Income Taxes (Tables)

12 Months Ended

Dec. 31, 2011

Income Taxes

Schedule of provision for taxes on earnings from continuing operations

	Year Ended December 31,
	2011		2010
Current:
Federal	$	—	$	(73	)
State	11		165
	11		92
Deferred:
Federal	—		—
State	—		—
Foreign	—		—
	—		—
Income Tax Expense	$	11	$	92

Schedule of reconciliation between effective tax rate on income from continuing operations and the statutory tax rate

	Year Ended December 31,
	2011					2010					2009
Pre tax income	$	(84,790	)			$	(61,251	)			$	(31,765	)
Statutory rate	(29,677		)	35.0	%	(21,438		)	35.0	%	(11,118		)	35.0	%
State income tax net of federal benefit	(4,870		)	5.7	%	(3,518		)	5.7	%	(1,825		)	5.7	%
Net change in federal valuation allowance	41,136			(48.5	)%	26,869			(43.9	)%	12,275			(38.6	)%
Tax credits	(4,202		)	5.0	%	(3,175		)	5.2	%	3,401			(10.7	)%
Expired NOL’s	—			—		—			—		(879		)	2.8	%
Noncontrolling interest	1,448			(1.7	)%	908			(1.5	)%	3,562			(11.2	)%
Deferred tax true-up	(4,236		)	5.0	%	—			—		—			—
Other	412			(0.5	)%	446			(0.7	)%	(2,225		)	7.0	%
Effective rate	$	11		(0.1	)%	$	92		(0.2	)%	3,191			(10.0	)%

Schedule of significant components of deferred tax assets and liabilities

	Year Ended December 31,
	2011			2010
Deferred Tax Assets:
Net operating loss carryovers	$	195,399		$	148,688
R&D credits	44,970			38,989
Capitalized R&D	23,212			26,932
Deferred revenue	20,541			38,409
Accrued restructuring	10,888			10,888
Other	25,606			19,396
Total deferred tax assets	$	320,616		$	283,302
Deferred Tax Liabilities:
Convertible debt	$	(9,426	)	$	(12,275	)
Intangible and capital assets	(3,702		)	(5,156		)
Net deferred tax asset	$	307,488		$	265,871
Valuation allowance	(307,488		)	(265,871		)
Net deferreds	$	—		$	—

Summary of the gross amounts of unrecognized tax benefits

Unrecognized tax benefits balance at January 1, 2011	$	8,968
Decrease for prior period tax positions	(97		)
Increase for current period tax positions	963
Unrecognized tax benefits balance at December 31, 2011	$	9,834