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Condensed Consolidated Statements of Cash Flows (USD $)
In Thousands, unless otherwise specified
 6 Months Ended
Jun. 30, 2014
Jun. 30, 2013
Cash flows from operating activities:    
Net loss $ (78,838) $ (97,811)
Adjustments to reconcile net loss to net cash used in operating activities:    
Non-cash royalty revenue related to sale of future royalties (10,610) (8,221)
Non-cash interest expense on liability related to sale of future royalties 10,521 11,028
Stock-based compensation 8,525 8,601
Depreciation and amortization 6,519 7,281
Other non-cash transactions 865 159
Changes in operating assets and liabilities:    
Accounts receivable, net (818) (236)
Inventory (659) (2,210)
Other assets 738 5,508
Accounts payable (1,818) 2,631
Accrued compensation (2,868) 2,314
Accrued expenses (314) 3,280
Accrued clinical trial expenses (3,697) (565)
Interest payable 0 (166)
Deferred revenue 7,636 (2,818)
Other liabilities (6,557) (1,223)
Net cash used in operating activities (71,375) (72,448)
Cash flows from investing activities:    
Maturities of investments 118,777 200,477
Purchases of investments (166,496) (109,400)
Purchases of property and equipment (5,192) (794)
Net cash (used in) provided by investing activities (52,911) 90,283
Cash flows from financing activities:    
Payment of capital lease obligations (1,650) (1,466)
Repayment of proceeds from sale of future royalties (7,000) (3,000)
Issuance of common stock, net of issuance costs 116,601 0
Proceeds from shares issued under equity compensation plans 7,961 2,621
Net cash provided by (used in) financing activities 115,912 (1,845)
Effect of exchange rates on cash and cash equivalents 6 5
Net (decrease) increase in cash and cash equivalents (8,368) 15,995
Cash and cash equivalents at beginning of period 39,067 25,437
Cash and cash equivalents at end of period 30,699 41,432
Supplemental disclosure of cash flow information:    
Cash paid for interest $ 8,622 $ 9,070