Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Cash flows from operating activities:
Net income (loss)	$ (220,872)	$ (123,603)	$ 85,248
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation, amortization and impairment charges	8,307	4,614	6,147
Stock-based compensation	20,341	7,675	4,836
Deferred executive compensation expense	2,810	1,719	1,477
Revaluation of warrant liability	15,924	46,715	19,532
Increase (decrease) from:
Other assets	(4,647)	(145)	814
Amounts due under license and collaboration agreements	(67)	373	3,176
Accounts payable	2,664	2,394	(1,684)
Accrued compensation and benefits	10,656	82	76
Accrued product development expenses	2,113	3,759	117
Other accrued expenses	4,669	1,271	(1,043)
Other liabilities	5,714	1,660	18
Deferred revenue	(230)	999	(111,611)
Deferred executive compensation paid	(1,063)	(775)	(685)
Net cash provided by (used in) operating activities	(153,681)	(53,262)	6,418
Cash flows from investing activities:
Acquisitions of marketable securities	(89,554)
Proceeds from maturities of marketable securities	44,500
Change in restricted cash	(289)
Investment in property and equipment	(4,424)	(1,452)	(1,344)
Investment in intangible assets	(633)	(671)	(691)
Net cash used in investing activities	(50,400)	(2,123)	(2,035)
Cash flows from financing activities:
Proceeds from long-term borrowings		4,375
Repayment of long-term borrowings	(1,400)	(1,400)	(1,925)
Principal payments under capital lease obligations	(54)	(66)	(118)
Proceeds from issuance of common stock, net of issuance costs		243,058	57,515
Proceeds from issuance of common stock pursuant to warrants	12,483	8,080	2,624
Proceeds from issuance of common stock pursuant to stock option and purchase plans	10,511	4,791	789
Payment of tax withholding obligations related to stock compensation	(4,336)	(827)
Net cash provided by financing activities	17,204	258,011	58,885
Net increase (decrease) in cash and cash equivalents	(186,877)	202,626	63,268
Cash and cash equivalents, beginning of year	306,256	103,630	40,362
Cash and cash equivalents, end of year	119,379	306,256	103,630
Supplemental disclosures:
Interest paid	206	230	182
Property and equipment acquired through capital lease			19
Non-cash transaction - property and equipment included in accounts payable or accruals	$ 579	$ 911