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Consolidated Statements of Operations (USD $)
In Thousands, except Per Share data, unless otherwise specified
 12 Months Ended
Dec. 31, 2013
Dec. 31, 2012
Dec. 31, 2011
Revenue:      
Product sales $ 44,846 $ 35,399 $ 24,864
Royalty revenue 1,148 4,874 10,327
Non-cash royalty revenue related to sale of future royalties 22,055 10,791  
License, collaboration and other revenue 80,872 30,127 36,289
Total revenue 148,921 81,191 71,480
Operating costs and expenses:      
Cost of goods sold 38,509 30,428 21,891
Research and development 190,010 148,675 126,766
General and administrative 40,532 41,614 46,760
Impairment of long-lived assets    1,675   
Total operating costs and expenses 269,051 222,392 195,417
Loss from operations (120,130) (141,201) (123,937)
Non-operating income (expense):      
Interest income 732 2,315 2,244
Interest expense (18,453) (15,489) (10,223)
Non-cash interest expense on liability related to sale of future royalties (22,309) (18,057)  
Other income (expense), net 392 983 (1,044)
Total non-operating expense, net (39,638) (30,248) (9,023)
Loss before provision for income taxes (159,768) (171,449) (132,960)
Provision for income taxes 2,245 406 1,018
Net loss $ (162,013) $ (171,855) $ (133,978)
Basic and diluted net loss per share $ (1.40) $ (1.50) $ (1.19)
Weighted average shares outstanding used in computing basic and diluted net loss per share 115,732 114,820 112,942