CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Cash flows from operating activities:
Net loss	$ (106,014)	$ (57,649)	$ (43,515)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	9,035	5,125	4,941
Deferred income taxes			10,742
Non-cash stock-based compensation	12,360	16,676	19,118
Charge for 401(k) company stock match	364	488	495
Equity in loss of joint venture (Regulus Therapeutics Inc.)	4,522	3,505	7,639
Tax benefit from stock-based compensation		120	220
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)		(4,421)
Benefit from intraperiod tax allocation on marketable securities	(10,572)
Changes in operating assets and liabilities:
Proceeds from landlord tenant improvements	1,780
Billed and unbilled collaboration receivables	1,364	1,982	2,594
Income taxes receivable		10,669	(10,669)
Prepaid expenses and other assets	1,780	2,731	(2,738)
Accounts payable	(1,736)	(3,512)	(3,177)
Income taxes payable			(5,516)
Accrued expenses and other	(3,591)	2,457	651
Deferred revenue	(8,562)	(70,255)	(60,705)
Net cash used in operating activities	(115,609)	(87,068)	(84,341)
Cash flows from investing activities:
Purchases of property and equipment	(8,348)	(1,291)	(4,732)
Increase in restricted cash	(162)
Purchases of marketable securities	(277,129)	(293,115)	(390,473)
Sales and maturities of marketable securities	289,013	376,365	413,043
Net cash provided by investing activities	3,374	81,959	17,838
Cash flows from financing activities:
Proceeds from exercise of stock options and other types of equity	6,971	738	2,670
Proceeds from issuance of common stock, net of offering costs	86,800
Payments for repurchase of common stock for employee tax withholding	(359)
Proceeds from issuance of shares to Novartis			993
Net cash provided by financing activities	93,412	738	3,663
Effect of exchange rate on cash			(29)
Net decrease in cash and cash equivalents	(18,823)	(4,371)	(62,869)
Cash and cash equivalents, beginning of period	70,228	74,599	137,468
Cash and cash equivalents, end of period	51,405	70,228	74,599
Supplemental disclosure of cash flows:
(Cash paid for income taxes) proceeds from income tax refunds	(17)	10,657	(5,767)
Supplemental disclosure of noncash investing activities:
Fixed asset expenditures included in accounts payable and accrued expenses	$ 1,441