Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities:
Net loss	$ (89,225)	$ (106,014)	$ (57,649)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	10,229	9,035	5,125
Non-cash stock-based compensation	20,703	12,360	16,676
Charge for 401(k) company stock match	449	364	488
Equity in loss of joint venture (Regulus Therapeutics Inc.)		4,522	3,505
Tax benefit from stock-based compensation			120
Other than temporary impairment on equity securities			595
Realized gain on sale of marketable securities		(255)
Gain on issuance of stock by joint venture		(16,084)
Benefit from intraperiod tax allocation on marketable securities	(2,695)	(10,572)
Changes in operating assets and liabilities:
Proceeds from landlord tenant improvements	204	1,780
Billed and unbilled collaboration receivables	(4,144)	1,364	1,982
Income taxes receivable			10,669
Prepaid expenses and other assets	(1,356)	1,780	2,731
Accounts payable	1,832	(1,736)	(3,512)
Accrued expenses and other	1,547	(3,591)	2,457
Deferred revenue	(6,201)	(8,562)	(70,255)
Net cash used in operating activities	(68,657)	(115,609)	(87,068)
Cash flows from investing activities:
Purchases of property and equipment	(4,006)	(8,348)	(1,291)
Increase in restricted cash		(162)
Purchases of marketable securities	(364,305)	(277,129)	(293,115)
Sales and maturities of marketable securities	237,806	289,013	376,365
Net cash (used in) provided by investing activities	(130,505)	3,374	81,959
Cash flows from financing activities:
Proceeds from exercise of stock options and other types of equity	28,743	6,971	738
Proceeds from issuance of common stock, net of offering costs	173,572	86,800
Payments for repurchase of common stock for employee tax withholding	(1,389)	(359)
Net cash provided by financing activities	200,926	93,412	738
Net increase (decrease) in cash and cash equivalents	1,764	(18,823)	(4,371)
Cash and cash equivalents, beginning of period	51,405	70,228	74,599
Cash and cash equivalents, end of period	53,169	51,405	70,228
Supplemental disclosure of cash flows:
Cash (paid for income taxes) proceeds from income tax refunds	(11)	(17)	10,657
Supplemental disclosure of noncash investing activities:
Fixed asset expenditures included in accounts payable and accrued expenses	161	1,441
Repurchase of common stock for employee tax withholding in accrued expenses	$ 600