Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013
Cash flows from operating activities:
Net income (loss)	$ 112,247	$ (45,381)
Adjustments for non-cash operating items:
Stock-based compensation	32,799	25,628
Amortization of deferred revenue	(12,698)	(21,163)
Amortization of debt discount and debt issuance costs	11,007	9,941
Depreciation on property and equipment	3,603	2,474
Asset impairment and other charges	1,112	35
Excess tax benefits from stock-based compensation	(362)
Accretion of discount on securities		(148)
Changes in operating assets and liabilities:
Receivable from collaboration partner	(100,880)	(32,126)
Prepaid expenses and other current assets	3,599	(6,567)
Other non-current assets	(4,289)	(1,468)
Accounts payable, accrued expenses and other current liabilities	28,460	14,484
Interest payable	1,698	1,698
Other non-current liabilities	16	(239)
Net cash provided by (used in) operating activities	76,312	(52,832)
Cash flows from investing activities:
Purchases of property and equipment	(9,223)	(6,321)
Change in restricted cash	(2,073)	(713)
Purchases of short-term investments		(144,926)
Maturities of short-term investments		285,000
Net cash (used in) provided by investing activities	(11,296)	133,040
Cash flows from financing activities:
Proceeds from issuance of common stock under equity incentive and stock purchase plans	26,891	6,459
Excess tax benefits from stock-based compensation	362
Repayment of Convertible Notes	(4)
Net cash provided by financing activities	27,249	6,459
Net increase in cash and cash equivalents	92,265	86,667
Cash and cash equivalents at beginning of period	228,788	71,301
Cash and cash equivalents at end of period	321,053	157,968
Non-cash investing and financing activities:
Amounts capitalized under build-to-suit lease transactions	18,085
Interest capitalized during construction period for build-to-suit lease transactions	945
Property and equipment expenditures incurred but not yet paid	$ 355	$ 23