Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009
Cash flows from operating activities:
Net income (loss)	$ 41,179	$ (754,626)	$ (642,178)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	35,041	30,459	30,107
Stock-based compensation expense	118,226	91,124	86,722
Other non-cash based compensation expense	8,525	6,552	6,044
Intangible asset impairment charge	105,800		7,200
Secured notes (due 2012) discount amortization expense	18,409	13,589	3,125
Change in fair value of derivative instruments	16,801	41,229	1,847
Deferred income taxes	(7,501)		(2,225)
Loss on disposal of property and equipment	55	39	2,211
Loss on exchanges of convertible senior subordinated notes (due 2013)			18,137
Other non-cash items, net	264	(31)
Changes in operating assets and liabilities, excluding the effects of the acquisitions of a variable interest entity (Alios) and business (ViroChem):
Accounts receivable, net	(170,606)	(2,923)	13,900
Inventories	(111,388)
Prepaid expenses and other current assets	(1,717)	(600)	2,070
Accounts payable	37,468	(1,182)	(15,057)
Accrued expenses and other liabilities	116,921	8,182	8,924
Excess tax benefit from share-based payment arrangements	(900)
Accrued restructuring expense	(3,282)	(4,422)	(47)
Accrued interest	(99)	3,031	(1,423)
Income taxes payable (Alios)	12,075
Deferred revenues	(71,536)	(65,863)	53,057
Net cash provided by (used in) operating activities	143,735	(635,442)	(427,586)
Cash flows from investing activities:
Purchases of marketable securities	(721,545)	(1,234,719)	(1,186,701)
Sales and maturities of marketable securities	1,016,040	1,284,806	788,263
Payment for acquisition of ViroChem, net of cash acquired			(87,422)
Payment for acquisition of a variable interest entity (Alios)	(60,000)
Expenditures for property and equipment	(34,595)	(38,054)	(23,496)
Increase in restricted cash and cash equivalents		(3,777)	(55)
Decrease in restricted cash and cash equivalents (Alios)	12,695
Decrease (increase) in other assets	(183)	(955)	679
Net cash provided by (used in) investing activities	212,412	7,301	(508,732)
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	900
Issuances of common stock from employee benefit plans, net	124,862	33,434	47,850
Issuances of common stock from stock offerings, net			801,385
Issuance of convertible senior subordinated notes (due 2015), net		391,645
Issuance of secured notes (due 2012) and sale of milestone payments, net			149,902
Payments to redeem secured notes (due 2012)	(155,000)
Settlement of milestone derivatives	(95,000)
Debt conversion/exchange costs		(22)	(131)
Net cash (used in) provided by financing activities	(124,238)	425,057	999,006
Effect of changes in exchange rates on cash	214	(377)	(5,145)
Net increase (decrease) in cash and cash equivalents	232,123	(203,461)	57,543
Cash and cash equivalents-beginning of period	243,197	446,658	389,115
Cash and cash equivalents-end of period	475,320	243,197	446,658
Supplemental disclosure of cash flow information:
Cash paid for interest	13,512	761	10,248
Cash paid for taxes	0
Conversion/exchange of convertible senior subordinated notes (due 2013) for common stock		32,071	255,429
Accrued interest offset to additional paid-in capital on conversion/exchange of convertible senior subordinated notes (due 2013)		140	3,355
Unamortized debt issuance costs of converted/exchanged convertible senior subordinated notes (due 2013) offset to additional paid-in capital		624	5,899
Capitalization of construction in-process related to financing lease transactions	54,655
Fair value of common stock issued to acquire ViroChem			$ 290,557