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Condensed Consolidated Statements of Cash Flows (USD $)
In Thousands, unless otherwise specified
 3 Months Ended
Mar. 31, 2014
Mar. 31, 2013
Cash flows from operating activities:    
Net loss $ (46,201) $ (55,063)
Adjustments to reconcile net loss to net cash used in operating activities:    
Non-cash royalty revenue related to sale of future royalties (5,773) (4,393)
Non-cash interest expense on liability related to sale of future royalties 5,387 5,543
Stock-based compensation 4,361 4,245
Depreciation and amortization 3,264 3,628
Other non-cash transactions 777 139
Changes in operating assets and liabilities:    
Accounts receivable, net 374 2,158
Inventory 580 (112)
Other assets (718) 3,844
Accounts payable (6,126) 1,355
Accrued compensation (4,827) 179
Accrued expenses 693 (1,130)
Accrued clinical trial expenses (3,179) 6,532
Interest payable (3,750) (3,916)
Deferred revenue (5,957) 2,710
Other liabilities (1,195) (3,830)
Net cash used in operating activities (62,290) (38,111)
Cash flows from investing activities:    
Maturities of investments 56,972 100,338
Purchases of investments (110,661) (56,336)
Purchases of property and equipment (4,524) (316)
Net cash (used in) provided by investing activities (58,213) 43,686
Cash flows from financing activities:    
Payment of capital lease obligations (825) (692)
Repayment of proceeds from sale of future royalties (7,000) (3,000)
Issuance of common stock, net of issuance costs 116,619  
Proceeds from shares issued under equity compensation plans 5,074 1,218
Net cash provided by (used in) financing activities 113,868 (2,474)
Effect of exchange rates on cash and cash equivalents 11 (7)
Net (decrease) increase in cash and cash equivalents (6,624) 3,094
Cash and cash equivalents at beginning of period 39,067 25,437
Cash and cash equivalents at end of period 32,443 28,531
Supplemental disclosure of cash flow information:    
Cash paid for interest $ 7,961 $ 8,250