Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Cash flows from operating activities:
Net income (loss)	$ 34,254	$ (32,068)
Adjustments for non-cash operating items:
Stock-based compensation	20,842	16,427
Amortization of deferred revenue	(8,465)	(16,931)
Amortization of debt discount and debt issuance costs	7,170	6,474
Depreciation on property and equipment	2,193	1,554
Accretion of discount on securities		(112)
Loss on disposal of equipment		35
Changes in operating assets and liabilities:
Receivable from collaboration partner	7,272	(28,861)
Prepaid expenses and other current assets	1,768	(3,733)
Other non-current assets	(4,847)	(1,383)
Accounts payable, accrued expenses and other current liabilities	(3,647)	10,405
Other non-current liabilities	(1)	(137)
Net cash provided by (used in) operating activities	56,539	(48,330)
Cash flows from investing activities:
Purchases of property and equipment	(4,506)	(4,651)
Change in restricted cash	(2,073)	(1,056)
Purchases of short-term investments		(144,926)
Maturities of short-term investments		225,000
Net cash (used in) provided by investing activities	(6,579)	74,367
Cash flows from financing activities:
Proceeds from issuance of common stock under equity incentive and stock purchase plans	11,289	3,649
Repayment of Convertible Notes	(1)
Net cash provided by financing activities	11,288	3,649
Net increase in cash and cash equivalents	61,248	29,686
Cash and cash equivalents at beginning of period	228,788	71,301
Cash and cash equivalents at end of period	290,036	100,987
Non-cash investing and financing activities:
Amounts capitalized under build-to-suit transactions	16,800
Interest capitalized during construction period for build-to-suit transactions	450
Property and equipment expenditures incurred but not yet paid	$ 3,082