Income Taxes (Tables)

12 Months Ended

Dec. 31, 2016

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,
	2016		2015			2014
Current:
Federal	$	1,067	$	379		$	263
State		1,867		(7	)		(4,295	)
Total current		2,934		372			(4,032	)
Deferred:
Federal		—		—			(8,948	)
State		—		—			(2,427	)
Total deferred		—		—			(11,375	)
Income tax expense (benefit)	$	2,934	$	372		$	(15,407	)

Reconciliation Between Effective and Statutory Tax Rate

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

	Year Ended December 31,
	2016					2015					2014
Pre-tax loss	$	(83,622	)			$	(87,906	)			$	(54,391	)
Statutory rate		(29,268	)	35.0	%		(30,767	)	35.0	%		(19,035	)	35.0	%
State income tax net of federal benefit		(276	)	0.3	%		1		0.0	%		(3,125	)	5.7	%
Net change in valuation allowance		55,927		(66.9	)%		69,499		(79.1	)%		29,547		(54.3	)%
Loss on debt extinguishment		—		0.0	%		—		0.0	%		2,406		(4.4	)%
Tax credits		(26,954	)	32.2	%		(41,284	)	47.0	%		(23,628	)	43.4	%
California franchise tax refund		—		0.0	%		—		0.0	%		(2,795	)	5.1	%
Deferred tax true-up		2,591		(3.1	)%		1,496		(1.7	)%		977		(1.8	)%
Other		914		(1.1	)%		1,427		(1.6	)%		246		(0.5	)%
Effective rate	$	2,934		(3.5	)%	$	372		(0.4	)%	$	(15,407	)	28.2	%

Deferred Tax Assets and Liabilities

Significant components of our deferred tax assets and liabilities as of December 31, 2016 and 2015 are as follows (in thousands):

	Year Ended December 31,
	2016			2015
Deferred Tax Assets:
Net operating loss carryovers	$	194,372		$	218,493
R&D credits		193,845			153,601
Deferred revenue		54,203			45,110
Stock-based compensation		48,209			31,093
Other		26,228			19,655
Total deferred tax assets	$	516,857		$	467,952
Deferred Tax Liabilities:
Convertible debt	$	(62,669	)	$	(55,928	)
Unrealized gain in other comprehensive income		-			(5,288	)
Intangible and capital assets		(2,030	)		(2,643	)
Net deferred tax asset	$	452,158		$	404,093
Valuation allowance		(452,158	)		(404,093	)
Net deferreds	$	—		$	—

Gross Unrecognized Tax Benefits

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

	Year Ended December 31,
	2016			2015		2014
Beginning balance of unrecognized tax benefits	$	51,257		$	27,365	$	23,964
Settlement of prior period tax positions		(4,033	)		—		—
Decrease for prior period tax positions		—			—		(1,653	)
Increase for prior period tax positions		7,928			215		—
Increase for current period tax positions		11,847			23,677		5,054
Ending balance of unrecognized tax benefits	$	66,999		$	51,257	$	27,365