Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013 Pfizer convertible subordinated note due 2014	Sep. 30, 2013 4.75% convertible senior notes due 2015
Cash flows from operating activities:
Net loss	$ (40,276)	$ (63,099)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization of debt discounts	20,355	22,214
Stock-based compensation	28,577	29,426
Debt exchange expense	11,262
Changes in operating assets and liabilities:
Accounts receivable	37,754	(10,125)
Prepaid expenses and other assets	2,644	8,370
Inventory	(6,554)	(1,672)
Accounts payable	4,251	(2,175)
Accrued and other current liabilities	13,075	(3,220)
Deferred revenue - Product revenues		(2,332)
Deferred revenue - Collaborative agreements	(50,219)	(50,209)
Net cash provided by (used in) operating activities	20,869	(72,822)
Cash flows from investing activities:
Capital expenditures	(2,236)	(1,909)
Purchases of marketable securities	(15,024)
Sales and maturities of marketable securities	(203)	421
Net cash used in investing activities	(17,463)	(1,488)
Cash flows from financing activities:
Proceeds from issuance of common stock under stock plans	55,921	40,229
Cash paid in connection with exchange of 4.75% convertible senior notes due 2015	(11,262)
Net cash provided by financing activities	44,659	40,229
Net increase (decrease) in cash and cash equivalents	48,065	(34,081)
Cash and cash equivalents at beginning of period	224,057	273,164
Cash and cash equivalents at end of period	272,122	239,083
Supplemental Schedule of Cash Flow Information
Interest paid	9,500	9,500
Income taxes paid	140	1
Non-cash reclassification to additional paid in capital in connection with conversion/exchange of debt instruments			$ 9,373	$ 149,915