Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2014	Mar. 31, 2013
Cash flows from operating activities:
Net loss	$ (13,665)	$ (27,170)
Adjustments for non-cash operating items:
Amortization of deferred revenue	(4,233)	(8,465)
Stock-based compensation	9,661	8,296
Amortization of debt discount and debt issuance costs	3,532	3,190
Depreciation on property and equipment	1,064	678
Accretion of discount on securities		(66)
Loss on disposal of equipment		35
Changes in operating assets and liabilities:
Receivable from collaboration partner	13,959	(4,684)
Prepaid expenses and other current assets	3,121	(1,548)
Other non-current assets	(4,806)	(173)
Accounts payable, accrued expenses and other current liabilities	(2,687)	2,862
Interest payable	1,698	1,698
Other non-current liabilities	(255)	140
Net cash provided by (used in) operating activities	7,389	(25,207)
Cash flows from investing activities:
Purchases of short-term investments		(59,969)
Maturities of short-term investments		125,000
Change in restricted cash	(2,073)
Purchases of property and equipment	(1,645)	(1,424)
Net cash (used in) provided by investing activities	(3,718)	63,607
Cash flows from financing activities:
Proceeds from issuance of common stock under equity incentive and stock purchase plans	9,010	1,823
Net cash provided by financing activities	9,010	1,823
Net increase in cash and cash equivalents	12,681	40,223
Cash and cash equivalents at beginning of period	228,788	71,301
Cash and cash equivalents at end of period	241,469	111,524
Non-cash investing activities:
Property and equipment expenditures incurred but not yet paid	$ 385	$ 2,499