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Condensed Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
 9 Months Ended
Sep. 30, 2016
Sep. 30, 2015
CASH FLOWS FROM OPERATING ACTIVITIES:    
Net income (loss) $ 71,690 $ (91,426)
Adjustments to reconcile net income (loss) to net cash used in operating activities:    
Depreciation and accretion 3,097 10,094
Stock-based compensation expense 4,130 6,378
Loss on disposal of property and equipment   27
Interest on note payable to our principal stockholder 2,172 2,193
Loss on foreign currency exchange 3,035  
Warrant fair value adjustment (7,879)  
Series A Warrant issuance costs included in financing 653  
Loss on extinguishment of debt   1,049
Interest incurred through borrowings under Sanofi Loan Facility 4,125 798
Other, net 717 (5)
Changes in operating assets and liabilities:    
Accounts receivable (3,114) 48,757
Inventory (5,124) (13,732)
Deferred costs from collaboration 13,539 (13,539)
Deferred costs from commercial product sales (279)  
Prepaid expenses and other current assets (516) 6,979
Other assets 307 (672)
Accounts payable (10,288) (2,698)
Accrued expenses and other current liabilities 6,575 (5,922)
Deferred sales from collaboration (17,503) 17,038
Deferred payment from collaboration (135,056)  
Deferred revenue 2,014  
Recognized loss on purchase commitments 2,367  
Net cash used in operating activities (65,338) (34,681)
CASH FLOWS FROM INVESTING ACTIVITIES:    
Purchase of property and equipment (1,144) (9,969)
Proceeds from sale of property and equipment 17 78
Net cash used in investing activities (1,127) (9,891)
CASH FLOWS FROM FINANCING ACTIVITIES:    
Proceeds from issuance of common stock 772 13,524
Proceeds from direct placement 50,000  
Issuance costs associated with direct placement (2,690)  
Payment of 2015 notes   (64,287)
Principal payments on notes payable to Deerfield (5,000)  
Payment of debt issuance costs on 2018 notes   (831)
Milestone payment   (4,219)
Other   40
Proceeds from issuance of common stock pursuant to at-the-market issuance   14,536
Issuance costs of at-the-market issuance   (271)
Payment of employment taxes related to vested restricted stock units (161) (1,833)
Net cash provided by (used in) financing activities 42,921 (43,341)
NET DECREASE IN CASH AND CASH EQUIVALENTS (23,544) (87,913)
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 59,074 120,841
CASH AND CASH EQUIVALENTS, END OF PERIOD 35,530 32,928
SUPPLEMENTAL CASH FLOWS DISCLOSURES:    
Interest paid in cash, net of amounts capitalized 7,198 11,439
Payment of 2015 Notes and interest through issuance of common stock   8,253
Reclassification of deferred payments from collaboration to Sanofi loan facility and loss share obligation $ 4,713 28,150
Cost incurred for construction in progress included in accounts payable and accrued liabilities   $ 192