Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Cash flows from operating activities:
Net loss	$ (53,916)	$ (162,013)	$ (171,855)
Adjustments to reconcile net loss to net cash used in operating activities:
Non-cash royalty revenue related to sale of future royalties	(21,937)	(22,055)	(10,791)
Non-cash interest expense on liability related to sale of future royalties	20,888	22,309	18,057
Stock-based compensation	17,017	17,708	16,199
Depreciation and amortization	12,927	14,275	14,508
Other non-cash transactions	(560)	664	2,520
Changes in assets and liabilities:
Accounts receivable, net	(1,378)	3,576	(867)
Inventory	500	4,817	(5,613)
Other assets	(3,294)	6,423	6,031
Accounts payable	(6,359)	6,199	(122)
Accrued compensation	(8,505)	5,481	(4,034)
Accrued expenses	273	(1,915)	1,495
Accrued clinical trial expenses	(9,197)	(595)	5,547
Interest payable		(166)	5,278
Deferred revenue	(4,664)	(12,399)	(9,384)
Liability related to receipt of refundable milestone payment	(70,000)	70,000
Other liabilities	(13,801)	9,164	3,275
Net cash used in operating activities	(142,006)	(38,527)	(129,756)
Cash flows from investing activities:
Maturities of investments	247,995	319,181	307,887
Purchases of investments	(297,251)	(268,068)	(164,662)
Sales of investments	21,661	2,887	5,378
Restricted cash			(25,000)
Purchases of property, plant and equipment	(9,976)	(4,091)	(10,583)
Net cash (used in) provided by investing activities	(37,571)	49,909	113,020
Cash flows from financing activities:
Payment of capital lease obligations	(3,536)	(2,992)	(2,437)
Issuance of common stock, net of issuance costs	116,536
(Repayment of) proceeds from sale of future royalties, net of $4.4 million of transaction costs in 2012	(7,000)	(3,000)	119,588
Proceeds from issuance of senior secured notes, net of $4.5 million of issuance costs			77,940
Repayment of convertible subordinated notes			(172,407)
Proceeds from shares issued under equity compensation plans	46,984	8,208	4,117
Net cash provided by financing activities	152,984	2,216	26,801
Effect of exchange rates on cash and cash equivalents	(109)	32	60
Net (decrease) increase in cash and cash equivalents	(26,702)	13,630	10,125
Cash and cash equivalents at beginning of year	39,067	25,437	15,312
Cash and cash equivalents at end of year	12,365	39,067	25,437
Supplemental disclosure of cash flow information:
Cash paid for interest	17,445	17,590	9,620
Cash paid for income taxes	964	1,014	1,021
Supplemental schedule of non-cash investing and financing activities:
Property and equipment acquired through capital leases and other financing	5,231	2,000
Retirement of convertible subordinated notes in exchange for senior secured notes			$ 42,548