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Condensed Consolidated Statements of Cash Flows (USD $)
In Thousands, unless otherwise specified
 9 Months Ended 283 Months Ended
Sep. 30, 2014
Sep. 30, 2013
Sep. 30, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:      
Net loss $ (161,941) $ (137,907) $ (2,458,343)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:      
Depreciation and accretion 15,574 10,109 156,408
Stock-based compensation expense 46,755 31,304 229,859
Stock expense for shares issued pursuant to research agreement     3,018
(Gain) loss on sale, abandonment/disposal or impairment of property and equipment   686 25,070
Accrued interest on investments, net of amortization of discounts     (191)
In-process research and development     19,726
Goodwill impairment     151,428
Loss on available-for-sale securities     990
Write-off of derivative liability (363)   (363)
Litigation settlement in stock     6,494
Fair value of forward purchase contract     1,237
Interest expense related to milestone payment 1,850   1,850
Other, net (7) (3) 1,094
Changes in assets and liabilities:      
State research and development credit exchange receivable (765) 242 (1,062)
Prepaid expenses and other current assets (14,768) (708) (18,303)
Other assets (130)   (360)
Accounts payable 13,692 (1,929) 17,039
Accrued expenses and other current liabilities (3,003) 3,525 35,721
Deferred up-front payment from collaboration agreement 150,000   150,000
Other liabilities 2,186   2,775
Net cash provided by (used in) operating activities 39,830 (94,681) (1,685,163)
CASH FLOWS FROM INVESTING ACTIVITIES:      
Purchase of marketable securities     (796,779)
Sales and maturities of marketable securities     796,393
Purchase of property and equipment (19,134) (1,821) (354,867)
Proceeds from sale of property and equipment     454
Net cash used in investing activities (9,884) (1,821) (345,549)
CASH FLOWS FROM FINANCING ACTIVITIES:      
Issuance of common stock and warrants, net of issuance costs 38,573 51,658 1,582,897
Collection of Series C convertible preferred stock subscriptions receivable     50,000
Issuance of Series B convertible preferred stock for cash     15,000
Cash received for common stock to be issued     3,900
Repurchase of common stock     (1,028)
Put shares sold to majority stockholder     623
Borrowings under lines of credit     4,220
Payment of 2013 notes     (115,000)
Proceeds from notes receivables     1,742
Proceeds from issuance of facility financing obligation & milestone rights 40,000 79,500 159,500
Proceeds from issuance of Tranche B of the facility financing obligation 20,000   20,000
Facility financing obligation & milestone rights issuance costs   (598) (598)
Borrowings on notes payable to principal stockholder     387,750
Principal payments on notes payable to principal stockholder     (70,000)
Borrowings on notes payable     3,460
Principal payments on notes payable     (1,667)
Proceeds from senior convertible notes     207,050
Payment of employment taxes related to vested restricted stock units (26,844) (2,095) (44,672)
Net cash provided by financing activities 71,729 128,465 2,203,177
NET INCREASE IN CASH AND CASH EQUIVALENTS 101,675 31,963 172,465
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 70,790 61,840  
CASH AND CASH EQUIVALENTS, END OF PERIOD 172,465 93,803 172,465
SUPPLEMENTAL CASH FLOWS DISCLOSURES:      
Cash paid for income taxes     26
Interest paid in cash, net of amounts capitalized 9,740 7,862 82,344
Accretion on redeemable convertible preferred stock     (952)
Issuance of common stock upon conversion of notes payable     3,331
Increase in additional paid-in capital resulting from merger     171,154
Issuance of common stock for notes receivable     2,758
Issuance of common stock pursuant to conversion of facility financing obligation 93,500   100,000
Issuance of put option by stockholder     (2,949)
Put option redemption by stockholder     1,921
Issuance of Series C convertible preferred stock subscriptions     50,000
Issuance of Series A redeemable convertible preferred stock     4,296
Conversion of Series A redeemable convertible preferred stock     (5,248)
Non-cash construction in progress and property and equipment 3,809 5,523 3,089
Capitalization of interest on note payable to principal stockholder     22,105
Reduction of principal on note payable to principal stockholder upon issuance of common stock and exercise of warrants     290,334
Forward purchase contract contribution to APIC     29,317
Reclassification of forward purchase contract to APIC     28,080
Reclassification of share-based awards to liability 22,963   22,963
Tranche B Commitment Asset 1,753   1,753
Intellectual property
      
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:      
Income from sale of intellectual property (9,250)   (9,250)
CASH FLOWS FROM INVESTING ACTIVITIES:      
Proceeds from sale of intellectual property $ 9,250   $ 9,250