Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2015	Mar. 31, 2014
Cash flows from operating activities:
Net loss	$ (3,118)	$ (13,665)
Adjustments for non-cash operating items:
Stock-based compensation	13,372	9,661
Change in fair value of contingent purchase consideration	4,000
Amortization of debt discount and debt issuance costs	3,910	3,532
Depreciation on property and equipment	1,531	1,064
Amortization of deferred revenue	(1,411)	(4,233)
Change in deferred income taxes	(1,402)
Asset impairment and other charges	73
Changes in operating assets and liabilities:
Receivable from collaboration partner	58,124	13,959
Prepaid expenses and other current assets	(520)	3,121
Other non-current assets	(1,335)	(4,806)
Accounts payable, accrued expenses and other current liabilities	(17,587)	(2,687)
Interest payable	1,698	1,698
Other non-current liabilities	(113)	(255)
Net cash provided by operating activities	57,222	7,389
Cash flows from investing activities:
Change in restricted cash	(1,574)	(2,073)
Purchases of property and equipment	(956)	(1,645)
Net cash used in investing activities	(2,530)	(3,718)
Cash flows from financing activities:
Proceeds from issuance of common stock under equity incentive and stock purchase plans	11,502	9,010
Reduction of build-to-suit lease obligation	(227)
Repayment of Convertible Notes	(8)
Net cash provided by financing activities	11,267	9,010
Net increase in cash and cash equivalents	65,959	12,681
Cash and cash equivalents at beginning of period	502,677	228,788
Cash and cash equivalents at end of period	568,636	241,469
Non-cash investing activities:
Interest capitalized during construction period for build-to-suit lease transactions	527
Property and equipment expenditures incurred but not yet paid	$ 918	$ 385