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Condensed Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
 6 Months Ended
Jun. 30, 2016
Jun. 30, 2015
CASH FLOWS FROM OPERATING ACTIVITIES:    
Net loss $ (54,831) $ (59,569)
Adjustments to reconcile net loss to net cash provided by (used) in operating activities:    
Depreciation and accretion 2,058 6,359
Stock-based compensation expense 2,628 3,778
Interest incurred through borrowings under Sanofi Loan Facility 2,604 265
Loss on disposal of property and equipment   12
Loss on foreign currency exchange 2,023  
Warrant fair value adjustment 5,306  
Warrant issuance cost 653  
Interest on note payable to principal stockholder 1,443 1,435
Other, net 717 (6)
Changes in assets and liabilities:    
Inventory (2,866) (10,146)
Receivables from Collaboration 23 45,688
Prepaid expenses and other current assets 2,595 6,130
Deferred costs from collaboration   (10,831)
Other assets (238) (866)
Accounts payable (12,532) (2,236)
Accrued expenses and other current liabilities 2,663 (7,800)
Deferred sales from collaboration 177 12,968
Deferred payment from collaboration 9,202  
Purchase commitment loss - current 8,312  
Non-current purchase commitment loss (12,204)  
Other liabilities   30
Net cash used in operating activities (42,267) (14,789)
CASH FLOWS FROM INVESTING ACTIVITIES:    
Purchase of property and equipment (1,144) (8,737)
Proceeds from sale of property and equipment 17  
Net cash used in investing activities (1,127) (8,737)
CASH FLOWS FROM FINANCING ACTIVITIES:    
Proceeds from issuance of common stock 734 12,820
Proceeds from direct placement 50,000  
Issuance costs associated with the direct placement (2,678)  
Milestone payment   (4,220)
Other   40
Proceeds from issuance of common stock pursuant to ATM issuance   2,050
Payment of employment taxes related to vested restricted stock units (3) (818)
Net cash provided by financing activities 48,053 9,872
NET INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS 4,659 (13,654)
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 59,074 120,841
CASH AND CASH EQUIVALENTS, END OF PERIOD 63,733 107,187
SUPPLEMENTAL CASH FLOWS DISCLOSURES:    
Interest paid in cash, net of amounts capitalized 4,608 6,644
Non-cash construction in progress and property and equipment   $ 623
Reclassification of deferred payments from collaboration to Sanofi Loan Facility and loss share obligation 5,003  
Reclassification of deferred costs from loss on purchase commitment to deferred costs from collaboration $ 9,202