Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Cash flows from operating activities
Net loss	$ (147,787)	$ (83,559)	$ (130,685)
Adjustments to reconcile net loss to net cash used in operating activities
Non-cash interest expense	8,217	8,511	4,548
Depreciation and amortization	4,288	3,223	2,589
Stock-based compensation	15,351	13,197	10,733
Purchased premiums and interest on marketable securities		858	(1,809)
Other non-cash items	4		579
Changes in operating assets and liabilities:
Accounts receivable	(3,170)	2,587	3,410
Prepaid expenses and other current assets	(850)	827	4,037
Inventory	(3,717)
Accounts payable, accrued expenses and other	13,557	(646)	13,304
Deferred revenues	6,377	19,482	(4,989)
Deferred rent and tax incentives	2,374	712	2,076
Other assets and liabilities, net			1,032
Net cash (used in) operating activities	(105,356)	(34,808)	(95,175)
Cash flows from investing activities
Purchase of marketable securities		(111,832)	(112,923)
Proceeds from sales and maturities of marketable securities	87,899	111,858	95,100
Purchase of property and equipment	(12,789)	(6,035)	(9,857)
Assignment of restricted cash			(57)
Other investing activities, net		(2)	(2)
Net cash provided by (used in) investing activities	75,110	(6,011)	(27,739)
Cash flows from financing activities
Proceeds from public offerings, net of issuance costs	38,560		26,716
Proceeds from exercise of options and warrants to purchase common stock	10,087	10,384	2,036
Proceeds from issuance of senior secured notes due 2022, net of issuance costs	169,434
Proceeds from issuance of preferred stock by Silver Creek Pharmaceuticals, Inc.	2,083
Proceeds from convertible notes issued by Silver Creek Pharmaceuticals, Inc., net of issuance costs		1,044	121,537
Repayment of loans payable to Hercules Technology Growth Capital, Inc.	(40,000)
Payments of dividends on Series B convertible preferred stock		(7)	(3)
Net cash provided by financing activities	180,164	11,421	150,286
Net increase (decrease) in cash and cash equivalents	149,918	(29,398)	27,372
Cash and cash equivalents, beginning of period	35,688	65,086	37,714
Cash and cash equivalents, end of period	185,606	35,688	65,086
Non-cash investing and financing activities
Issuance of derivative liability			35
Value of conversion feature of convertible senior notes, classified in Stockholders' Deficit			51,876
Property, plant and equipment in accounts payable and accrued expenses	816	704
Receivables related to stock option exercises in prepaid expenses and other current assets	14
Disposals of fully-depreciated property and equipment	303	1,603	210
Reclassification of deferred financing costs to stockholders' deficit			278
Conversion of Silver Creek Pharmaceuticals, Inc. convertible notes		1,044	2,603
Supplemental disclosure of cash flows
Cash paid for interest	$ 10,087	$ 9,510	$ 3,915