Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Cash flows from operating activities:
Net income (loss)	$ 244,725	$ 276,452	$ (42,613)
Adjustments for non-cash operating items:
Stock-based compensation	54,862	45,134	37,078
Impairment of intangible assets	30,000
Loss on extinguishment of Convertible Notes	21,087
Amortization of debt discount and debt issuance costs	8,613	14,898	13,456
Depreciation on property and equipment	7,023	5,239	3,449
Excess tax benefits from stock-based compensation	(100,243)	(16,965)
Changes in deferred income taxes	(8,270)	(3,827)
Change in fair value of contingent purchase consideration	(10,674)
Amortization of deferred revenue	(2,822)	(14,109)	(25,396)
Release of valuation allowance for deferred income taxes		(33,403)
Other non-cash items	52	1,124	(10)
Changes in operating assets and liabilities:
Receivable from collaboration partners	(206,821)	(77,527)	(71,752)
Prepaid expenses and other current assets	(4,556)	301	(3,953)
Other non-current assets	3,279	(401)	(7,353)
Accounts payable, accrued expenses and other current liabilities	145,997	41,965	27,852
Current taxes payable	30,459	1,970	37
Other non-current liabilities	7,228	(252)	996
Net cash provided by (used) in operating activities	219,939	240,599	(68,209)
Cash flows from investing activities:
Purchases of short-term investments	(90,381)		(144,926)
Sales or maturities of short-term investments	90,224		370,000
Purchases of property and equipment	(19,459)	(10,544)	(7,535)
Change in restricted cash	(1,371)	(1,866)	(713)
Net cash (used in) provided by investing activities	(430,987)	(17,410)	216,826
Cash flows from financing activities:
Principal repayment of Convertible Notes	(258,742)	(12)
Cash settlement of Convertible Notes conversion premium	(1,126)
Proceeds from borrowings under Revolving Credit Facility	150,000
Principal repayment of borrowings under Revolving Credit Facility	(75,000)
Financing transaction costs	(1,715)
Excess tax benefits from stock-based compensation	100,243	16,965
Proceeds from issuance of common stock under equity incentive and stock purchase plans	21,459	33,882	8,870
Reduction of build-to-suit lease obligation	(895)	(135)
Net cash (used in) provided by financing activities	(65,776)	50,700	8,870
Net (decrease) increase in cash and cash equivalents	(276,824)	273,889	157,487
Cash and cash equivalents at beginning of year	502,677	228,788	71,301
Cash and cash equivalents at end of year	225,853	502,677	228,788
Supplemental disclosures of cash flow information:
Interest	3,577	6,792	6,792
Income taxes, net of refunds	2,122	1,525	(127)
Non-cash investing and financing activities:
Reacquisition of Convertible Notes equity component upon conversion	324,177
Fair value of common stock issued for conversion of Convertible Notes	312,990
Derecognition of build-to-suit lease asset	3,241
Derecognition of build-to-suit lease obligations	3,176
Property and equipment expenditures incurred but not yet paid	5,828	242	$ 99
Interest capitalized during construction period for build-to-suit lease transactions	2,024	1,459
Accrued interest payable forfeited upon conversion of Convertible Notes	1,686
Amounts capitalized under build-to-suit lease transactions	44	18,085
BioMarin Pharmaceutical Inc. [Member]
Cash flows from investing activities:
Payments under Agreement	$ (410,000)
CureTech Ltd [Member]
Cash flows from investing activities:
Payments under Agreement		$ (5,000)