Summary of Significant Accounting Policies (Tables)

3 Months Ended

Mar. 31, 2014

Common Shares Excluded from the Calculation of Net Loss Per Common Share

The following table sets forth for the period presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:

	At March 31,
	2014		2013
Options to purchase common stock		8,185		8,568
Unvested restricted common stock		10		604
Other		378		—
		8,573		9,172

Fair Value Measured on Recurring Basis

Financial assets measured at fair value on a recurring basis are summarized as follows, in thousands:

Description	At March 31, 2014		Quoted Prices in Active Markets (Level 1)		Significant Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	344,211	$	342,208	$	2,003	$	—
Marketable securities (fixed income):
Corporate notes		512,081		—		512,081		—
U.S. Government obligations		65,930		—		65,930		—
Commercial paper		71,915		—		71,915		—
Marketable securities (Regulus equity holdings)		55,478		55,478		—		—
Total	$	1,049,615	$	397,686	$	651,929	$	—
Description	At December 31, 2013		Quoted Prices in Active Markets (Level 1)		Significant Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	32,571	$	32,571	$	—	$	—
Marketable securities (fixed income):
Corporate notes		228,462		—		228,462		—
U.S. Government obligations		56,863		—		56,863		—
Commercial paper		11,978		—		11,978		—
Marketable securities (Regulus equity holdings)		45,452		45,452		—		—
Total	$	375,326	$	78,023	$	297,303	$	—

Summary of Fair Value Accumulated Other Comprehensive Income and Intraperiod Tax Allocation in Available-for-Sale Marketable Securities

The following table summarizes the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding our investment in Regulus available-for-sale marketable securities at March 31, 2014 and 2013 and the activity for the three months ended March 31, 2014 and 2013, in thousands:

Description	At December 31, 2013			Three Months Ended March 31, 2014			Balance at March 31, 2014
Carrying value	$	12,449		$	—		$	12,449
Accumulated other comprehensive income, before tax		33,003			10,026			43,029
Investment in equity securities of Regulus, as reported	$	45,452		$	10,026		$	55,478
Accumulated other comprehensive income, before tax	$	33,003		$	10,026		$	43,029
Intraperiod tax allocation recorded as a benefit from income taxes		(13,267	)		(2,699	)		(15,966	)
Intraperiod tax allocation recorded as an accrued liability		—			(1,380	)		(1,380	)
Accumulated other comprehensive income, net of tax	$	19,736		$	5,947		$	25,683
Description	At December 31, 2012			Three Months Ended March 31, 2013			Balance at March 31, 2013
Carrying value	$	12,449		$	—		$	12,449
Accumulated other comprehensive income, before tax		26,299			8,918			35,217
Investment in equity securities of Regulus, as reported	$	38,748		$	8,918		$	47,666
Accumulated other comprehensive income, before tax	$	26,299		$	8,918		$	35,217
Intraperiod tax allocation recorded as a benefit from income taxes		(10,572	)		(562	)		(11,134	)
Intraperiod tax allocation recorded as an accrued liability		—			(3,023	)		(3,023	)
Accumulated other comprehensive income, net of tax	$	15,727		$	5,333		$	21,060

Summary of Company's Marketable Securities

The following tables summarize our marketable securities, other than our holdings in Regulus noted above, at March 31, 2014 and December 31, 2013, in thousands:

	At March 31, 2014
Description	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Commercial paper (Due within 1 year)	$	71,940	$	—	$	(25	)	$	71,915
Corporate notes (Due within 1 year)		223,039		49		(137	)		222,951
Corporate notes (Due after 1 year through 2 years)		289,659		32		(561	)		289,130
U.S. Government obligations (Due within 1 year)		20,024		11		—			20,035
U.S. Government obligations (Due after 1 year through 2 years)		45,916		7		(28	)		45,895
Total	$	650,578	$	99	$	(751	)	$	649,926
	At December 31, 2013
Description	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Commercial paper (Due within 1 year)	$	11,983	$	—	$	(5	)	$	11,978
Corporate notes (Due within 1 year)		154,175		33		(46	)		154,162
Corporate notes (Due after 1 year through 2 years)		74,312		23		(35	)		74,300
U.S. Government obligations (Due within 1 year)		26,553		8		—			26,561
U.S. Government obligations (Due after 1 year through 2 years)		30,300		2		—			30,302
Total	$	297,323	$	66	$	(86	)	$	297,303