Selected Quarterly Financial Data (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended								12 Months Ended
	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2010	Sep. 30, 2010	Jun. 30, 2010	Mar. 31, 2010	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009
Quarterly Financial Data
Product sales	$ 6,073	$ 7,677	$ 8,641	$ 2,474	$ 10,700	$ 5,485	$ 9,398	$ 1,828	$ 24,864	$ 27,412	$ 30,116
Royalty revenues	3,095	2,545	2,367	2,319	1,999	1,745	1,756	1,756	10,327	7,255	5,172
License, collaboration and other revenue	6,614	16,846	6,323	6,506	32,615	30,695	31,409	29,653	36,289	124,372	36,643
Total revenue	15,782	27,068	17,331	11,299	45,314	37,925	42,563	33,237	71,480	159,039	71,931
Gross profit on product sales	623	2,639	501	(789)	463	(760)	4,509	(2,468)
Research and development expenses	33,302	31,018	32,270	30,176	31,455	27,724	25,600	23,286	126,766	108,065	95,109
General and administrative expenses	11,498	12,350	11,185	11,727	11,585	10,181	10,207	9,013	46,760	40,986	41,006
Impairment of long-lived assets					12,576				0	12,576	0
Total operating costs and expenses	50,250	48,406	51,595	45,166	65,853	44,150	40,696	36,595	195,417	187,294	167,063
Operating (loss) income	(34,468)	(21,338)	(34,264)	(33,867)	(20,539)	(6,225)	1,867	(3,358)	(123,937)	(28,255)	(95,132)
Interest expense	2,525	2,543	2,570	2,585	2,488	2,826	2,909	2,951	(10,223)	(11,174)	(12,176)
Net loss	$ (37,495)	$ (24,068)	$ (36,381)	$ (36,034)	$ (22,580)	$ (8,711)	$ (517)	$ (6,130)	$ (133,978)	$ (37,938)	$ (102,519)
Basic and diluted net loss per share	$ (0.33)	$ (0.21)	$ (0.32)	$ (0.33)	$ (0.24)	$ (0.09)	$ (0.01)	$ (0.07)	$ (1.19)	$ (0.40)	$ (1.11)