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Condensed Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
 9 Months Ended
Sep. 30, 2015
Sep. 30, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:    
Net loss $ (91,426) $ (161,941)
Adjustments to reconcile net loss to net cash (used in) provided by operating activities:    
Depreciation and accretion 10,094 15,574
Stock-based compensation expense 6,378 46,755
Loss on disposal of property and equipment 27  
Loss on extinguishment of debt 1,049  
Interest paid through borrowings under Sanofi Loan Facility 798  
Write off of derivative liability   (363)
Income from sale of intellectual property   (9,250)
Interest expense related to milestone payment   1,850
Other, net (5) (7)
Changes in assets and liabilities:    
Inventory (13,732)  
Receivables from Collaboration 48,757  
Prepaid expenses and other current assets 6,979 (14,768)
Deferred product costs from collaboration (13,539)  
Other assets (672) (895)
Accounts payable (2,698) 13,692
Accrued expenses and other current liabilities (5,922) (3,003)
Deferred product sales from collaboration 17,038  
Deferred up-front payment from collaboration agreement   150,000
Other liabilities 2,193 2,186
Net cash (used in) provided by operating activities (34,681) 39,830
CASH FLOWS FROM INVESTING ACTIVITIES:    
Purchase of property and equipment (9,969) (19,134)
Proceeds from sale of property and equipment 78  
Proceeds from sale of intellectual property   9,250
Net cash used in investing activities (9,891) (9,884)
CASH FLOWS FROM FINANCING ACTIVITIES:    
Proceeds from issuance of common stock and warrants 13,524 38,573
Proceeds from issuance of facility financing obligation & milestone rights   40,000
Proceeds from issuance of Tranche B of the facility financing obligation   20,000
Payment of 2015 notes (64,287)  
Payment of debt issuance costs on 2018 notes (831)  
Milestone payment (4,219)  
Other 40  
Proceeds from issuance of common stock pursuant to ATM issuance 14,536  
Issuance costs of ATM (271)  
Payment of employment taxes related to vested restricted stock units (1,833) (26,844)
Net cash (used in) provided by financing activities (43,341) 71,729
NET (DECREASE) INCREASE IN CASH AND CASH EQUIVALENTS (87,913) 101,675
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 120,841 70,790
CASH AND CASH EQUIVALENTS, END OF PERIOD 32,928 172,465
SUPPLEMENTAL CASH FLOWS DISCLOSURES:    
Interest paid in cash, net of amounts capitalized 11,439 9,740
Issuance of common stock pursuant to conversion of facility financing obligation   93,500
Non-cash construction in progress and property and equipment 192 3,809
Reclassification of share-based awards to liability   22,963
Tranche B Commitment Asset   $ 1,753
Payment of 2015 notes and interest through issuance of common stock 8,253  
Reclassification of deferred payments from collaboration to Sanofi loan facility $ 28,150