Income Taxes (Tables)

12 Months Ended

Dec. 31, 2015

Income Taxes [Abstract]

Provision for Income Taxes

The provisions for income taxes on income from continuing operations were as follows (in thousands):

	Year Ended December 31,
	2015			2014			2013
Current:
Federal	$	379		$	263		$	—
State		(7	)		(4,295	)		2
Total current		372			(4,032	)		2
Deferred:
Federal		—			(8,948	)		(5,082	)
State		—			(2,427	)		(834	)
Total deferred		—			(11,375	)		(5,916	)
Income tax expense (benefit)	$	372		$	(15,407	)	$	(5,914	)

Reconciliation Between Effective and Statutory Tax Rate

The reconciliation between our effective tax rate on income from continuing operations and the statutory U.S. tax rate is as follows (in thousands):

	Year Ended December 31,
	2015					2014					2013
Pre-tax loss	$	(87,906	)			$	(54,391	)			$	(66,558	)
Statutory rate		(30,767	)	35.0	%		(19,035	)	35.0	%		(23,295	)	35.0	%
State income tax net of federal benefit		1		0.0	%		(3,125	)	5.7	%		(3,823	)	5.7	%
Net change in valuation allowance		69,499		(79.1	)%		29,547		(54.3	)%		28,850		(43.3	)%
Loss on debt extinguishment		—		0.0	%		2,406		(4.4	)%		—		0.0	%
Tax credits		(41,284	)	47.0	%		(23,628	)	43.4	%		(15,839	)	23.8	%
California franchise tax refund		—		0.0	%		(2,795	)	5.1	%		—		0.0	%
Deferred tax true-up		1,496		(1.7	)%		977		(1.8	)%		8,023		(12.1	)%
Other		1,427		(1.6	)%		246		(0.5	)%		170		(0.2	)%
Effective rate	$	372		(0.4	)%	$	(15,407	)	28.2	%	$	(5,914	)	8.9	%

Deferred Tax Assets and Liabilities

Significant components of our deferred tax assets and liabilities as of December 31, 2015 and 2014 are as follows (in thousands):

	Year Ended December 31,
	2015			2014
Deferred Tax Assets:
Net operating loss carryovers	$	218,493		$	231,654
R&D credits		153,601			93,594
Deferred revenue		45,110			58,836
Stock-based compensation		31,093			21,553
Other		19,655			15,549
Total deferred tax assets	$	467,952		$	421,186
Deferred Tax Liabilities:
Convertible debt	$	(55,928	)	$	(73,733	)
Unrealized gain in other comprehensive income		(5,288	)		(27,878	)
Intangible and capital assets		(2,643	)		(3,641	)
Net deferred tax asset	$	404,093		$	315,934
Valuation allowance		(404,093	)		(315,934	)
Net deferreds	$	—		$	—

Gross Unrecognized Tax Benefits

The following table summarizes our gross unrecognized tax benefits (in thousands):

	Year Ended December 31,
	2015		2014			2013
Beginning balance of unrecognized tax benefits	$	27,365	$	23,964		$	10,872
Decrease for prior period tax positions		—		(1,653	)		—
Increase for prior period tax positions		215		—			9,821
Increase for current period tax positions		23,677		5,054			3,271
Ending balance of unrecognized tax benefits	$	51,257	$	27,365		$	23,964