Income Taxes (Tables)

12 Months Ended

Dec. 31, 2015

Income Tax Disclosure [Abstract]

Loss Before Provision (Benefit) for Income Taxes

Loss before provision (benefit) for income taxes includes the following components (in thousands):

	Year Ended December 31,
	2015			2014			2013
Domestic	$	(81,931	)	$	(56,414	)	$	(161,068	)
Foreign		1,260			1,986			1,300
Loss before provision (benefit) for income taxes	$	(80,671	)	$	(54,428	)	$	(159,768	)

Provision (Benefit) for Income Taxes

The provision (benefit) for income taxes consists of the following (in thousands):

	Year Ended December 31,
	2015			2014			2013
Current:
Federal	$	—		$	—		$	—
State		(1	)		1			1
Foreign		529			(482	)		1,838
Total Current		528			(481	)		1,839
Deferred:
Federal		—			—			422
State		—			—			49
Foreign		(22	)		(31	)		(65	)
Total Deferred		(22	)		(31	)		406
Provision (benefit) for income taxes	$	506		$	(512	)	$	2,245

Income Tax Provision Related to Continuing Operations

Income tax provision related to continuing operations differs from the amount computed by applying the statutory income tax rate of 35% to pretax loss as follows (in thousands):

	Year Ended December 31,
	2015			2014			2013
U.S. federal provision (benefit)
At statutory rate	$	(28,235	)	$	(19,050	)	$	(55,919	)
State taxes		(1	)		1			50
Change in valuation allowance		22,210			11,831			55,042
Non-cash interest expense on liability related to sale of    future royalties		7,217			7,311			7,808
Stock-based compensation		674			2,832			271
Foreign tax inclusion		1,773			—			—
Foreign tax differential		(7	)		(17	)		(20	)
Research credits		(4,529	)		(2,933	)		(6,273	)
Other		1,404			(487	)		1,286
Provision (benefit) for income taxes	$	506		$	(512	)	$	2,245

Significant Components of Deferred Tax Assets and Liabilities

Significant components of our deferred tax assets for federal and state income taxes are as follows (in thousands):

	December 31,
	2015			2014
Deferred tax assets:
Net operating loss carryforwards	$	447,761		$	423,776
Research and other credits		70,258			66,666
Deferred revenue		29,658			29,758
Stock-based compensation		22,832			21,948
Capitalized research expenses		12,440			14,795
Sale of future royalties		12,319			20,153
Reserves and accruals		8,309			8,288
Property, plant and equipment		6,451			8,264
Other		3,158			2,218
Deferred tax assets before valuation allowance		613,186			595,866
Valuation allowance for deferred tax assets		(612,996	)		(595,690	)
Total deferred tax assets		190			176
Total deferred tax liabilities		—			—
Net deferred tax assets	$	190		$	176

Unrecognized Tax Benefits

We have the following activity relating to unrecognized tax benefits (in thousands):

	December 31,
	2015			2014			2013
Beginning balance	$	27,522		$	16,363		$	14,067
Tax positions related to current year
Additions:
Federal		529			502			477
State		443			6,141			381
Reductions		—			—			—
Tax positions related to prior year
Additions:
Federal		—			—			636
State		—			5,258			—
Foreign		—			—			802
Reductions		(11,110	)		(742	)		—
Settlements		—			—			—
Lapses in statute of limitations		—			—			—
Ending balance	$	17,384		$	27,522		$	16,363