INCOME TAXES (Tables)

12 Months Ended

Dec. 31, 2012

Schedule of Deferred Tax Assets and Liabilities

 Components of the net deferred tax (liability) asset at December 31, 2012 and 2011 are as follows, in thousands:

	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	102,819		$	46,230
Research and development credits		17,443			12,405
AMT credits		788			788
Foreign tax credits		3,196			3,196
Capitalized research and development and start-up costs		16,102			3,974
Deferred revenue		30,776			53,485
Deferred compensation		24,804			21,855
Intangible assets		2,540			4,302
Partnership interest		7,118			5,338
Other		4,173			2,850
Total deferred tax assets		209,759			154,423
Deferred tax liabilities:
Intangible assets		(38	)		(91	)
Unrealized gain on available-for-sale securities		(10,572	)		—
Gain on issuance of stock by Regulus		(6,466	)		—
Deferred tax asset valuation allowance		(192,721	)		(154,423	)
Net deferred tax liability	$	(38	)	$	(91	)

Provision for Income Taxes

The (benefit from) provision for income taxes for the years ended December 31, 2012, 2011 and 2010 are as follows, in thousands:

	2012			2011			2010
U.S.:
Current	$	52		$	52		$	(9,928	)
Deferred		(10,572	)		—			10,494
Total U.S.		(10,520	)		52			566
Foreign:
Current		—			—			—
Deferred		(52	)		(52	)		(52	)
Total Foreign		(52	)		(52	)		(52	)
Provision for income taxes	$	(10,572	)	$	—		$	514

Effective Income Tax Rate

The Company’s effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2012, 2011 and 2010:

	2012			2011			2010
At U.S. federal statutory rate		35.0	%		35.0	%		35.0	%
State taxes, net of federal effect		4.9			4.6			4.2
Stock compensation		(0.7	)		(3.3	)		(5.0	)
Other permanent items		(1.6	)		(0.2	)		1.3
Valuation allowance		(28.5	)		(36.1	)		(36.7	)
Effective income tax rate		9.1	%		—	%		(1.2	)%

Reconciliation of Unrecognized Tax Benefits

A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows, in thousands:

Balance at December 31, 2010	$	428
Subtractions for tax positions related to the prior years		(300	)
Balance at December 31, 2011		128
Subtractions for tax positions related to the prior years		(128	)
Balance at December 31, 2012	$	—