000			4,777,000
Severance charge		1,510,000			—			1,510,000			—
Total operating expenses		4,946,000			2,317,000			11,574,000			10,155,000
Loss from operations		(4,946,000	)		(2,320,000	)		(11,264,000	)		(9,822,000	)
Other income (expense)
Gain (loss) on derivative liabilities		24,334,000			(41,548,000	)		34,026,000			(45,617,000	)
Amortization of note discount and patents		—			(23,000	)		—			(2,660,000	)
Interest expense, net		—			(9,000	)		—			(233,000	)
Other income (expense), net		24,334,000			(41,580,000	)		34,026,000			(48,510,000	)
Net income (loss)	$	19,388,000		$	(43,900,000	)	$	22,762,000		$	(58,332,000	)
Other comprehensive income (loss)
Net unrealized gain (loss) on foreign currency translations		(93,000	)		(21,000	)		(113,000	)		(24,000	)
Comprehensive income (loss)	$	19,295,000		$	(43,921,000	)	$	22,649,000		$	(58,356,000	)
Net income (loss) per share – basic	$	0.10		$	(0.44	)	$	0.12		$	(0.68	)
Weighted average number of shares of common stock outstanding – basic		187,159,093			99,156,809			184,445,172			85,688,356
Net income (loss) per share – diluted	$	0.06		$	(0.44	)	$	0.07		$	(0.68	)
Weighted average number of shares of common stock outstanding – diluted		315,990,084			99,156,809			323,604,642			85,688,356

See accompanying condensed notes to consolidated financial statements.

4

AMPLIPHI BIOSCIENCES CORPORATION

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (DEFICIT)

	Preferred Stock						Common Stock
	Shares			Amount			Shares			Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Income			Total Stockholders' Equity (Deficit)
Balances, December 31, 2012 (Restated)		—			—			66,908,810		$	669,000	$	332,806,000		$	(320,426,000	)	$	(106,000	)	$	12,943,000
Net loss		—			—			—			—		—			(57,648,000	)		—			(57,648,000	)
Stock-based compensation		—			—			—			—		1,437,000			—			—			1,437,000
Beneficial conversion feature and warrants associated with issuance of convertible loan notes		—			—			—			—		2,635,000			—			—			2,635,000
Shares issued for Intrexon		—			—			24,000,000			240,000		2,760,000			—			—			3,000,000
Issuance of preferred stock from conversion of convertible loan notes		5,016,081			50,000			—			—		—			—			—			50,000
Issuance of preferred stock		4,999,999			50,000			—			—		—			—			—			50,000
Preferred stock converted to common stock		(1,156,102	)		(11,000	)		11,561,020			115,000		6,511,000			—			—			6,615,000
Stock options exercised		—			—			61,018			1,000		12,000			—			—			13,000
Shares released from escrow		—			—			8,000,000			80,000		(80,000	)		—			—			—
Issuance of common stock for December financing		—			—			72,007,000			720,000		14,744,000			—			—			15,464,000
Escheat shares		—			—			(2,286	)		—		—			—			—			—
Foreign currency translations		—			—			—			—		—			—			41,000			41,000
Balances, December 31, 2013 (Restated)		8,859,978		$	89,000			182,535,562		$	1,825,000	$	360,825,000		$	(378,074,000	)	$	(65,000	)	$	(15,400,000	)
Net income		—			—			—			—		—			22,762,000			—			22,762,000
Warrants exercised		—			—			2,734,151			28,000		1,730,000			—			—			1,758,000
Preferred stock converted to common stock		(188,938	)		(2,000	)		1,889,380			19,000		724,000			—			—			741,000
Stock-based compensation		—			—			—			—		759,000			—			—			759,000
Stock-based compensation - severance		—			—			—			—		831,000			—			—			831,000
Foreign currency translations		—			—			—			—		—			—			(113,000	)		(113,000	)
Balances, September 30, 2014 (Unaudited)		8,671,040		$	87,000			187,159,093		$	1,872,000	$	364,869,000		$	(355,312,000	)	$	(178,000	)	$	11,338,000

See accompanying condensed notes to consolidated financial statements.

5

AMPLIPHI BIOSCIENCES CORPORATION

CONSOLIDATED STATEMENTS OF CASH FLOWS

	Nine Months Ended September 30,
	2014			2013
	(Unaudited)			(Unaudited)
Cash flows from operating activities
Net income (loss) from operations	$	22,762,000		$	(58,332,000	)
Adjustments required to reconcile net income (loss) to cash used in operating activities:
Derivative liability (gain) loss		(34,026,000	)		45,617,000
Shares issued for technology access fee		—			3,000,000
Amortization of patents		23,000			23,000
Amortization of note discount		—			2,637,000
Warrants issued as investment fees		—			759,000
Depreciation		59,000			66,000
Stock-based compensation		759,000			1,206,000
Stock-based compensation - severance		831,000			—
Changes in operating assets and liabilities net of acquisitions:
Accounts receivable		(19,000	)		(125,000	)
Tax refund		—			618,000
Accounts payable and accrued expenses		(307,000	)		(453,000	)
Accrued severance		659,000			—
Prepaid expenses and other current assets		(108,000	)		(153,000	)
Interest on loan notes		—			233,000
Net cash used in operating activities		(9,367,000	)		(4,904,000	)
Cash flows from investing activities
Purchases of property and equipment		(1,089,000	)		(97,000	)
Net cash used in investing activities		(1,089,000	)		(97,000	)
Cash flows from financing activities
Proceeds from Preferred Series B		—			7,000,000
Proceeds from convertible loan notes		—			2,000,000
Payment of convertible loan note		—			(26,000	)
Net cash provided by financing activities		—			8,974,000
Effect of exchange rates		(113,000	)		24,000
Net increase (decrease) in cash and cash equivalents		(10,569,000	)		3,997,000
Cash and cash equivalents, beginning of period		20,355,000			862,000
Cash and cash equivalents, end of period	$	9,786,000		$	4,859,000

See accompanying condensed notes to consolidated financial statements.

6

AMPLIPHI BIOSCIENCES CORPORATION

CONDENSED NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

September 30, 2014

(Unaudited)

1. Nature of Business and Significant Accounting Policies

Nature of Business

AmpliPhi Biosciences Corporation (the “Company”) was incorporated in the state of Washington in 1989. The Company, headquartered in Richmond, Virginia, is dedicated to developing novel antibacterial solutions called bacteriophage (phage). Phages are naturally occurring viruses that preferentially target and kill their bacterial targets.

Basis of Presentation

The interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries - Biocontrol, Ampliphi d.o.o., and AmpliPhi Australia. All significant intercompany accounts and transactions have been eliminated. All amounts on the financial statements and disclosures have been rounded to the nearest $1,000 except share and per share data.

The interim consolidated financial statements included herein have been prepared by the Company, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC. In the opinion of the Company’s management, all adjustments (consisting of normal recurring adjustments, reclassifications, and non-recurring adjustments) necessary to present fairly our results of operations for the three months and nine months ended September 30, 2014 and 2013, our cash flows for the nine months ended September 30, 2014 and 2013 and our financial position as of September 30, 2014 have been made. The results of operations for such interim periods are not necessarily indicative of the operating results to be expected for the full year.

Certain information and disclosures normally included in the notes to the annual financial statements have been condensed or omitted from these interim consolidated financial statements. Accordingly, these interim consolidated financial statements should be read in conjunction with the 2013 audited consolidated financial statements and notes.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Cash and Cash Equivalents

The Company considers cash equivalents to be short-term investments that have a maturity at the time of purchase of three months or less, are readily convertible into cash and have an insignificant level of valuation risk attributable to potential changes in interest rates. Cash equivalents are recorded at cost, which approximates fair market value, and consist primarily of money market accounts.

Accounts Receivable

Accounts receivable amounts are stated at their face amounts less any allowance. Provisions for doubtful accounts are estimated based on assessment of the probable collection from specific customer accounts and other known factors. If an account was determined to be uncollectible (payment has not been made in accordance with contract terms), it would be written off against the allowance. As of September 30, 2014 and December 31, 2013, management determined no allowance for doubtful accounts was required.

7

Property and Equipment

Property and equipment are recorded at cost and are depreciated using the straight-line method over the estimated useful lives of the related assets, generally three to seven years. 

Prepaid Expenses and Other Current Assets

Prepaid and other current assets as of September 30, 2014 and December 31, 2013 consist primarily of prepaid insurance and deposits.

Goodwill

Investments in purchased companies in excess of the underlying fair value of net assets at the date of acquisition are recorded as goodwill and assessed annually for impairment. If considered impaired, goodwill will be written down to fair value and a corresponding impairment loss recognized.

In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired in a business combination with an aggregate value of $7,172,000. Goodwill in the amount of $2,381,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired in a business combination with an aggregate value of $8,584,000. Goodwill in the amount of $1,948,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

Patents

Patents are recorded at cost and are amortized using the straight-line method over the estimated useful lives of the patents.

In 2011, the rights to Biocontrol Limited’s patents were acquired in a business combination. Patents in the amount of $493,000 have been recorded. These patents are being amortized over their useful life through December 2026.

Stock-Based Compensation

The Company accounts for stock-based payments under the guidance of Financial Accounting Standards Board (FASB) Accounting Standards Codification (ASC) 718, Stock Compensation, which requires measurement of compensation cost for all share-based payment awards at fair value on the date of grant and recognition of compensation cost over the requisite service period (typically the vesting period) for awards expected to vest.

Warrant and Preferred Shares Conversion Feature Liability

The Company accounts for warrants and the preferred shares conversion feature of the Company’s Series B preferred stock with anti-dilution (“down-round”) provisions under the guidance of ASC 815, Derivatives, and Hedging and Emerging Issue Task Force Statement 07-5: Determining Whether an Instrument (or Embedded Feature) Is Indexed to an Entity’s Own Stock, which require such warrants and the Series B preferred shares conversion feature to be recorded as a liability and adjusted to fair value in each reporting period.

Fair Value of Financial Assets and Liabilities — Derivative Instruments

The Company measures the fair value of financial assets and liabilities in accordance with GAAP, which defines fair value, establishes a framework for measuring fair value, and requires certain disclosures about fair value measurements.

8

GAAP defines fair value as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. GAAP also establishes as fair value hierarchy, which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. GAAP describes three levels of inputs that may be used to measure fair value:

Level 1 — quoted prices in active markets for identical assets or liabilities.

Level 2 — quoted prices for similar assets and liabilities in active markets or inputs that are observable.

Level 3 — inputs that are unobservable.

The Company does not use derivative financial instruments to hedge exposures to cash-flow, market or foreign-currency risks. However, the Company has entered into certain financial instruments and contracts, such as convertible loan notes with detachable common stock warrants and the issuance of preferred stock with detachable common stock warrants with features that are either i) not afforded equity classification, ii) embody risks not clearly and closely related to host contracts, or iii) may be net-cash settled by the counterparty. These instruments are required to be carried as derivative liabilities, at fair value.

The Company estimates fair values of these derivatives utilizing Level 2 inputs. The Company uses the Monte Carlo valuation technique as it embodies all of the requisite assumptions (including trading volatility, remaining term to maturity, market price, strike price, and risk free rates) necessary to fair value these instruments.

Estimating fair values of derivative financial instruments, including Level 2 instruments, require the use of significant and subjective inputs that may, and are likely to, change over the duration of the instrument with related changes in internal and external market factors. In addition, option-based techniques are volatile and sensitive to changes in our trading market price, the trading market price of various peer companies and other key assumptions. Since derivative financial instruments are initially and subsequently carried at fair value, our income will reflect this sensitivity of internal and external factors.

Revenue Recognition

The Company generates revenue from technology licenses. Revenue under technology licenses typically consists of nonrefundable, up-front license fees, technology access fees and various other payments. The Company recognizes revenue associated with performance milestones as earned, typically based upon the achievement of the specific milestones defined in the applicable agreements.

The Company recognizes revenue under research and development contracts as the related costs are incurred. When contracts include multiple elements, the Company follows ASC 605-25, Multiple Element Arrangements, which requires the Company to satisfy the following before revenue can be recognized:

• The delivered items have value to the customer on a stand-alone basis;

• Any undelivered items have objective and reliable evidence of fair value; and

• Delivery or performance is probable and within the Company’s control for any delivered items that have a right of return.

The Company classifies advance payments received in excess of amounts earned as deferred revenue.

Based upon the terms specified in its collaboration agreements, the Company receives advance payments from some of its collaboration partners before the project has been performed. These payments are deferred and recognized as revenue when the costs are incurred.

9

Research and Development

Research and development costs include salaries, costs of outside collaborators and outside services, royalty and license costs and allocated facility, occupancy and utility expenses. The Company expenses research and development costs as incurred.

In Process Research & Development (IPR&D) assets represent capitalized incomplete research projects that the Company acquired through business combinations. Such assets are initially measured at their acquisition date fair values. The fair value of the research projects is recorded as intangible assets on the consolidated balance sheet rather than expensed regardless of whether these assets have an alternative future use. The amounts capitalized are being accounted for as indefinite-lived intangible assets, subject to impairment testing until completion or abandonment of research and development efforts associated with the projects. Upon successful completion of each project, the Company will make a determination as to the then remaining useful life of the intangible asset and begin amortization. The Company tests its indefinite-lived intangibles, including IPR&D assets, for impairment at least annually. In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired by a business combination for $7,172,000. In 2012, IPR&D in the amount of $5,161,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired by a business combination $8,584,000. In 2011, IPR&D in the amount of $7,285,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

Net Income (Loss) per Common Share

Net income (loss) per common share is based on net income (loss) divided by the weighted average number of common shares outstanding during the period. For the three months ended September 30, 2014 and the nine months ended September 30, 2014, both basic and diluted net income (loss) are disclosed in the Consolidated Statements of Operations and Comprehensive Income. For the three months ended September 30, 2013 and the nine months ended September 30, 2013, the diluted net loss per share is the same as the basic net loss per share because all stock options, warrants, contingent shares, and Series B Preferred shares were antidilutive with respect to computing the net loss per share and therefore were excluded from the calculation of diluted net loss per share. The total number of shares that the Company excluded from the calculations of net loss per share was 150,283,630 shares for the three month period ending September 30, 2013 and 63,155,331 shares for the nine month period ending September 30, 2013.

Recent Accounting Pronouncements

On February 5, 2013, the FASB issued ASU no. 2013-02 which adds new disclosure requirements for items reclassified out of accumulated other comprehensive income (AOCI). The ASU is intended to help entities improve the transparency of changes in other comprehensive income (OCI) and items reclassified out of AOCI in their financial statements. It does not amend any existing requirements for reporting net income or OCI in the financial statements. For public entities, the new disclosure requirements are effective for fiscal years, and interim periods within those years, beginning after December 15, 2012. For nonpublic entities, the ASU is effective for fiscal years beginning after December 15, 2013, and interim and annual periods thereafter. The Company elected to early adopt this standard which did not result in any changes to the consolidated financial statements.

2. Liquidity

The Company has prepared the accompanying consolidated financial statements on a going concern basis, which assumes that the Company will realize its assets and satisfy its liabilities in the normal course of business. However, the Company has incurred net losses since its inception, has negative operating cash flows and has an accumulated deficit of $355.3 million as of September 30, 2014. These circumstances raise substantial doubt about the Company’s ability to continue as a going concern. The accompanying financial statements do not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classifications of liabilities that may result from the outcome of the uncertainty concerning the Company’s ability to continue as a going concern.

10

The Company believes that its current resources will only be sufficient to fund operations through the first quarter of 2015. This estimate is based on the Company’s ability to manage its staffing expenses and its working capital. Actual results could differ from its estimates. The Company intends to seek additional financing in order to fund operations through 2015; however, the Company cannot provide assurances that it will be successful in obtaining additional financing for these periods or as needed in the future. If the Company does not raise additional funds by the first quarter of 2015, it plans to implement cost reduction measures, such as a reduction in workforce, reducing its intellectual property prosecution, reducing other operating activities, and/or the pursuit of alternative financing transactions that would likely be on terms disadvantageous to the Company and dilutive to its shareholders. The Company could also be required to relinquish rights to its technology or product candidates or in-licensed technology on unfavorable terms, either of which would reduce the ultimate value of the technology or product candidates, or to sell assets likely at values significantly below their potential worth. If the Company is unable to secure additional capital, it may be required to cease operations, declare bankruptcy or otherwise wind-up its business.

3. Preferred Shares

On June 13, 2013, the Company’s Board of Directors approved a resolution designating 10,016,080 shares of Preferred Stock as Series B Convertible Preferred Stock with an initial stated value of $1.40 and par value of $0.01. Each Series B preferred share is convertible into 10 shares of common stock and is entitled to the number of votes equal to the number of shares of common stock. These Series B shares may be converted to common stock by the holder of the shares at any time. The Series B shares shall be automatically converted into common shares upon the closing of an underwritten initial public offering with aggregate proceeds to the Company of at least $7 million and a price per share to the public of at least the Series B stated value upon the closing of which the shares of common stock of the Company shall be listed for trading on the New York Stock Exchange. The Series B shares are also convertible into common shares upon the election of the holders of two-thirds of the outstanding Series B shares. Until conversion, the holders of Series B Preferred shares shall be entitled to receive dividends of 10% of the Series B stated value per annum.

In connection with the private placement of Series B Convertible Preferred Stock, the Company recorded a liability for a complex embedded derivative that required bifurcation under ASC Section 815. The embedded derivative includes a redemption feature, multiple dividend features, as well as multiple conversion features with a down-round ratchet provision. The Company estimates the fair values of the conversion feature using a Monte Carlo valuation model. The Company measured the fair value of the conversion feature on June 26, 2013 and July 15, 2013(dates of issuance) and recorded the initial liability as part of the private placement proceeds.

On June 26, 2013, the Company issued 4,999,999 shares of the Company’s newly-created Series B Convertible Preferred Stock and warrants to purchase 12,499,996 shares of common stock at an exercise price of $0.14 per share for an aggregate purchase price of $7.0 million. The value of the derivative liability related to the warrants was $1,886,000 and the value of the derivative liability related to the preferred shares was $5,064,000. As part of the same transaction, the Company converted $5,491,001 in outstanding convertible loan notes (principal and interest) into 4,357,936 shares of Series B Convertible Preferred Stock and warrants to purchase 10,894,839 shares of common stock at an exercise price of $0.14 per share. The value of the derivative liability related to the warrants was $1,644,000 and the value of the derivative liability related to the preferred shares was $3,804,000. As part of this issuance, the Company issued warrants to purchase 4,999,999 shares of common stock at an exercise price of $0.14 per share with an initial fair value of $759,000 and paid $350,000 to the placement agents. As a result of this financing, all outstanding convertible notes were converted into shares of Series B Convertible Preferred Stock and warrants to purchase common stock. On July 15, 2013, the remaining outstanding convertible loan notes, totaling $829,277 in principal and interest, were converted into 658,145 shares of Series B Convertible Preferred Stock and warrants to purchase 1,645,361 shares of common stock at an exercise price of $0.14 per share. The value of the derivative liability related to the warrants was $674,000 and the value of the derivative liability related to the preferred shares was $155,000.

In connection with the private placement of Series B Convertible Preferred Stock, the Company recorded a liability for the conversion feature that contains a provision that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision). The Company estimates the fair values of the conversion feature using a Monte Carlo valuation model. The Company measured the fair value of the conversion feature on June 26, 2013 and July 15, 2013 and recorded the initial liability as part of the private placement proceeds.

11

On May 16, 2014, 188,938 preferred shares were converted into 1,889,380 shares of common stock. Due to this conversion, a gain on derivative liabilities of $118,000 was recognized and $741,000 was reclassified out of the derivative liability account and into equity.

The Company re-measured the fair value of the conversion feature at September 30, 2014 and recorded an $18.4 million gain on derivative liabilities during the third quarter to adjust the liability associated with the conversion feature to an estimated fair value of $7.6 million. The change in fair value and the associated gain was attributable to a decline in the market value of our common stock as of September 30, 2014.

4. Warrants and Warrants Liability

The Company follows ASC 815-40, Contracts in an Entity’s Own Equity, as it relates to outstanding warrants.

In connection with the December 2013 private placement of 72,007,000 shares of the Company's common stock at a price per share of $0.25, the Company issued an aggregate of warrants to purchase 4,320,420 shares of common stock at an exercise price of $0.25 per share to the placement agents. These warrants expire December 2018. These warrants contain provisions that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision) and contain net settlement provisions. Due to these provisions, the Company accounted for these warrants as liabilities instead of equity.

In connection with the private placement of Series B Convertible Preferred Stock, which occurred through two closings on June 26, 2013 and July 15, 2013, respectively, the Company issued an aggregate of warrants to purchase 30,040,194 shares of common stock at an exercise price of $0.14 per share. These warrants expire June 2018. These warrants contain provisions that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision) and contain net settlement provisions. Due to these provisions, the Company accounted for these warrants as liabilities instead of equity. The Company measured the fair value of these warrants on June 26, 2013 and July 15, 2013 and recorded the initial liability as part of the private placement proceeds and expensed $1.4 million for the warrants issued to the placement agent.

We estimate the fair values of these securities using a Monte Carlo valuation model. The following warrants were issued in 2013 using the Monte Carlo valuation method with the key inputs as follows:

	June 26, 2013			July 15, 2013			December 23, 2013
Warrants issued		28,394,834			1,645,360			4,320,420
Risk free interest rate		.0109			.0109			0.0167
Volatility		160.94	%		163.08	%		155.24	%
Expected term		5 years			5 years			5 years
Exercise price	$	0.14		$	0.14		$	0.25

From February through May 2013, in connection with the issuance of new convertible promissory notes, the Company issued warrants to purchase up to 7,030,387 shares of its common stock. These warrants expire February through May 2018 and are exercisable at a price of $0.14 per share. These warrants are considered to be equity.

In 2011, in connection with the Biocontrol business combination, the Company issued warrants to purchase up to 1,355,164 shares of its common stock. These warrants expire in December 2016 and are exercisable at a price of $0.46 per share. These warrants are considered to be equity.

On June 26, 2014, 3,855,714 warrants, issued on June 26, 2013, were exercised. Due to this exercise, 2,734,151 shares of common stock were issued, a gain on derivative liabilities of $398,000 was recognized, and $1,729,000 was classified out of the derivative liability account and into equity.

12

The Company re-measured the fair value of the liability warrants at September 30, 2014 and recorded a $5.9 million gain on derivative liabilities during the third quarter to adjust the liabilities associated with the warrants to their estimated fair values totaling $6.9 million. The change in fair value and the resulting gain was attributable to a decline in the market value of our common stock as of September 30, 2014.

5. Stock Options

In October 2012, our board of directors approved and adopted the 2012 Stock Incentive Plan, which we refer to as the 2012 Plan. Under the 2012 Plan, we are authorized to issue up to 35,000,000 shares of our common stock in stock incentive awards to employees, directors and consultants.

In March 2009, our board of directors and shareholders adopted the 2009 Stock Incentive Plan, which we refer to as the 2009 Stock Incentive Plan. Under the 2009 Plan, we are authorized to issue up to 4,200,000 shares of our common stock in stock incentive awards to employees, directors and consultants.

In December 2013, our board of directors adopted the 2013 Plan. Under the 2013 Plan, we are authorized to issue up to 40,000,000 shares of our common stock in stock incentive awards to employees, directors and consultants. Our shareholders approved the 2013 Plan in February 2014.

The Company’s 2013 Stock Incentive Plan provides for the issuance of long-term incentive awards, or Awards, in the form of non-qualified and incentive stock options, or Options, stock appreciation rights, stock grants and restricted stock units. The Awards may be granted by the Company’s Board of Directors to its employees, directors and officers and to consultants, agents, advisors and independent contractors who provide services to the Company. The exercise price for Options must not be less than the fair market value of the underlying shares on the date of grant. Options expire no later than ten years from the date of grant and generally vest and become exercisable over a four-year period following the date of grant. Under the 2012 Plan, every non-employee member of the Company’s Board of Directors may elect to receive a non-qualified Option or restricted stock unit grant in lieu of certain cash compensation. Upon the exercise of Options, the Company issues the resulting shares from shares reserved for issuance under the Company’s Incentive Plans.

Under ASC 718 Stock Compensation, the Company is required to expense the fair value of share-based payments granted over the vesting period. The Company values Awards granted at their grant date fair value in accordance with the provisions of ASC 718 and recognizes stock-based compensation expense on a straight-line basis over the service period of each award.

Stock-based compensation expense is reduced by an estimated forfeiture rate derived from historical employee termination behavior. If the actual number of forfeitures differs from the Company’s estimates, the Company may record adjustments to increase or decrease compensation expense in future periods. There were no significant adjustments related to changes in the Company’s estimates for the three and nine month periods ended September 30, 2013 and 2014.

Following is a summary of the amount included as stock-based compensation expense in the accompanying consolidated statements of operations and comprehensive income (loss):

	Three Months Ended				Nine Months Ended
	September 30, 2014		September 30, 2013		September 30, 2014		September 30, 2013
Income statement category:
Research and development	$	38,000	$	40,000	$	116,000	$	153,000
General and administrative		195,000		208,000		643,000		1,053,000
Severance charge		831,000		—		831,000		—
Total stock-based compensation expense	$	1,064,000	$	248,000	$	1,590,000	$	1,206,000

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The following table summarizes Option activity:

	Shares		Weighted Average Exercise Price		Average Remaining Contractual Term (Years)		Intrinsic Value
Outstanding at December 31, 2013		25,721,000	$	0.19
Granted		—		—
Exercised		—		—
Forfeited		3,137,378		0.19
Expired		2,000		13.10
Outstanding at September 30, 2014		22,581,622	$	0.19		2.15	$	862,982
Exercisable at September 30, 2014		19,972,558	$	0.19		1.35	$	822,989

The aggregate intrinsic value is determined using the closing price of the Company’s common stock of $0.22 on September 30, 2014.

As of September 30, 2014, the Company had unrecognized compensation cost related to unvested Options of approximately $559,358 net of estimated forfeitures, which the Company expects to recognize over a weighted average period of approximately two and a half years.

As of September 30, 2014, the Company had reserved shares of its common stock for future issuance as follows:

	Shares Reserved
Stock options outstanding		22,581,622
Available for future grants under the 2013 Stock Incentive Plan		39,250,000
Warrants		38,890,451
Total shares reserved		100,722,073

6. Severance Charge

On September 15, 2014, by mutual agreement of the Board of Directors (the “Board”) of the Company and Philip J. Young, Mr. Young stepped down from his role as President and Chief Executive Officer of the Company, effective September 15, 2014. In accordance with Mr. Young’s employment agreements, the Company recorded a severance charge in the quarter ended September 30, 2014 of $1,510,000 related to severance-period compensation and benefits, as well as stock-based compensation expense related to the accelerated vesting of stock options .The composition of the severance charge is as follows:

Compensation and benefits	$	679,000
Stock-based compensation expenses related to accelerated vesting		831,000
Total severance charge	$	1,510,000

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

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with “Selected Consolidated Financial Data” and the Unaudited Condensed Consolidated Financial Statements and related Notes included in Part I Item 1 of this Form 10-Q.

This discussion contains forward-looking statements that involve risks and uncertainties. Such statements, which include statements concerning product development plans, the use of bacteriophages to kill bacterial pathogens, future revenue sources, selling and marketing expenses, general and administrative expenses, clinical trial and other research and development expenses, capital resources, capital expenditures, tax credits and carry-forwards, the Company’s ability to raise capital through additional financings or borrowings, are subject to risks and uncertainties, including, but not limited to, those discussed below and elsewhere in this Form 10-Q and in Item 1A of Amendment No. 4 to Form 10, filed on November 14, 2014, that could cause actual results to differ materially from those projected. The forward-looking statements set forth in this Form 10-Q are as of the close of business on November 14, 2014, and we do not intend to update this forward-looking information.

Overview

AmpliPhi Biosciences is a biotechnology company focused on the discovery, development and commercialization of novel phage therapeutics. Our proprietary pipeline is based on the use of bacteriophages, a family of viruses that infect only bacteria. Phages have powerful and highly selective mechanisms of action that permit them to target and kill specific bacterial pathogens, including the so-called multi-drug-resistant (MDR) or “Superbug” strains.

We are combining our proprietary approach and expertise in identifying, characterizing and developing naturally occurring bacteriophages with that of our collaboration partners in bacteriophage biology, drug engineering, development and manufacturing, to develop second-generation bacteriophage products. We believe that phages represent a promising means to treat bacterial infections, especially those that have developed resistance to current medicines.

Our lead program is AmpliPhage-002, for the treatment of methicillin-resistant S. aureus (MRSA) infections. We have two other product candidates in development: AmpliPhage-001 for the treatment of P. Aeruginosa lung infections in CF patients and AmpliPhage-004 for the treatment of C. difficile infections.

We have incurred net losses since our inception. Our operations to date have been limited to research and development and raising capital. Since November 2010, we have raised approximately $5.6 million through the sale and issuance of convertible notes and warrants to purchase common stock. In June and July of 2013, we completed a private placement of shares of Series B Convertible Preferred Stock and warrants to purchase common stock, with proceeds to the Company of approximately $7.0 million. At the same time we converted approximately $6.3 million in outstanding convertible notes to Series B Convertible Preferred Stock. In December 2013, we completed a private placement of shares of common stock, with gross proceeds of approximately $18 million, prior to commissions. To date, we have not generated any meaningful revenue and have primarily financed our operations through the sale and issuance of convertible notes and the private placement of our equity securities. As of September 30, 2014, we had an accumulated deficit of $355.3 million. We recorded annual net losses of $57.7 million in 2013 and $1.1 million in 2012. We anticipate that a substantial portion of our capital resources and efforts in the foreseeable future will be focused on completing the development and obtaining regulatory approval of our product candidates.

We expect our research and development expenses to expand as we increase our development activities and commence clinical trials to pursue regulatory approval for our product candidates. We also expect to incur additional expenses associated with operating as a public company. As a result, we expect to continue to incur significant and increasing operating losses at least for the next several years. We do not expect to generate product revenue unless and until we successfully complete development and obtain marketing approval for at least one of our product candidates.

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We currently expect to use our existing cash and cash equivalents for the continued research and development of our product candidates and for working capital and other general corporate purposes.

We may also use a portion of our cash and cash equivalents for the potential acquisition of, or investment in, product candidates, technologies, formulations or companies that complement our business, although we have no current understandings, commitments or agreements to do so. We expect that our current cash and cash equivalents will not be sufficient to enable us to complete all necessary development of any potential product candidates. Accordingly, we will be required to obtain further funding through other public offerings, debt financing, collaboration and licensing arrangements or other sources. Adequate additional funding may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed or on attractive terms, we would be forced to delay, reduce or eliminate our research and development programs.

Results of Operations

Revenue

We recognized no revenues for the quarter ended September 30, 2014. For the nine month period ending September 30, 2014, we recognized revenues of $310,000 in revenue from sublicensing arrangements, a decrease from $333,000 for the same period in 2013, as a result of reduced grant revenue.

Research and Development

Research and development expenses were $1.8 million for the quarter ended September 30, 2014, up $0.7 million from the $1.1 million recorded for the quarter ended September 30, 2013. Research and development expenses were $4.7 million for the nine month period ended September 30, 2014, compared to $5.4 million for the nine month period ended September 30, 2013. Research and development costs for the nine month period in 2013 included a $3.0 million non-cash one-time technology access fee which was incurred in April 2013. Adjusted for this one-time item, research and development expense for the nine months of 2014 represented an increase of $2.3 million. The increase in research and development expense for both the three month and nine month periods ended September 30, 2014 were due to an increase in discovery, laboratory, nonclinical testing, research and development collaborations, consulting, and clinical development planning expenses for all of our product candidates.

Adjusted for the one-time non-cash technology access fee incurred in 2013, research and development expenses are expected to increase in 2014 compared to 2013 as we plan to continue investing substantial resources to research and development as we prepare to initiate clinical trials and continue our discovery efforts.

General and Administrative

General and administrative expenses were $1.6 million for the quarter ended September 30, 2014 compared to $1.2 million for the quarter ended September 30, 2013. The $0.4 million increase in general and administrative expense was due primarily to a $0.3 million accrual for payments to certain shareholders as required by the terms of our Series B Preferred Stock Purchase Agreement.

General and administrative expenses were $5.4 million for the nine month period ended September 30, 2014 compared to $4.8 million for the nine month period ended September 30, 2013. This increase of $0.6 million was attributable to the accrual of payments to certain shareholders outlined above and higher legal, accounting, and staffing expenses incurred to satisfy our obligations as a public company. Partially offsetting these cost increases were reduced investment fees resulting from the fees incurred in 2013 for our Series B private placement.

We currently expect our general and administrative expenses to increase in 2014 compared to 2013 due to additional costs associated with being a public company.

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Severance Charge

The Company recorded a severance charge in the quarter ended September 30, 2014 of $1.5 million related to severance-period compensation and benefits and stock-based compensation expense related to the acceleration of vested stock options related to the termination of the Company’s Chief Executive Officer during the quarter.

Derivative Liabilities

During the quarter ended September 30, 2014, we recognized a gain on derivative liabilities of $24.3 million related to reductions in the fair value of derivative liabilities for warrants issued in June, July, and December 2013 and the conversion feature of the shares of Series B Preferred Stock issued in June and July 2013. The reduction in fair value was attributable to a decline in the market value of our common stock at September 30, 2014. During the quarter ended September 30, 2013, we recognized a loss on derivative liabilities of $41.5 million for warrants issued in June 2013 and the conversion feature of the shares of Series B Preferred Stock issued in June 2013.

For the nine month period ended September 30, 2014, we recognized a gain on derivative liabilities of $34.0 million compared to $45.6 million loss for the nine month period ended September 30, 2013.

Derivative liabilities are adjusted to fair value each reporting period and are influenced by several factors including the price of the Company’s common stock as of the balance sheet date. On September 30, 2014, the price per share of the Company’s common stock was $0.22 per share compared to $0.50 per share at December 31, 2013.

Income Taxes

We incurred net operating losses for the years ended December 31, 2013 and 2012 and, accordingly, we did not pay any U.S. federal or state income taxes. As of December 31, 2013, we had accumulated approximately $175.4 million in U.S. and UK operating loss carry-forwards and research tax credit carry-forwards of approximately $3.7 million. The carry-forwards began to expire in 2012. Our net operating loss carry-forwards are subject to certain limitations on annual utilization as a result of changes in ownership of the Company, as defined by federal and state tax laws.

Net Operating Losses

We have not recorded a benefit from our net operating loss or research credit carry-forwards because we believe that it is uncertain that we will have sufficient income from future operations to realize the carry-forwards prior to their expiration. Accordingly, we have established a 100% valuation allowance against the deferred tax asset arising from the carry-forwards.

Liquidity and Capital Resources

We have incurred net losses since inception through September 30, 2014 of $355.3 million, of which $315.5 million was incurred in the Company’s prior focus on gene therapy in 2010 and years earlier. We have not generated any product revenues and do not expect to generate revenue from the sale of product candidates in the near term.

We had cash and cash equivalents of $9.8 million and $20.4 million at September 30, 2014 and December 31, 2013, respectively.

Net cash used in operating activities for the nine month period ended September 30, 2014 was $9.4 million. We recorded net income for the nine-month period of $22.8 million, including a non-cash gain on derivative liabilities of $34.0 million. Other items in uses of funds from operations included non-cash charges related to stock-based compensation expense, depreciation expenses, and patent amortization, which collectively totaled $1.7 million. Increases in accounts payable and accrued liabilities increased net cash from operating activities by $0.3 million, partially offset by an increase in receivables and prepaid expenses of $0.1 million.

17

Net cash used in operating activities for the nine month period ended September 30, 2013 was $4.9 million. We recorded a net loss of $58.3 for the period, including a non-cash charge on derivative liabilities of $45.6 million. The net impact of these two factors was a use of funds of $12.7 million. Other items in uses of funds from operations included non-cash charges for a technology access, amortization of loan discount, stock-based compensation expense, depreciation expenses, warrant-based investment fees, and a loss on disposal of equipment, which collectively totaled $6.4 million. Net changes in accrued liabilities, receivables and other assets also generated $0.1 million in cash.

Net cash used in investing activities for the nine month period ended September 30, 2014 and September 30, 2013 were $1.1 million and $0.9 million, respectively, due to purchases of equipment.

Net cash provided by financing activities for the nine month period ended September 30, 2013 was $9.0 million due to proceeds from our issuance of shares of Series B Preferred Stock and convertible loan notes. We expect 2014 cash requirements to be in the range of $15.0 million to $17.0 million. We believe that our cash as of September 30, 2014, will be sufficient to fund our projected operating requirements through the first quarter of 2015.

Our total use of cash in the nine month period ended September 30, 2014 was $10.6 million.

We expect to need to raise additional capital or incur indebtedness to continue to fund our future operations. We may seek to raise capital through a variety of sources, including:

· the public equity market;

· private equity financing;

· collaborative arrangements;

· licensing arrangements; and/or

· public or private debt.

Our ability to raise additional funds will depend on our clinical and regulatory developments, our product development activities, our ability to identify promising in-licensing opportunities and factors related to financial, economic and market conditions, many of which are beyond our control. We cannot be certain that sufficient funds will be available to us when required or on satisfactory terms. If adequate funds are not available, we may be required to significantly reduce or refocus our operations or to obtain funds through arrangements that may require us to relinquish rights to certain of our products, technologies or potential markets, any of which could delay or require that we curtail our development programs or otherwise have a material adverse effect on our business, financial condition and results of operations. To the extent that additional capital is raised through the sale of equity or convertible debt securities, the issuance of such securities would result in ownership dilution to our existing stockholders.

If we are unable to secure additional financing on a timely basis or on terms favorable to us, we may be required to cease or reduce certain research and development projects, to sell some or all of our technology or assets or to merge all or a portion of our business with another entity. Insufficient funds may require us to delay, scale back or eliminate some or all of our activities, and if we are unable to obtain additional funding, there is uncertainty regarding our continued existence.

Off-Balance Sheet Arrangements

As of September 30, 2014, we did not have any relationships with unconsolidated entities or financial partnerships, such as entities often referred to as structured finance or special purpose entities, which would have been established for the purpose of facilitating off-balance sheet arrangements or other contractually narrow or limited purposes. In addition, we do not engage in trading activities involving non-exchange traded contracts. Therefore, we are not materially exposed to any financing, liquidity, market or credit risk that could arise if we had engaged in these relationships.

Recent Accounting Pronouncements

None.

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Item 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

We are a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and are not required to provide the information required under this item.

Item 4. CONTROLS AND PROCEDURES

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our Principal Executive Officer and Principal Financial Officer, has evaluated the effectiveness of our disclosure controls and procedures (as such term is defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act), as of the end of the period covered by this report. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed in the reports we file or submit under the Exchange Act is accumulated and communicated to management, including our Principal Executive Officer and Principal Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. Based on this evaluation, our Principal Executive Officer and Principal Financial Officer, have concluded that our financial disclosure controls and procedures were effective during the period covered by this report. 

Changes in Internal Controls Over Financial Reporting.

There were no changes in our internal control over financial reporting during the first nine months of 2014 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

We are not a party to any material legal proceedings.

Item 1A. Risk Factors

 There have been no material changes from the risk factors disclosed in Part I, Item 1A, of our Annual Report on Form 10-K/A for the fiscal year ended December 31, 2013 as amended and filed with the SEC on September 12, 2014.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

None.

Item 3. Defaults upon Senior Securities

None.

Item 4. Mine Safety Disclosures

Not applicable.

Item 5. Other Information

None.

Item 6. Exhibits

(a)   Exhibits

19

Number		Description
	3.1	Amended and Restated Articles of Incorporation, effective May 21, 2009 (incorporated by reference to Exhibit 3.1 to the Registration Statement on Form 10 filed December 16, 2013).
	3.2	Articles of Amendment to Amended and Restated Articles of Incorporation, effective June 26, 2013 (incorporated by reference to Exhibit 3.2 to the Registration Statement on Form 10 filed December 16, 2013).
	3.3	Articles of Correction to Amended and Restated Articles of Incorporation, effective June 26, 2013 (incorporated by reference to Exhibit 3.3 to the Registration Statement on Form 10 filed December 16, 2013).
	3.4	Amended and Restated Bylaws (incorporated by reference to Exhibit 3.4 to the Registration Statement on Form 10 filed December 16, 2013).
	4.1	Specimen stock certificate evidencing shares of common stock (incorporated by reference to Exhibit 4.1 to the Registration Statement on Form 10 filed December 16, 2013).
	4.2	Form of Warrant to Purchase Shares of Common Stock (incorporated by reference to Exhibit 4.2 to the Registration Statement on Form 10 filed December 16, 2013).
	4.3	Subscription Agreement to Purchase Series B Preferred Stock and Warrants, dated June 26, 2013 (incorporated by reference to Exhibit 4.3 to the Registration Statement on Form 10 filed December 16, 2013).
	4.4	Registration Rights Agreement, dated December 16, 2013 (incorporated by reference to Exhibit 4.4 to the Registration Statement on Form 10 filed December 16, 2013).
	4.5	Subscription Agreement, dated December 16, 2013 (incorporated by reference to Exhibit 4.5 to the Registration Statement on Form 10 filed December 16, 2013).
	10.1*	Interim Chief Operating Officer Agreement, dated September 18, 2014, by and between the Company and Wendy S. Johnson.
	31.1*	Certification of the Chief Executive Officer required by Rule 13a-14(a)/Rule 15d-14(a).
	31.2*	Certification of Chief Financial Officer required by Rule 13a-14(a)/Rule 15d-14(a).
	32.1*	Certification of the Principal Executive Officer Required by 18 U.S.C. 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
	32.2*	Certification of the Principal Financial Officer Required by 18 U.S.C. 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.PRE	XBRL Taxonomy Extension Presentation Linkbase Document.
	101.LAB	XBRL Taxonomy Extension Label Linkbase Document.

* Furnished electronically with this report.

20

AMPLIPHI BIOSCIENCES CORPORATION

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

	AMPLIPHI BIOSCIENCES CORPORATION
Date: November 14, 2014	By	/s/ David E. Bosher
		Name: David E. Bosher
		Title: Interim Chief Financial Officer

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EX-10.1

Exhibit 10.1

AMPLIPHI BIOSCIENCES CORPORATION

INTERIM CHIEF OPERATING OFFICER AGREEMENT

This Interim Chief Operating Officer Agreement (“Agreement”) is entered into by and between AmpliPhi Biosciences Corporation, a Washington corporation (the “Company”) and Wendy S. Johnson (“Consultant”), on September 18, 2014, and shall be deemed to be effective as of September 1, 2014. The Company desires to retain Consultant as an independent contractor to perform services for the Company on an interim basis, and Consultant is willing to perform such services, on the terms described below. In consideration of the mutual promises contained herein, the parties agree as follows:

1.           Services and Compensation. Consultant agrees to perform for the Company the services described in Exhibit A (the “Services”), and the Company agrees to pay Consultant the compensation described in Exhibit A for Consultant’s performance of the Services.

2.           Confidentiality.

(a)           Definition. “Confidential Information” means any and all information and materials, in whatever form, tangible or intangible, whether disclosed to or learned or developed by Consultant before or after the execution of this Agreement, whether or not marked or identified as confidential or proprietary, pertaining in any manner to the business of or used by the Company and its affiliates, or pertaining in any manner to any person or entity to whom the Company owes a duty of confidentiality. Confidential Information includes, but is not limited to, the following types of information and materials: (i) trade secrets, inventions, ideas, processes, formulas, algorithms, pre-clinical and clinical data, formulations, programs, other works of authorship, know-how, improvements, discoveries, developments, designs and techniques; (ii) information regarding plans for research, development, new products, marketing and selling, business plans, business methods, budgets and unpublished financial statements, licenses, prices and costs, suppliers and customers; (iii) sensitive personnel information including the skills and compensation of other employees of the Company; and (iv) any other information or materials relating to the past, present, planned or foreseeable business, products, developments, technology or activities of the Company. Consultant understands that Confidential Information includes, but is not limited to, information pertaining to any aspect of the Company’s business which is either information not known by actual or potential competitors of the Company or other third parties not under confidentiality obligations to the Company, or is otherwise proprietary information of the Company or its customers or suppliers, whether of a technical nature or otherwise. Consultant further understands that Confidential Information does not include any of the foregoing items which has become publicly and widely known and made generally available through no wrongful act of Consultant or of others who were under confidentiality obligations as to the item or items involved.

(b)           Nonuse and Nondisclosure. Consultant will not, during or subsequent to the term of this Agreement, (i) use the Confidential Information for any purpose whatsoever other than the performance of the Services on behalf of the Company or (ii) disclose the Confidential Information to any third party except as reasonably required to perform the Services and under appropriate confidentiality agreements. Consultant agrees that all Confidential Information will remain the sole property of the Company. Consultant also agrees to take all reasonable precautions to prevent any unauthorized disclosure of such Confidential Information.

(c)           Former Client Confidential Information. Consultant agrees that Consultant will not, during the term of this Agreement, improperly use or disclose any proprietary information or trade secrets of any former or current employer of Consultant or other person or entity with which Consultant has an agreement or duty to keep in confidence information acquired by Consultant, if any. Consultant also agrees that Consultant will not bring onto the Company’s premises any unpublished document or proprietary information belonging to any such employer, person or entity unless consented to in writing by such employer, person or entity.

(d)           Third Party Confidential Information. Consultant recognizes that the Company has received and in the future will receive from third parties their confidential or proprietary information subject to a duty on the Company’s part to maintain the confidentiality of such information and to use it only for certain limited purposes. Consultant agrees that, during the term of this Agreement and thereafter, Consultant owes the Company and such third parties a duty to hold all such confidential or proprietary information in the strictest confidence and not to disclose it to any person, firm or corporation or to use it except as necessary in carrying out the Services for the Company consistent with the Company’s agreement with such third party.

1

(e)           Return of Materials. Upon the termination of this Agreement, or upon Company’s earlier request, Consultant will deliver to the Company all of the Company’s property, including but not limited to all electronically stored information and passwords to access such property, or Confidential Information that Consultant may have in Consultant’s possession or control.

3.           Ownership.

(a)           Assignment. Consultant agrees that all inventions (whether or not patentable), copyrightable material, notes, records, drawings, designs, improvements, developments, discoveries and trade secrets conceived, discovered, developed or reduced to practice by Consultant, solely or in collaboration with others, during the term of this Agreement that relate in any manner to the business of the Company that Consultant may be directed to undertake, investigate or experiment with or that Consultant may become associated with in work, investigation or experimentation in the Company’s line of business in performing the Services under this Agreement (collectively, “Inventions”), are the sole property of the Company. Consultant also agrees to assign (or cause to be assigned) and hereby assigns fully to the Company all Inventions and any copyrights, patents, mask work rights or other intellectual property rights relating to all Inventions.

(b)           Further Assurances. Consultant agrees to assist Company, or its designee, at the Company’s expense, in every proper way to secure the Company’s rights in Inventions and any copyrights, patents, mask work rights or other intellectual property rights relating to all Inventions in any and all countries, including the disclosure to the Company of all pertinent information and data with respect to all Inventions, the execution of all applications, specifications, oaths, assignments and all other instruments that the Company may deem necessary in order to apply for and obtain such rights and in order to assign and convey to the Company, its successors, assigns and nominees the sole and exclusive right, title and interest in and to all Inventions, and any copyrights, patents, mask work rights or other intellectual property rights relating to all Inventions. Consultant also agrees that Consultant’s obligation to execute or cause to be executed any such instrument or papers shall continue after the termination of this Agreement.

(c)           Pre-Existing Materials. Attached as Exhibit B is a list describing with particularity all inventions, improvements, developments, concepts, discoveries or other proprietary information which were (i) made by Consultant prior to becoming a Consultant to the Company and (ii) could reasonably be deemed to be in or related to the business of the Company (collectively referred to as “Prior Inventions”), which belong solely to Consultant or belong to Consultant jointly with another, which relate in any way to any of the Company’s proposed businesses, products or research and development, and which are not assigned to the Company hereunder; or, if no such list is attached, Consultant represents that there are no such Prior Inventions. Subject to Section 3(a), Consultant agrees that if, in the course of performing the Services, Consultant incorporates into any Invention developed under this Agreement any Prior Invention owned by Consultant or in which Consultant has an interest, (i) Consultant will inform Company, in writing before incorporating such Prior Invention into any Invention, and (ii) the Company is hereby granted a nonexclusive, royalty-free, perpetual, irrevocable, worldwide license to make, have made, modify, use and sell such Prior Invention as part of or in connection with such Invention. Consultant will not incorporate any invention, improvement, development, concept, discovery or other proprietary information owned by any third party into any Invention without Company’s prior written permission.

(d)           Attorney-in-Fact. Consultant agrees that, if the Company is unable because of Consultant’s unavailability, dissolution, mental or physical incapacity, or for any other reason, to secure Consultant’s signature for the purpose of applying for or pursuing any application for any United States or foreign patents or mask work or copyright registrations covering the Inventions assigned to the Company in Section 3(a), then Consultant hereby irrevocably designates and appoints the Company and its duly authorized officers and agents as Consultant’s agent and attorney-in-fact, to act for and on Consultant’s behalf to execute and file any such applications and to do all other lawfully permitted acts to further the prosecution and issuance of patents, copyright and mask work registrations with the same legal force and effect as if executed by Consultant.

2

4.           Conflicting Obligations. Consultant certifies that Consultant has no outstanding agreement or obligation that is in conflict with any of the provisions of this Agreement or that would preclude Consultant from complying with the provisions of this Agreement. Consultant will not enter into any such conflicting agreement during the term of this Agreement. Consultant’s violation of this Section 4(a) will be considered a breach of a material provision of this Agreement under Section 6(b).

5.           Reports. Consultant also agrees that Consultant will, from time to time during the term of this Agreement or any extension thereof, keep the Company advised as to Consultant’s progress in performing the Services under this Agreement. Consultant further agrees that Consultant will, as requested by the Company, prepare written reports with respect to such progress.

6.           Term and Termination.

(a)         Term. The term of this Agreement will begin on the date of this Agreement and will continue until the earliest of (i) December 31, 2014, (ii) such time as the Company hires a new Chief Executive Officer or (iii) termination as provided in Section 6(b). The term of this Agreement may be extended upon mutual written agreement of the parties.

(b)         Termination. Either party may terminate this Agreement upon giving the other party 30 days’ prior written notice of such termination pursuant to Section 9(e) of this Agreement. The Company may terminate this Agreement immediately and without prior notice if Consultant refuses to or is unable to perform the Services or is in breach of any material provision of this Agreement.

(c)         Survival. Upon such termination, all rights and duties of the Company and Consultant toward each other shall cease except:

(i)           The Company will pay, within 30 days after the effective date of termination, all amounts owing to Consultant for Services completed and accepted by the Company prior to the termination date and related expenses, if any, submitted in accordance with the Company’s policies and in accordance with the provisions of Section 1 of this Agreement; and

(ii)           Section 2 (Confidentiality), Section 3 (Ownership), Section 7 (Independent Contractor; Benefits) and Section 9 (Miscellaneous) will survive termination of this Agreement.

7.           Independent Contractor; Benefits.

(a)         Independent Contractor. It is the express intention of the Company and Consultant that Consultant perform the Services as an independent contractor to the Company. Nothing in this Agreement shall in any way be construed to constitute Consultant as an employee of the Company. Consultant agrees to furnish (or reimburse the Company for) all tools and materials necessary to accomplish this Agreement and shall incur all expenses associated with performance, except as expressly provided in Exhibit A. Consultant acknowledges and agrees that Consultant is obligated to report as income all compensation received by Consultant pursuant to this Agreement. Consultant agrees to and acknowledges the obligation to pay all self-employment and other taxes on such income.

(b)         Benefits. The Company and Consultant agree that Consultant will receive no Company-sponsored benefits from the Company. If Consultant is reclassified by a state or federal agency or court as Company’s employee, Consultant will become a reclassified employee and will receive no benefits from the Company, except those mandated by state or federal law, even if by the terms of the Company’s benefit plans or programs of the Company in effect at the time of such reclassification, Consultant would otherwise be eligible for such benefits.

8.           Indemnification Agreement. The Company and Consultant acknowledge that the Company and Consultant have entered into that certain Indemnification Agreement, dated June 1, 2014 (the “Indemnification Agreement”), and that nothing herein is intended to limit or modify the parties’ rights or obligations under the Indemnification Agreement.

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9.           Miscellaneous.

(a)           Governing Law. This Agreement shall be governed by the laws of the Commonwealth of Virginia without regard to conflicts of law rules.

(b)           Assignability. Except as otherwise provided in this Agreement, Consultant may not sell, assign or delegate any rights or obligations under this Agreement. The Company may assign (i) this Agreement to a Company affiliate or (ii) this Agreement in the event of a merger, acquisition or sale of all or substantially all of the assets of the Company. Subject to the foregoing, this Agreement will be binding upon and inure to the benefit of the parties hereto, their successors and assigns.

(c)           Entire Agreement. This Agreement and the Indemnification Agreement constitute the entire agreement between the parties with respect to the subject matter hereof and thereof and supersede all prior written and oral agreements between the parties regarding the subject matter hereof and thereof.

(d)           Headings. Headings are used in this Agreement for reference only and shall not be considered when interpreting this Agreement.

(e)           Notices. Any notice or other communication required or permitted by this Agreement to be given to a party shall be in writing and shall be deemed given if delivered personally or by commercial messenger or courier service, or mailed by U.S. registered or certified mail (return receipt requested), or sent via facsimile (with receipt of confirmation of complete transmission) to the party at the party’s address or facsimile number written below or at such other address or facsimile number as the party may have previously specified by like notice. If by mail, delivery shall be deemed effective 3 business days after mailing in accordance with this Section 9(e).

(i) If to the Company, to:

4870 Sadler Road, Suite 300

Glen Allen, VA 23060

Attention: Chief Executive Officer

(ii)          If to Consultant, to the address for notice on the signature page to this Agreement or, if no such address is provided, to the last address of Consultant provided by Consultant to the Company.

(f)           Attorneys’ Fees. In any court action at law or equity that is brought by one of the parties to this Agreement to enforce or interpret the provisions of this Agreement, the prevailing party will be entitled to reasonable attorneys’ fees, in addition to any other relief to which that party may be entitled.

(g)           Severability. If any provision of this Agreement is found to be illegal or unenforceable, the other provisions shall remain effective and enforceable to the greatest extent permitted by law.

(h)           Amendments. This Agreement may be amended or waived only upon written consent of the Consultant and the Company.

(i)           Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original and all of which together shall constitute one instrument.

[Remainder of page intentionally left blank.]

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IN WITNESS WHEREOF, the parties hereto have executed this Interim Chief Operating Officer Agreement as of the date first written above.

CONSULTANT		AMPLIPHI BIOSCIENCES CORPORATION
By:	/s/ Wendy S. Johnson	By:	/s/ Jeremy Laurence Curnock Cook
Name:	Wendy S. Johnson	Name:	Jeremy Laurence Curnock Cook
		Title:	Interim CEO
Address for Notice:
5350 Renaissance Avenue
San Diego CA 92122

Signature Page to Interim Chief Operating Officer Agreement

EXHIBIT A

SERVICES AND COMPENSATION

1.           Services. Consultant shall serve as the interim Chief Operating Officer of the Company and shall perform the duties, and have the responsibilities, that are customary for persons serving in such office. Consultant will report to the Interim Chief Executive Officer of the Company.

2.           Compensation.

A.           The Company will compensate Consultant at a rate of $20,000 per month, payable on the last business day of each month, during the term of this Agreement.

B.           The Company will reimburse Consultant for reasonable travel and other business expenses incurred by Consultant in the performance of her duties, consistent with the Company’s reimbursement policies. Consultant will provide receipts to the Company documenting such expenses.

3.           Other Engagements. Consultant may accept other consulting assignments, and engage in other business activities, so long as they do not interfere with her obligations under this Agreement.

EXHIBIT B

LIST OF PRIOR INVENTIONS EXCLUDED UNDER SECTION 3(C)

Title Date Identifying Number or Brief Description

x No inventions or improvements

¨ Additional Sheets Attached

Signature of Consultant:  /s/ Wendy Johnson

Print Name of Consultant:  Wendy Johnson

Date:  September 17, 2014

EX-31.1

Exhibit 31.1

AMPLIPHI BIOSCIENCES CORPORATION

CERTIFICATION

 I, Jeremy Curnock Cook, certify that:

1. I have reviewed this quarterly report on Form 10-Q of AmpliPhi Biosciences Corporation;

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 officers 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(s) 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: November 14, 2014

/s/ Jeremy Curnock Cook

Jeremy Curnock Cook

Chairman and Interim Chief Executive Officer

EX-31.2

Exhibit 31.2

AMPLIPHI BIOSCIENCES CORPORATION

CERTIFICATION

I, David E. Bosher, certify that:

1. I have reviewed this quarterly report on Form 10-Q of AmpliPhi Biosciences Corporation;

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 officers 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(s) 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: November 14, 2014

/s/ David E. Bosher

David E. Bosher

Interim Chief Financial Officer

EX-32.1

Exhibit 32.1

AMPLIPHI BIOSCIENCES CORPORATION

CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER

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 AmpliPhi Biosciences Corporation (the “Company”) on Form 10-Q for the period ended September 30, 2014 as filed with the Securities and Exchange Commission (the “Report”), I, Jeremy Curnock Cook, Chairman and Interim Chief Executive Officer of the Company, hereby certify as of the date hereof, solely for purposes of Title 18, Chapter 63, Section 1350 of the United States Code, that to the best of my knowledge:

(1) the Report fully complies with the requirements of Section 13(a) or 15(d), as applicable, of the Securities Exchange Act of 1934, and

(2) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company at the dates and for the periods indicated.

A signed original of this written statement required by Section 906, or other document authenticating, acknowledging, or otherwise adopting the signature that appears in typed form within the electronic version of this written statement required by Section 906, has been provided to the Company and will be retained by the Company and furnished to the Securities and Exchange Commission or its staff upon request.

This Certification has not been, and shall not be deemed, “filed” with the Securities and Exchange Commission.

Date: November 14, 2014

/s/ Jeremy Curnock Cook

Jeremy Curnock Cook

Chairman and Interim Chief Executive Officer

EX-32.2

Exhibit 32.2

AMPLIPHI BIOSCIENCES CORPORATION

CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER

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 AmpliPhi Biosciences Corporation (the “Company”) on Form 10-Q for the period ended September 30, 2014 as filed with the Securities and Exchange Commission (the “Report”), I, David E. Bosher, Chief Financial Officer of the Company, hereby certify as of the date hereof, solely for purposes of Title 18, Chapter 63, Section 1350 of the United States Code, that to the best of my knowledge:

(1) the Report fully complies with the requirements of Section 13(a) or 15(d), as applicable, of the Securities Exchange Act of 1934, and

(2) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company at the dates and for the periods indicated.

A signed original of this written statement required by Section 906, or other document authenticating, acknowledging, or otherwise adopting the signature that appears in typed form within the electronic version of this written statement required by Section 906, has been provided to the Company and will be retained by the Company and furnished to the Securities and Exchange Commission or its staff upon request.

This Certification has not been, and shall not be deemed, “filed” with the Securities and Exchange Commission.

Date: November 14, 2014

/s/ David E. Bosher

David E. Bosher

Interim Chief Financial Officer

XML

Stock Options (Details Textual) (USD $)	9 Months Ended
	Sep. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Grant Date Intrinsic Value	$ 0.22
Employee Service Share-based Compensation, Nonvested Awards, Compensation Not yet Recognized, Stock Options	$ 559,358
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition	2 years 6 months
2012 Stock Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Authorized	35,000,000
2009 Stock Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Authorized	4,200,000
2013 Stock Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Authorized	40,000,000

XML

Preferred Shares

9 Months Ended

Sep. 30, 2014

Equity [Abstract]

Preferred Stock [Text Block]

3. Preferred Shares

On June 13, 2013, the Company’s Board of Directors approved a resolution designating 10,016,080 shares of Preferred Stock as Series B Convertible Preferred Stock with an initial stated value of $1.40 and par value of $0.01. Each Series B preferred share is convertible into 10 shares of common stock and is entitled to the number of votes equal to the number of shares of common stock. These Series B shares may be converted to common stock by the holder of the shares at any time. The Series B shares shall be automatically converted into common shares upon the closing of an underwritten initial public offering with aggregate proceeds to the Company of at least $7 million and a price per share to the public of at least the Series B stated value upon the closing of which the shares of common stock of the Company shall be listed for trading on the New York Stock Exchange. The Series B shares are also convertible into common shares upon the election of the holders of two-thirds of the outstanding Series B shares. Until conversion, the holders of Series B Preferred shares shall be entitled to receive dividends of 10% of the Series B stated value per annum.

In connection with the private placement of Series B Convertible Preferred Stock, the Company recorded a liability for a complex embedded derivative that required bifurcation under ASC Section 815. The embedded derivative includes a redemption feature, multiple dividend features, as well as multiple conversion features with a down-round ratchet provision. The Company estimates the fair values of the conversion feature using a Monte Carlo valuation model. The Company measured the fair value of the conversion feature on June 26, 2013 and July 15, 2013(dates of issuance) and recorded the initial liability as part of the private placement proceeds.

On June 26, 2013, the Company issued 4,999,999 shares of the Company’s newly-created Series B Convertible Preferred Stock and warrants to purchase 12,499,996 shares of common stock at an exercise price of $0.14 per share for an aggregate purchase price of $7.0 million. The value of the derivative liability related to the warrants was $1,886,000 and the value of the derivative liability related to the preferred shares was $5,064,000. As part of the same transaction, the Company converted $5,491,001 in outstanding convertible loan notes (principal and interest) into 4,357,936 shares of Series B Convertible Preferred Stock and warrants to purchase 10,894,839 shares of common stock at an exercise price of $0.14 per share. The value of the derivative liability related to the warrants was $1,644,000 and the value of the derivative liability related to the preferred shares was $3,804,000. As part of this issuance, the Company issued warrants to purchase 4,999,999 shares of common stock at an exercise price of $0.14 per share with an initial fair value of $759,000 and paid $350,000 to the placement agents. As a result of this financing, all outstanding convertible notes were converted into shares of Series B Convertible Preferred Stock and warrants to purchase common stock. On July 15, 2013, the remaining outstanding convertible loan notes, totaling $829,277 in principal and interest, were converted into 658,145 shares of Series B Convertible Preferred Stock and warrants to purchase 1,645,361 shares of common stock at an exercise price of $0.14 per share. The value of the derivative liability related to the warrants was $674,000 and the value of the derivative liability related to the preferred shares was $155,000.

In connection with the private placement of Series B Convertible Preferred Stock, the Company recorded a liability for the conversion feature that contains a provision that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision). The Company estimates the fair values of the conversion feature using a Monte Carlo valuation model. The Company measured the fair value of the conversion feature on June 26, 2013 and July 15, 2013 and recorded the initial liability as part of the private placement proceeds.

On May 16, 2014, 188,938 preferred shares were converted into 1,889,380 shares of common stock. Due to this conversion, a gain on derivative liabilities of $118,000 was recognized and $741,000 was reclassified out of the derivative liability account and into equity.

The Company re-measured the fair value of the conversion feature at September 30, 2014 and recorded an $18.4 million gain on derivative liabilities during the third quarter to adjust the liability associated with the conversion feature to an estimated fair value of $7.6 million. The change in fair value and the associated gain was attributable to a decline in the market value of our common stock as of September 30, 2014.

XML

Liquidity

9 Months Ended

Sep. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Liquidation Basis of Accounting [Text Block]

2. Liquidity

The Company has prepared the accompanying consolidated financial statements on a going concern basis, which assumes that the Company will realize its assets and satisfy its liabilities in the normal course of business. However, the Company has incurred net losses since its inception, has negative operating cash flows and has an accumulated deficit of $355.3 million as of September 30, 2014. These circumstances raise substantial doubt about the Company’s ability to continue as a going concern. The accompanying financial statements do not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classifications of liabilities that may result from the outcome of the uncertainty concerning the Company’s ability to continue as a going concern.

The Company believes that its current resources will only be sufficient to fund operations through the first quarter of 2015. This estimate is based on the Company’s ability to manage its staffing expenses and its working capital. Actual results could differ from its estimates. The Company intends to seek additional financing in order to fund operations through 2015; however, the Company cannot provide assurances that it will be successful in obtaining additional financing for these periods or as needed in the future. If the Company does not raise additional funds by the first quarter of 2015, it plans to implement cost reduction measures, such as a reduction in workforce, reducing its intellectual property prosecution, reducing other operating activities, and/or the pursuit of alternative financing transactions that would likely be on terms disadvantageous to the Company and dilutive to its shareholders. The Company could also be required to relinquish rights to its technology or product candidates or in-licensed technology on unfavorable terms, either of which would reduce the ultimate value of the technology or product candidates, or to sell assets likely at values significantly below their potential worth. If the Company is unable to secure additional capital, it may be required to cease operations, declare bankruptcy or otherwise wind-up its business.

XML

CONSOLIDATED BALANCE SHEETS (USD $)	Sep. 30, 2014	Dec. 31, 2013
Current assets
Cash and cash equivalents	$ 9,786,000	$ 20,355,000
Accounts receivable	27,000	8,000
Prepaid expenses and other current assets	279,000	171,000
Total current assets	10,092,000	20,534,000
Property and equipment, net of accumulated depreciation of $559,000 and $473,000 as of September 30, 2014 and December 31, 2013, respectively	1,175,000	145,000
Intangible assets
In process research and development	12,446,000	12,446,000
Patents, net of accumulated amortization of $116,000 and $93,000 as of September 30, 2014 and December 31, 2013, respectively	377,000	400,000
Goodwill	4,329,000	4,329,000
Total intangible assets	17,152,000	17,175,000
Total assets	28,419,000	37,854,000
Current liabilities
Accounts payable and accrued expenses	1,840,000	2,147,000
Accrued severance	659,000	0
Total current liabilities	2,499,000	2,147,000
Long term liabilities
Derivative preferred shares conversion liability	7,633,000	34,443,000
Derivative warrants liability	6,949,000	16,664,000
Total long term liabilities	14,582,000	51,107,000
Total liabilities	17,081,000	53,254,000
Stockholders' equity (deficit)
Preferred stock, $0.01 par value, 10,000,000 shares authorized; 8,671,040 shares issued and outstanding at September 30, 2014 and 8,859,978 shares issued and outstanding at December 31, 2013	87,000	89,000
Common stock, $0.01 par value, 445,000,000 shares authorized, 187,159,093 shares issued and outstanding at September 30, 2014 and 182,535,562 shares issued and outstanding at December 31, 2013	1,872,000	1,825,000
Additional paid-in capital	363,032,000	358,988,000
Paid-in-capital - contingent shares	1,837,000	1,837,000
Accumulated other comprehensive loss	(178,000)	(65,000)
Accumulated deficit	(355,312,000)	(378,074,000)
Total stockholders' equity (deficit)	11,338,000	(15,400,000)
Total liabilities and stockholders' equity (deficit)	$ 28,419,000	$ 37,854,000

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CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013
Cash flows from operating activities
Net income (loss) from operations	$ 22,762,000	$ (58,332,000)
Adjustments required to reconcile net income (loss) to cash used in operating activities:
Derivative liability (gain) loss	(34,026,000)	45,617,000
Shares issued for technology access fee	0	3,000,000
Amortization of patents	23,000	23,000
Amortization of note discount	0	2,637,000
Warrants issued as investment fees	0	759,000
Depreciation	59,000	66,000
Stock-based compensation	759,000	1,206,000
Stock-based compensation - severance	831,000	0
Changes in operating assets and liabilities net of acquisitions:
Accounts receivable	(19,000)	(125,000)
Tax refund	0	618,000
Accounts payable and accrued expenses	(307,000)	(453,000)
Accrued severance	659,000	0
Prepaid expenses and other current assets	(108,000)	(153,000)
Interest on loan notes	0	233,000
Net cash used in operating activities	(9,367,000)	(4,904,000)
Cash flows from investing activities
Purchases of property and equipment	(1,089,000)	(97,000)
Net cash used in investing activities	(1,089,000)	(97,000)
Cash flows from financing activities
Proceeds from Preferred Series B	0	7,000,000
Proceeds from convertible loan notes	0	2,000,000
Payment of convertible loan note	0	(26,000)
Net cash provided by financing activities	0	8,974,000
Effect of exchange rates	(113,000)	24,000
Net increase (decrease) in cash and cash equivalents	(10,569,000)	3,997,000
Cash and cash equivalents, beginning of period	20,355,000	862,000
Cash and cash equivalents, end of period	$ 9,786,000	$ 4,859,000

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Stock Options (Details) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 1,064,000	$ 248,000	$ 1,590,000	$ 1,206,000
General and administrative expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	195,000	208,000	643,000	1,053,000
Research and development expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	831,000	0	831,000	0
Research and Development [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Allocated Share-based Compensation Expense	$ 38,000	$ 40,000	$ 116,000	$ 153,000

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Stock Options (Details 2) (Employee Stock Option [Member])	Sep. 30, 2014	Dec. 31, 2013
Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options outstanding	22,581,622	25,721,000
Available for future grants under the 2013 Stock Incentive Plan	39,250,000
Warrants	38,890,451
Total shares reserved	100,722,073

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Nature of Business and Significant Accounting Policies

9 Months Ended

Sep. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Business Description and Accounting Policies [Text Block]

1. Nature of Business and Significant Accounting Policies

Nature of Business

AmpliPhi Biosciences Corporation (the “Company”) was incorporated in the state of Washington in 1989. The Company, headquartered in Richmond, Virginia, is dedicated to developing novel antibacterial solutions called bacteriophage (phage). Phages are naturally occurring viruses that preferentially target and kill their bacterial targets.

Basis of Presentation

The interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries - Biocontrol, Ampliphi d.o.o., and AmpliPhi Australia. All significant intercompany accounts and transactions have been eliminated. All amounts on the financial statements and disclosures have been rounded to the nearest $1,000 except share and per share data.

The interim consolidated financial statements included herein have been prepared by the Company, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC. In the opinion of the Company’s management, all adjustments (consisting of normal recurring adjustments, reclassifications, and non-recurring adjustments) necessary to present fairly our results of operations for the three months and nine months ended September 30, 2014 and 2013, our cash flows for the nine months ended September 30, 2014 and 2013 and our financial position as of September 30, 2014 have been made. The results of operations for such interim periods are not necessarily indicative of the operating results to be expected for the full year.

Certain information and disclosures normally included in the notes to the annual financial statements have been condensed or omitted from these interim consolidated financial statements. Accordingly, these interim consolidated financial statements should be read in conjunction with the 2013 audited consolidated financial statements and notes.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Cash and Cash Equivalents

The Company considers cash equivalents to be short-term investments that have a maturity at the time of purchase of three months or less, are readily convertible into cash and have an insignificant level of valuation risk attributable to potential changes in interest rates. Cash equivalents are recorded at cost, which approximates fair market value, and consist primarily of money market accounts.

Accounts Receivable

Accounts receivable amounts are stated at their face amounts less any allowance. Provisions for doubtful accounts are estimated based on assessment of the probable collection from specific customer accounts and other known factors. If an account was determined to be uncollectible (payment has not been made in accordance with contract terms), it would be written off against the allowance. As of September 30, 2014 and December 31, 2013, management determined no allowance for doubtful accounts was required.

Property and Equipment

Property and equipment are recorded at cost and are depreciated using the straight-line method over the estimated useful lives of the related assets, generally three to seven years. 

Prepaid Expenses and Other Current Assets

Prepaid and other current assets as of September 30, 2014 and December 31, 2013 consist primarily of prepaid insurance and deposits.

Goodwill

Investments in purchased companies in excess of the underlying fair value of net assets at the date of acquisition are recorded as goodwill and assessed annually for impairment. If considered impaired, goodwill will be written down to fair value and a corresponding impairment loss recognized.

In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired in a business combination with an aggregate value of $7,172,000. Goodwill in the amount of $2,381,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired in a business combination with an aggregate value of $8,584,000. Goodwill in the amount of $1,948,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

Patents

Patents are recorded at cost and are amortized using the straight-line method over the estimated useful lives of the patents.

In 2011, the rights to Biocontrol Limited’s patents were acquired in a business combination. Patents in the amount of $493,000 have been recorded. These patents are being amortized over their useful life through December 2026.

Stock-Based Compensation

The Company accounts for stock-based payments under the guidance of Financial Accounting Standards Board (FASB) Accounting Standards Codification (ASC) 718, Stock Compensation, which requires measurement of compensation cost for all share-based payment awards at fair value on the date of grant and recognition of compensation cost over the requisite service period (typically the vesting period) for awards expected to vest.

Warrant and Preferred Shares Conversion Feature Liability

The Company accounts for warrants and the preferred shares conversion feature of the Company’s Series B preferred stock with anti-dilution (“down-round”) provisions under the guidance of ASC 815, Derivatives, and Hedging and Emerging Issue Task Force Statement 07-5: Determining Whether an Instrument (or Embedded Feature) Is Indexed to an Entity’s Own Stock, which require such warrants and the Series B preferred shares conversion feature to be recorded as a liability and adjusted to fair value in each reporting period.

Fair Value of Financial Assets and Liabilities — Derivative Instruments

The Company measures the fair value of financial assets and liabilities in accordance with GAAP, which defines fair value, establishes a framework for measuring fair value, and requires certain disclosures about fair value measurements.

GAAP defines fair value as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. GAAP also establishes as fair value hierarchy, which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. GAAP describes three levels of inputs that may be used to measure fair value:

Level 1 — quoted prices in active markets for identical assets or liabilities.

Level 2 — quoted prices for similar assets and liabilities in active markets or inputs that are observable.

Level 3 — inputs that are unobservable.

The Company does not use derivative financial instruments to hedge exposures to cash-flow, market or foreign-currency risks. However, the Company has entered into certain financial instruments and contracts, such as convertible loan notes with detachable common stock warrants and the issuance of preferred stock with detachable common stock warrants with features that are either i) not afforded equity classification, ii) embody risks not clearly and closely related to host contracts, or iii) may be net-cash settled by the counterparty. These instruments are required to be carried as derivative liabilities, at fair value.

The Company estimates fair values of these derivatives utilizing Level 2 inputs. The Company uses the Monte Carlo valuation technique as it embodies all of the requisite assumptions (including trading volatility, remaining term to maturity, market price, strike price, and risk free rates) necessary to fair value these instruments.

Estimating fair values of derivative financial instruments, including Level 2 instruments, require the use of significant and subjective inputs that may, and are likely to, change over the duration of the instrument with related changes in internal and external market factors. In addition, option-based techniques are volatile and sensitive to changes in our trading market price, the trading market price of various peer companies and other key assumptions. Since derivative financial instruments are initially and subsequently carried at fair value, our income will reflect this sensitivity of internal and external factors.

Revenue Recognition

The Company generates revenue from technology licenses. Revenue under technology licenses typically consists of nonrefundable, up-front license fees, technology access fees and various other payments. The Company recognizes revenue associated with performance milestones as earned, typically based upon the achievement of the specific milestones defined in the applicable agreements.

The Company recognizes revenue under research and development contracts as the related costs are incurred. When contracts include multiple elements, the Company follows ASC 605-25, Multiple Element Arrangements, which requires the Company to satisfy the following before revenue can be recognized:

• The delivered items have value to the customer on a stand-alone basis;

• Any undelivered items have objective and reliable evidence of fair value; and

• Delivery or performance is probable and within the Company’s control for any delivered items that have a right of return.

 

The Company classifies advance payments received in excess of amounts earned as deferred revenue.

Based upon the terms specified in its collaboration agreements, the Company receives advance payments from some of its collaboration partners before the project has been performed. These payments are deferred and recognized as revenue when the costs are incurred.

Research and Development

Research and development costs include salaries, costs of outside collaborators and outside services, royalty and license costs and allocated facility, occupancy and utility expenses. The Company expenses research and development costs as incurred.

In Process Research & Development (IPR&D) assets represent capitalized incomplete research projects that the Company acquired through business combinations. Such assets are initially measured at their acquisition date fair values. The fair value of the research projects is recorded as intangible assets on the consolidated balance sheet rather than expensed regardless of whether these assets have an alternative future use. The amounts capitalized are being accounted for as indefinite-lived intangible assets, subject to impairment testing until completion or abandonment of research and development efforts associated with the projects. Upon successful completion of each project, the Company will make a determination as to the then remaining useful life of the intangible asset and begin amortization. The Company tests its indefinite-lived intangibles, including IPR&D assets, for impairment at least annually. In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired by a business combination for $7,172,000. In 2012, IPR&D in the amount of $5,161,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired by a business combination $8,584,000. In 2011, IPR&D in the amount of $7,285,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

Net Income (Loss) per Common Share

Net income (loss) per common share is based on net income (loss) divided by the weighted average number of common shares outstanding during the period. For the three months ended September 30, 2014 and the nine months ended September 30, 2014, both basic and diluted net income (loss) are disclosed in the Consolidated Statements of Operations and Comprehensive Income. For the three months ended September 30, 2013 and the nine months ended September 30, 2013, the diluted net loss per share is the same as the basic net loss per share because all stock options, warrants, contingent shares, and Series B Preferred shares were antidilutive with respect to computing the net loss per share and therefore were excluded from the calculation of diluted net loss per share. The total number of shares that the Company excluded from the calculations of net loss per share was 150,283,630 shares for the three month period ending September 30, 2013 and 63,155,331 shares for the nine month period ending September 30, 2013.

Recent Accounting Pronouncements

On February 5, 2013, the FASB issued ASU no. 2013-02 which adds new disclosure requirements for items reclassified out of accumulated other comprehensive income (AOCI). The ASU is intended to help entities improve the transparency of changes in other comprehensive income (OCI) and items reclassified out of AOCI in their financial statements. It does not amend any existing requirements for reporting net income or OCI in the financial statements. For public entities, the new disclosure requirements are effective for fiscal years, and interim periods within those years, beginning after December 15, 2012. For nonpublic entities, the ASU is effective for fiscal years beginning after December 15, 2013, and interim and annual periods thereafter. The Company elected to early adopt this standard which did not result in any changes to the consolidated financial statements.

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CONSOLIDATED BALANCE SHEETS [Parenthetical] (USD $)	Sep. 30, 2014	Dec. 31, 2013
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment (in dollars)	$ 559,000	$ 473,000
Preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	10,000,000	10,000,000
Preferred stock, shares issued	8,671,040	8,859,978
Preferred stock, shares outstanding	8,671,040	8,859,978
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	445,000,000	445,000,000
Common stock, shares issued	187,159,093	182,535,562
Common stock, shares outstanding	187,159,093	182,535,562
Patents [Member]
Finite-Lived Intangible Assets, Accumulated Amortization	$ 116,000	$ 93,000

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Nature of Business and Significant Accounting Policies (Details Textual) (USD $)	3 Months Ended	9 Months Ended				12 Months Ended
	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013	Dec. 31, 2011 Patents [Member]	Dec. 31, 2012 SPH Holdings Pty Ltd [Member]	Dec. 31, 2011 Biocontrol Limited [Member]	Dec. 31, 2012 In Process Research and Development [Member] SPH Holdings Pty Ltd [Member]	Dec. 31, 2011 In Process Research and Development [Member] Biocontrol Limited [Member]
Significant Policies [Line Items]
Business Combination, Consideration Transferred, Total						$ 7,172,000	$ 8,584,000
Goodwill		4,329,000		4,329,000		2,381,000	1,948,000
Intangible Assets, Net (Excluding Goodwill)		12,446,000		12,446,000				5,161,000	7,285,000
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	150,283,630		63,155,331
Property, Plant and Equipment, Estimated Useful Lives		three to seven years
Finite-Lived Intangible Assets, Net					$ 493,000

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Document And Entity Information	9 Months Ended
	Sep. 30, 2014	Oct. 20, 2014
Document Information [Line Items]
Entity Registrant Name	AmpliPhi Biosciences Corp
Entity Central Index Key	0000921114
Current Fiscal Year End Date	--12-31
Entity Filer Category	Smaller Reporting Company
Trading Symbol	APHB
Entity Common Stock, Shares Outstanding		187,159,093
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2014
Document Fiscal Period Focus	Q3
Document Fiscal Year Focus	2014

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Liquidity (Details Textual) (USD $)	Sep. 30, 2014	Dec. 31, 2013
Liquidity Disclosure [Line Items]
Retained Earnings (Accumulated Deficit), Total	$ (355,312,000)	$ (378,074,000)

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CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Revenue	$ 0	$ (3,000)	$ 310,000	$ 333,000
Operating expenses
Research and development	1,804,000	1,106,000	4,687,000	5,378,000
General and administrative	1,632,000	1,211,000	5,377,000	4,777,000
Severance charge	1,510,000	0	1,510,000	0
Total operating expenses	4,946,000	2,317,000	11,574,000	10,155,000
Loss from operations	(4,946,000)	(2,320,000)	(11,264,000)	(9,822,000)
Other income (expense)
Gain (loss) on derivative liabilities	24,334,000	(41,548,000)	34,026,000	(45,617,000)
Amortization of note discount and patents	0	(23,000)	0	(2,660,000)
Interest expense, net	0	(9,000)	0	(233,000)
Other income (expense), net	24,334,000	(41,580,000)	34,026,000	(48,510,000)
Net income (loss)	19,388,000	(43,900,000)	22,762,000	(58,332,000)
Other comprehensive income (loss)
Net unrealized gain (loss) on foreign currency translations	(93,000)	(21,000)	(113,000)	(24,000)
Comprehensive income (loss)	$ 19,295,000	$ (43,921,000)	$ 22,649,000	$ (58,356,000)
Net income (loss) per share - basic (in dollars per share)	$ 0.10	$ (0.44)	$ 0.12	$ (0.68)
Weighted average number of shares of common stock outstanding - basic (in shares)	187,159,093	99,156,809	184,445,172	85,688,356
Net income (loss) per share - diluted (in dollars per share)	$ 0.06	$ (0.44)	$ 0.07	$ (0.68)
Weighted average number of shares of common stock outstanding - diluted (in shares)	315,990,084	99,156,809	323,604,642	85,688,356

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Severance Charge

9 Months Ended

Sep. 30, 2014

Severance Charge Abstract [Abstract]

Severance Charge Disclosure [Text Block]

6. Severance Charge

On September 15, 2014, by mutual agreement of the Board of Directors (the “Board”) of the Company and Philip J. Young, Mr. Young stepped down from his role as President and Chief Executive Officer of the Company, effective September 15, 2014. In accordance with Mr. Young’s employment agreements, the Company recorded a severance charge in the quarter ended September 30, 2014 of $1,510,000 related to severance-period compensation and benefits, as well as stock-based compensation expense related to the accelerated vesting of stock options .The composition of the severance charge is as follows:

Compensation and benefits	$	679,000
Stock-based compensation expenses related to accelerated vesting		831,000
Total severance charge	$	1,510,000

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Stock Options

9 Months Ended

Sep. 30, 2014

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

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

5. Stock Options

In October 2012, our board of directors approved and adopted the 2012 Stock Incentive Plan, which we refer to as the 2012 Plan. Under the 2012 Plan, we are authorized to issue up to 35,000,000 shares of our common stock in stock incentive awards to employees, directors and consultants.

In March 2009, our board of directors and shareholders adopted the 2009 Stock Incentive Plan, which we refer to as the 2009 Stock Incentive Plan. Under the 2009 Plan, we are authorized to issue up to 4,200,000 shares of our common stock in stock incentive awards to employees, directors and consultants.

In December 2013, our board of directors adopted the 2013 Plan. Under the 2013 Plan, we are authorized to issue up to 40,000,000 shares of our common stock in stock incentive awards to employees, directors and consultants. Our shareholders approved the 2013 Plan in February 2014.

The Company’s 2013 Stock Incentive Plan provides for the issuance of long-term incentive awards, or Awards, in the form of non-qualified and incentive stock options, or Options, stock appreciation rights, stock grants and restricted stock units. The Awards may be granted by the Company’s Board of Directors to its employees, directors and officers and to consultants, agents, advisors and independent contractors who provide services to the Company. The exercise price for Options must not be less than the fair market value of the underlying shares on the date of grant. Options expire no later than ten years from the date of grant and generally vest and become exercisable over a four-year period following the date of grant. Under the 2012 Plan, every non-employee member of the Company’s Board of Directors may elect to receive a non-qualified Option or restricted stock unit grant in lieu of certain cash compensation. Upon the exercise of Options, the Company issues the resulting shares from shares reserved for issuance under the Company’s Incentive Plans.

Under ASC 718 Stock Compensation, the Company is required to expense the fair value of share-based payments granted over the vesting period. The Company values Awards granted at their grant date fair value in accordance with the provisions of ASC 718 and recognizes stock-based compensation expense on a straight-line basis over the service period of each award.

Stock-based compensation expense is reduced by an estimated forfeiture rate derived from historical employee termination behavior. If the actual number of forfeitures differs from the Company’s estimates, the Company may record adjustments to increase or decrease compensation expense in future periods. There were no significant adjustments related to changes in the Company’s estimates for the three and nine month periods ended September 30, 2013 and 2014.

Following is a summary of the amount included as stock-based compensation expense in the accompanying consolidated statements of operations and comprehensive income (loss):

	Three Months Ended				Nine Months Ended
	September 30,		September 30,		September 30,		September 30,
	2014		2013		2014		2013
Income statement category:
Research and development	$	38,000	$	40,000	$	116,000	$	153,000
General and administrative		195,000		208,000		643,000		1,053,000
Severance charge		831,000		—		831,000		—
Total stock-based compensation expense	$	1,064,000	$	248,000	$	1,590,000	$	1,206,000

The following table summarizes Option activity:

				Average Remaining
			Weighted Average	Contractual Term
	Shares		Exercise Price	(Years)		Intrinsic Value
Outstanding at December 31, 2013	25,721,000	$	0.19
Granted	—		—
Exercised	—		—
Forfeited	3,137,378		0.19
Expired	2,000		13.10
Outstanding at September 30, 2014	22,581,622	$	0.19	2.15	$	862,982
Exercisable at September 30, 2014	19,972,558	$	0.19	1.35	$	822,989

The aggregate intrinsic value is determined using the closing price of the Company’s common stock of $0.22 on September 30, 2014.

As of September 30, 2014, the Company had unrecognized compensation cost related to unvested Options of approximately $559,358 net of estimated forfeitures, which the Company expects to recognize over a weighted average period of approximately two and a half years.

As of September 30, 2014, the Company had reserved shares of its common stock for future issuance as follows:

	Shares Reserved
Stock options outstanding	22,581,622
Available for future grants under the 2013 Stock Incentive Plan	39,250,000
Warrants	38,890,451
Total shares reserved	100,722,073

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Stock Options (Details 1) (Employee Stock Option [Member], USD $)	9 Months Ended
	Sep. 30, 2014
Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares, Outstanding at December 31, 2013	25,721,000
Shares, Granted	0
Shares, Exercised	0
Shares, Forfeited	3,137,378
Shares, Expired	2,000
Shares, Outstanding at September 30, 2014	22,581,622
Shares, Exercisable at September 30, 2014	19,972,558
Weighted Average Exercise Price, Outstanding at December 31, 2013	$ 0.19
Weighted Average Exercise Price, Granted	$ 0
Weighted Average Exercise Price, Exercised	$ 0
Weighted Average Exercise Price, Forfeited	$ 0.19
Weighted Average Exercise Price, Expired	$ 13.10
Weighted Average Exercise Price, Outstanding at September 30, 2014	$ 0.19
Weighted Average Exercise Price, Exercisable at September 30, 2014	$ 0.19
Average Remaining Contractual Term (Years), Outstanding at September 30, 2014	2 years 1 month 24 days
Average Remaining Contractual Term (Years), Exercisable at September 30, 2014	1 year 4 months 6 days
Intrinsic Value, Outstanding at September 30, 2014	$ 862,982
Intrinsic Value, Exercisable at September 30, 2014	$ 822,989

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Preferred Shares (Details Textual) (USD $)	9 Months Ended			9 Months Ended		12 Months Ended	9 Months Ended		12 Months Ended			12 Months Ended			12 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013	Sep. 30, 2014 Common Stock [Member]	Sep. 30, 2014 Preferred Stock [Member]	Dec. 31, 2013 Preferred Stock [Member]	Sep. 30, 2014 Warrant [Member]	Dec. 31, 2013 Warrant [Member]	Dec. 31, 2013 Convertible Notes Payable One [Member]	Dec. 31, 2013 Convertible Notes Payable One [Member] Preferred Stock [Member]	Dec. 31, 2013 Convertible Notes Payable One [Member] Warrant [Member]	Dec. 31, 2013 Convertible Notes Payable Two [Member]	Dec. 31, 2013 Convertible Notes Payable Two [Member] Preferred Stock [Member]	Dec. 31, 2013 Convertible Notes Payable Two [Member] Warrant [Member]	Dec. 31, 2013 Series B Convertible Preferred Stock [Member]	Dec. 31, 2013 Series B Convertible Preferred Stock [Member] Convertible Notes Payable One [Member]	Dec. 31, 2013 Series B Convertible Preferred Stock [Member] Convertible Notes Payable Two [Member]
Class of Stock [Line Items]
Preferred Stock, Shares Authorized	10,000,000		10,000,000												10,016,080
Preferred Stock, Initial Stated Value Per Share															$ 1.40
Preferred Stock, Par or Stated Value Per Share	$ 0.01		$ 0.01												$ 0.01
Debt Instrument, Convertible, Number of Equity Instruments															10
Preferred Stock, Dividend Rate, Percentage															10.00%
Debt Instrument, Convertible, If-initial public offering proceeds meets Least amount															$ 7,000,000
Stock Issued During Period, Shares, New Issues1						4,999,999									4,999,999
Warrants Issued During the Period, Number of Warrants												1,645,361			12,499,996	10,894,839
Warrants Issued During the Period, Exercise Price of Warrants															$ 0.14	$ 0.14
Warrants Issued During the Period, Value of Warrants															7,000,000
Debt Conversion, Original Debt, Amount									5,491,001			829,277
Debt Conversion, Converted Instrument, Shares Issued																4,357,936	658,145
Debt Instrument, Convertible, Beneficial Conversion Feature	18,400,000
Derivative preferred shares conversion liability	7,633,000		34,443,000
Derivative Liability						5,064,000		1,886,000		3,804,000	1,644,000		155,000	674,000
Warrants Issued During Period Number Of Warrants1									4,999,999
Warrants Issued During Period Exercise Price Of Warrants1									$ 0.14			$ 0.14
Fair Value Adjustment of Warrants	0	759,000							759,000
Payments of Stock Issuance Costs									350,000
Conversion of Stock, Shares Converted				1,889,380	188,938
Conversion of Stock, Shares Issued							118,000
Reclassification From Derivative Liability To Equity	$ 741,000

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Stock Options (Tables)

9 Months Ended

Sep. 30, 2014

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

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]

Following is a summary of the amount included as stock-based compensation expense in the accompanying consolidated statements of operations and comprehensive income (loss):

	Three Months Ended				Nine Months Ended
	September 30,		September 30,		September 30,		September 30,
	2014		2013		2014		2013
Income statement category:
Research and development	$	38,000	$	40,000	$	116,000	$	153,000
General and administrative		195,000		208,000		643,000		1,053,000
Severance charge		831,000		—		831,000		—
Total stock-based compensation expense	$	1,064,000	$	248,000	$	1,590,000	$	1,206,000

Schedule of Share-based Compensation, Stock Options, Activity [Table Text Block]

The following table summarizes Option activity:

				Average Remaining
			Weighted Average	Contractual Term
	Shares		Exercise Price	(Years)		Intrinsic Value
Outstanding at December 31, 2013	25,721,000	$	0.19
Granted	—		—
Exercised	—		—
Forfeited	3,137,378		0.19
Expired	2,000		13.10
Outstanding at September 30, 2014	22,581,622	$	0.19	2.15	$	862,982
Exercisable at September 30, 2014	19,972,558	$	0.19	1.35	$	822,989

Schedule of Common Stock, Capital Shares Reserved for Future Issuance [Table Text Block]

As of September 30, 2014, the Company had reserved shares of its common stock for future issuance as follows:

	Shares Reserved
Stock options outstanding	22,581,622
Available for future grants under the 2013 Stock Incentive Plan	39,250,000
Warrants	38,890,451
Total shares reserved	100,722,073

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Nature of Business and Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2014

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Accounting, Policy [Policy Text Block]

Basis of Presentation

The interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries - Biocontrol, Ampliphi d.o.o., and AmpliPhi Australia. All significant intercompany accounts and transactions have been eliminated. All amounts on the financial statements and disclosures have been rounded to the nearest $1,000 except share and per share data.

The interim consolidated financial statements included herein have been prepared by the Company, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC. In the opinion of the Company’s management, all adjustments (consisting of normal recurring adjustments, reclassifications, and non-recurring adjustments) necessary to present fairly our results of operations for the three months and nine months ended September 30, 2014 and 2013, our cash flows for the nine months ended September 30, 2014 and 2013 and our financial position as of September 30, 2014 have been made. The results of operations for such interim periods are not necessarily indicative of the operating results to be expected for the full year.

Certain information and disclosures normally included in the notes to the annual financial statements have been condensed or omitted from these interim consolidated financial statements. Accordingly, these interim consolidated financial statements should be read in conjunction with the 2013 audited consolidated financial statements and notes.

Use of Estimates, Policy [Policy Text Block]

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenue and expenses during the reporting period. Actual results could differ from those estimates.

Cash and Cash Equivalents, Policy [Policy Text Block]

Cash and Cash Equivalents

The Company considers cash equivalents to be short-term investments that have a maturity at the time of purchase of three months or less, are readily convertible into cash and have an insignificant level of valuation risk attributable to potential changes in interest rates. Cash equivalents are recorded at cost, which approximates fair market value, and consist primarily of money market accounts.

Trade and Other Accounts Receivable, Policy [Policy Text Block]

Accounts Receivable

Accounts receivable amounts are stated at their face amounts less any allowance. Provisions for doubtful accounts are estimated based on assessment of the probable collection from specific customer accounts and other known factors. If an account was determined to be uncollectible (payment has not been made in accordance with contract terms), it would be written off against the allowance. As of September 30, 2014 and December 31, 2013, management determined no allowance for doubtful accounts was required.

Property, Plant and Equipment, Policy [Policy Text Block]

Property and Equipment

Property and equipment are recorded at cost and are depreciated using the straight-line method over the estimated useful lives of the related assets, generally three to seven years. 

Other Current Assets [Text Block]

Prepaid Expenses and Other Current Assets

Prepaid and other current assets as of September 30, 2014 and December 31, 2013 consist primarily of prepaid insurance and deposits.

Goodwill and Intangible Assets, Goodwill, Policy [Policy Text Block]

Goodwill

Investments in purchased companies in excess of the underlying fair value of net assets at the date of acquisition are recorded as goodwill and assessed annually for impairment. If considered impaired, goodwill will be written down to fair value and a corresponding impairment loss recognized.

In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired in a business combination with an aggregate value of $7,172,000. Goodwill in the amount of $2,381,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired in a business combination with an aggregate value of $8,584,000. Goodwill in the amount of $1,948,000 was recorded. In management’s opinion, no goodwill has been impaired as of September 30, 2014 and December 31, 2013.

Goodwill and Intangible Assets, Intangible Assets, Policy [Policy Text Block]

Patents

Patents are recorded at cost and are amortized using the straight-line method over the estimated useful lives of the patents.

In 2011, the rights to Biocontrol Limited’s patents were acquired in a business combination. Patents in the amount of $493,000 have been recorded. These patents are being amortized over their useful life through December 2026.

Share-based Compensation, Option and Incentive Plans Policy [Policy Text Block]

Stock-Based Compensation

The Company accounts for stock-based payments under the guidance of Financial Accounting Standards Board (FASB) Accounting Standards Codification (ASC) 718, Stock Compensation, which requires measurement of compensation cost for all share-based payment awards at fair value on the date of grant and recognition of compensation cost over the requisite service period (typically the vesting period) for awards expected to vest.

Warrant and Preferred Shares Conversion Feature Liability, Policy [Policy Text Block]

Warrant and Preferred Shares Conversion Feature Liability

The Company accounts for warrants and the preferred shares conversion feature of the Company’s Series B preferred stock with anti-dilution (“down-round”) provisions under the guidance of ASC 815, Derivatives, and Hedging and Emerging Issue Task Force Statement 07-5: Determining Whether an Instrument (or Embedded Feature) Is Indexed to an Entity’s Own Stock, which require such warrants and the Series B preferred shares conversion feature to be recorded as a liability and adjusted to fair value in each reporting period.

Derivatives, Policy [Policy Text Block]

Fair Value of Financial Assets and Liabilities — Derivative Instruments

The Company measures the fair value of financial assets and liabilities in accordance with GAAP, which defines fair value, establishes a framework for measuring fair value, and requires certain disclosures about fair value measurements.

GAAP defines fair value as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. GAAP also establishes as fair value hierarchy, which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. GAAP describes three levels of inputs that may be used to measure fair value:

Level 1 — quoted prices in active markets for identical assets or liabilities.

Level 2 — quoted prices for similar assets and liabilities in active markets or inputs that are observable.

Level 3 — inputs that are unobservable.

The Company does not use derivative financial instruments to hedge exposures to cash-flow, market or foreign-currency risks. However, the Company has entered into certain financial instruments and contracts, such as convertible loan notes with detachable common stock warrants and the issuance of preferred stock with detachable common stock warrants with features that are either i) not afforded equity classification, ii) embody risks not clearly and closely related to host contracts, or iii) may be net-cash settled by the counterparty. These instruments are required to be carried as derivative liabilities, at fair value.

The Company estimates fair values of these derivatives utilizing Level 2 inputs. The Company uses the Monte Carlo valuation technique as it embodies all of the requisite assumptions (including trading volatility, remaining term to maturity, market price, strike price, and risk free rates) necessary to fair value these instruments.

Estimating fair values of derivative financial instruments, including Level 2 instruments, require the use of significant and subjective inputs that may, and are likely to, change over the duration of the instrument with related changes in internal and external market factors. In addition, option-based techniques are volatile and sensitive to changes in our trading market price, the trading market price of various peer companies and other key assumptions. Since derivative financial instruments are initially and subsequently carried at fair value, our income will reflect this sensitivity of internal and external factors.

Revenue Recognition, Policy [Policy Text Block]

Revenue Recognition

The Company generates revenue from technology licenses. Revenue under technology licenses typically consists of nonrefundable, up-front license fees, technology access fees and various other payments. The Company recognizes revenue associated with performance milestones as earned, typically based upon the achievement of the specific milestones defined in the applicable agreements.

The Company recognizes revenue under research and development contracts as the related costs are incurred. When contracts include multiple elements, the Company follows ASC 605-25, Multiple Element Arrangements, which requires the Company to satisfy the following before revenue can be recognized:

• The delivered items have value to the customer on a stand-alone basis;

• Any undelivered items have objective and reliable evidence of fair value; and

• Delivery or performance is probable and within the Company’s control for any delivered items that have a right of return.

 

The Company classifies advance payments received in excess of amounts earned as deferred revenue.

Based upon the terms specified in its collaboration agreements, the Company receives advance payments from some of its collaboration partners before the project has been performed. These payments are deferred and recognized as revenue when the costs are incurred.

Research and Development Expense, Policy [Policy Text Block]

Research and Development

Research and development costs include salaries, costs of outside collaborators and outside services, royalty and license costs and allocated facility, occupancy and utility expenses. The Company expenses research and development costs as incurred.

In Process Research & Development (IPR&D) assets represent capitalized incomplete research projects that the Company acquired through business combinations. Such assets are initially measured at their acquisition date fair values. The fair value of the research projects is recorded as intangible assets on the consolidated balance sheet rather than expensed regardless of whether these assets have an alternative future use. The amounts capitalized are being accounted for as indefinite-lived intangible assets, subject to impairment testing until completion or abandonment of research and development efforts associated with the projects. Upon successful completion of each project, the Company will make a determination as to the then remaining useful life of the intangible asset and begin amortization. The Company tests its indefinite-lived intangibles, including IPR&D assets, for impairment at least annually. In 2012, the rights to SPH Holdings Pty Ltd’s know-how and phage libraries were acquired by a business combination for $7,172,000. In 2012, IPR&D in the amount of $5,161,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

In 2011, the rights to Biocontrol Limited’s patents and phage libraries were acquired by a business combination $8,584,000. In 2011, IPR&D in the amount of $7,285,000 was recorded. In management’s opinion, this IPR&D has not been impaired as of September 30, 2014 and December 31, 2013.

Earnings Per Share, Policy [Policy Text Block]

Net Income (Loss) per Common Share

Net income (loss) per common share is based on net income (loss) divided by the weighted average number of common shares outstanding during the period. For the three months ended September 30, 2014 and the nine months ended September 30, 2014, both basic and diluted net income (loss) are disclosed in the Consolidated Statements of Operations and Comprehensive Income. For the three months ended September 30, 2013 and the nine months ended September 30, 2013, the diluted net loss per share is the same as the basic net loss per share because all stock options, warrants, contingent shares, and Series B Preferred shares were antidilutive with respect to computing the net loss per share and therefore were excluded from the calculation of diluted net loss per share. The total number of shares that the Company excluded from the calculations of net loss per share was 150,283,630 shares for the three month period ending September 30, 2013 and 63,155,331 shares for the nine month period ending September 30, 2013.

New Accounting Pronouncements, Policy [Policy Text Block]

Recent Accounting Pronouncements

On February 5, 2013, the FASB issued ASU no. 2013-02 which adds new disclosure requirements for items reclassified out of accumulated other comprehensive income (AOCI). The ASU is intended to help entities improve the transparency of changes in other comprehensive income (OCI) and items reclassified out of AOCI in their financial statements. It does not amend any existing requirements for reporting net income or OCI in the financial statements. For public entities, the new disclosure requirements are effective for fiscal years, and interim periods within those years, beginning after December 15, 2012. For nonpublic entities, the ASU is effective for fiscal years beginning after December 15, 2013, and interim and annual periods thereafter. The Company elected to early adopt this standard which did not result in any changes to the consolidated financial statements.

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Warrants and Warrants Liability (Tables)

9 Months Ended

Sep. 30, 2014

Stockholders Equity Note [Abstract]

Schedule of Stockholders Equity Note, Warrants or Rights [Table Text Block]

We estimate the fair values of these securities using a Monte Carlo valuation model. The following warrants were issued in 2013 using the Monte Carlo valuation method with the key inputs as follows:

	June 26, 2013			July 15, 2013			December 23, 2013
Warrants issued		28,394,834			1,645,360			4,320,420
Risk free interest rate		.0109			.0109			0.0167
Volatility		160.94	%		163.08	%		155.24	%
Expected term		5 years			5 years			5 years
Exercise price	$	0.14		$	0.14		$	0.25

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Severance Charge (Tables)

9 Months Ended

Sep. 30, 2014

Severance Charge Abstract [Abstract]

Severance Charge [Table Text Block]

The composition of the severance charge is as follows:

Compensation and benefits	$	679,000
Stock-based compensation expenses related to accelerated vesting		831,000
Total severance charge	$	1,510,000

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Warrants and Warrants Liability (Details Textual) (USD $)	9 Months Ended		9 Months Ended	12 Months Ended
	Sep. 30, 2014	Dec. 31, 2013	Sep. 30, 2014 Warrants Issued on June 26, 2013 Member [Member]	Dec. 31, 2013 Warrants Issued on June 26, 2013 Member [Member]	Dec. 31, 2011 Biocontrol Limited [Member]	Dec. 31, 2013 Convertible Notes Payable [Member]	Dec. 31, 2013 Series B Convertible Preferred Stock [Member]	Dec. 31, 2013 Common Stock [Member]	Dec. 31, 2013 Private Placement [Member] Series B Convertible Preferred Stock [Member]	Dec. 31, 2013 Private Placement [Member] Common Stock [Member]
Class of Warrant or Right [Line Items]
Stock Issued During Period, Shares, New Issues2								72,007,000		72,007,000
Stock Issued During Period, Exercise Price, New Issues2										$ 0.25
Warrants Issued During the Period, Terms Of Expiration					December 2016	February through May 2018			June 2018	December 2018
Warrants Issued During the Period, Number of Warrants				28,394,834	1,355,164	7,030,387	12,499,996		30,040,194
Warrants Issued During the Period, Exercise Price of Warrants					$ 0.46	$ 0.14	$ 0.14		$ 0.14
Warrants Issuance Costs									$ 1,400,000
Derivative warrants liability	6,949,000	16,664,000
Warrants Exercised During Period Value			3,855,714
Common Stock Issued During Period Value Warrants Exercised			2,734,151
Derivative, Gain on Derivative	5,900,000		398,000
Reclassifications of Temporary to Permanent Equity			$ 1,729,000

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Severance Charge (Details) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Severance Charge [Line Items]
Compensation and benefits			$ 679,000
Stock-based compensation expenses related to accelerated vesting			831,000	0
Total severance charge	$ 1,510,000	$ 0	$ 1,510,000	$ 0

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CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (DEFICIT) (USD $)	Total	Preferred Stock [Member]	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]
Balances at Dec. 31, 2012	$ 12,943,000	$ 0	$ 669,000	$ 332,806,000	$ (320,426,000)	$ (106,000)
Balances (in shares) at Dec. 31, 2012		0	66,908,810
Net income (loss)	(57,648,000)	0	0	0	(57,648,000)	0
Beneficial conversion feature and warrants associated with issuance of convertible loan notes	2,635,000	0	0	2,635,000	0	0
Shares issued for Intrexon	3,000,000	0	240,000	2,760,000	0	0
Shares issued for Intrexon (in shares)			24,000,000
Issuance of preferred stock from conversion of convertible loan notes	50,000	50,000	0	0	0	0
Issuance of preferred stock from conversion of convertible loan notes (in shares)		5,016,081	0
Issuance of preferred stock	50,000	50,000	0	0	0	0
Issuance of preferred stock (in shares)		4,999,999
Preferred stock converted to common stock	6,615,000	(11,000)	115,000	6,511,000	0	0
Preferred stock converted to common stock (in shares)		(1,156,102)	11,561,020
Stock-based compensation	1,437,000	0	0	1,437,000	0	0
Stock options exercised	13,000	0	1,000	12,000	0	0
Stock options exercised (in shares)			61,018
Shares released from escrow	0	0	80,000	(80,000)	0	0
Shares released from escrow (in shares)			8,000,000
Issuance of common stock for December financing	15,464,000	0	720,000	14,744,000	0	0
Issuance of common stock for December financing (in shares)			72,007,000
Escheat shares	0	0	0	0	0	0
Escheat shares (in shares)			(2,286)
Foreign currency translations	41,000	0	0	0	0	41,000
Balances at Dec. 31, 2013	(15,400,000)	89,000	1,825,000	360,825,000	(378,074,000)	(65,000)
Balances (in shares) at Dec. 31, 2013		8,859,978	182,535,562
Net income (loss)	22,762,000	0	0	0	22,762,000	0
Warrants exercised	1,758,000	0	28,000	1,730,000	0	0
Warrants exercised (in shares)			2,734,151
Preferred stock converted to common stock	741,000	(2,000)	19,000	724,000	0	0
Preferred stock converted to common stock (in shares)		(188,938)	1,889,380
Stock-based compensation	759,000	0	0	759,000	0	0
Stock-based compensation - severance	831,000	0	0	831,000	0	0
Foreign currency translations	(113,000)	0	0	0	0	(113,000)
Balances at Sep. 30, 2014	$ 11,338,000	$ 87,000	$ 1,872,000	$ 364,869,000	$ (355,312,000)	$ (178,000)
Balances (in shares) at Sep. 30, 2014		8,671,040	187,159,093

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Warrants and Warrants Liability

9 Months Ended

Sep. 30, 2014

Stockholders Equity Note [Abstract]

Stockholders Equity Note Warrants Disclosure [Text Block]

4. Warrants and Warrants Liability

The Company follows ASC 815-40, Contracts in an Entity’s Own Equity, as it relates to outstanding warrants.

In connection with the December 2013 private placement of 72,007,000 shares of the Company's common stock at a price per share of $0.25, the Company issued an aggregate of warrants to purchase 4,320,420 shares of common stock at an exercise price of $0.25 per share to the placement agents. These warrants expire December 2018. These warrants contain provisions that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision) and contain net settlement provisions. Due to these provisions, the Company accounted for these warrants as liabilities instead of equity.

In connection with the private placement of Series B Convertible Preferred Stock, which occurred through two closings on June 26, 2013 and July 15, 2013, respectively, the Company issued an aggregate of warrants to purchase 30,040,194 shares of common stock at an exercise price of $0.14 per share. These warrants expire June 2018. These warrants contain provisions that protect holders from a decline in the issue price of the Company’s common stock (“down-round” provision) and contain net settlement provisions. Due to these provisions, the Company accounted for these warrants as liabilities instead of equity. The Company measured the fair value of these warrants on June 26, 2013 and July 15, 2013 and recorded the initial liability as part of the private placement proceeds and expensed $1.4 million for the warrants issued to the placement agent.

We estimate the fair values of these securities using a Monte Carlo valuation model. The following warrants were issued in 2013 using the Monte Carlo valuation method with the key inputs as follows:

	June 26, 2013			July 15, 2013			December 23, 2013
Warrants issued		28,394,834			1,645,360			4,320,420
Risk free interest rate		.0109			.0109			0.0167
Volatility		160.94	%		163.08	%		155.24	%
Expected term		5 years			5 years			5 years
Exercise price	$	0.14		$	0.14		$	0.25

From February through May 2013, in connection with the issuance of new convertible promissory notes, the Company issued warrants to purchase up to 7,030,387 shares of its common stock. These warrants expire February through May 2018 and are exercisable at a price of $0.14 per share. These warrants are considered to be equity.

In 2011, in connection with the Biocontrol business combination, the Company issued warrants to purchase up to 1,355,164 shares of its common stock. These warrants expire in December 2016 and are exercisable at a price of $0.46 per share. These warrants are considered to be equity.

On June 26, 2014, 3,855,714 warrants, issued on June 26, 2013, were exercised. Due to this exercise, 2,734,151 shares of common stock were issued, a gain on derivative liabilities of $398,000 was recognized, and $1,729,000 was classified out of the derivative liability account and into equity.

The Company re-measured the fair value of the liability warrants at September 30, 2014 and recorded a $5.9 million gain on derivative liabilities during the third quarter to adjust the liabilities associated with the warrants to their estimated fair values totaling $6.9 million. The change in fair value and the resulting gain was attributable to a decline in the market value of our common stock as of September 30, 2014.

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Warrants and Warrants Liability (Details) (USD $)	12 Months Ended
	Dec. 31, 2013
Warrants Issued on June 26, 2013 Member [Member]
Class of Warrant or Right [Line Items]
Warrants Issued	28,394,834
Risk free interest rate	0.0109%
Volatility	160.94%
Expected term	5 years
Exercise price	$ 0.14
Warrants Issued on July 15, 2013 Member [Member]
Class of Warrant or Right [Line Items]
Warrants Issued	1,645,360
Risk free interest rate	0.0109%
Volatility	163.08%
Expected term	5 years
Exercise price	$ 0.14
Warrants Issued on December 23, 2013 Member [Member]
Class of Warrant or Right [Line Items]
Warrants Issued	4,320,420
Risk free interest rate	0.0167%
Volatility	155.24%
Expected term	5 years
Exercise price	$ 0.25