Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012
Cash flows from operating activities:
Net loss	$ (34,328)	$ (38,433)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation of property and equipment	976	666
Loss on disposal of property and equipment	91
Stock-based compensation	5,660	4,024
Amortization of deferred license fees	(3,108)	(3,108)
Warrant licensing expense		152
Restricted stock licensing expense		1,000
Amortization of premium on short-term investments	458	359
Changes in assets and liabilities:
Prepaid expenses and other current assets	(311)	(218)
Accounts payable	(3,047)	265
Accrued expenses	3,013	1,483
Lease incentive obligation	871
Accrued interest	16	15
Net cash used in operating activities	(29,709)	(33,795)
Cash flows from investing activities:
Purchases of marketable securities	(89,261)	(90,408)
Maturities of marketable securities	45,488	41,823
Purchases of property and equipment	(4,413)	(586)
Net cash used in investing activities	(48,186)	(49,171)
Cash flows from financing activities:
Proceeds from sale of common stock, net of issuance costs	73,296	57,755
Proceeds from exercise of common stock options and stock purchase plan	1,212	2,090
Payments on capital lease obligations	(248)
Net cash provided by financing activities	74,260	59,845
Net increase (decrease) in cash and cash equivalents	(3,635)	(23,121)
Cash and cash equivalents, beginning of period	13,345	35,781
Cash and cash equivalents, end of period	9,710	12,660
Supplemental disclosure of non-cash investing and financing activities:
Unrealized gain (loss) on available-for-sale investments	40	106
Issuance of 30,534 and 32,872 shares of common stock to fund the Company's 401(k) matching contribution for 2012 and 2011, respectively	354	274
Conversion of accrued expenses into 34,442 and 34,336 shares of common stock in connection with the Company's Employee Stock Purchase Plan for 2013 and 2012, respectively.	261	194
Laboratory equipment acquired with a capital lease		$ 1,151