Income Taxes (Tables)

12 Months Ended

Dec. 31, 2013

Income Tax Disclosure [Abstract]

Schedule of Income Tax (Expense) Benefit

Income tax (expense) benefit for the periods presented consisted of the following:

	Years Ended December 31,
	2013			2012			2011
Current:
Federal	$	(7	)	$	(7	)	$	4,309
State		(108	)		—			22
Total current		(115	)		(7	)		4,331
Deferred:
Federal		—			—			—
State		—			—			—
Total deferred		—			—			—
Total income tax (expense) benefit	$	(115	)	$	(7	)	$	4,331

Schedule of Reconciliation of Statutory Federal Income Tax Rate

A reconciliation of the statutory Federal income tax rate of 35% to the Company’s effective income tax rates is as follows:

	Years Ended December 31,
	2013			2012			2011
Federal tax provision at statutory rate		35.00	%		35.00	%		35.00	%
State taxes (net of Federal benefit)		1.43	%		10.81	%		2.27	%
Change in tax reserve		(2.31	%)		(0.06	%)		(0.94	%)
Orphan drug credit		—			0.25	%		(0.70	%)
Stock-based compensation		(0.25	%)		1.50	%		0.06	%
Non-deductible officer compensation		(1.79	%)		(1.86	%)		0.20	%
Change in valuation allowance		(52.09	%)		(45.48	%)		(29.94	%)
Research and development credits		19.37	%		—			7.05	%
Net proceeds from stockholder securities law settlement		—			—			(2.43	%)
Other		0.37	%		(0.19	%)		(0.53	%)
Benefit (provision) for taxes		(0.27	)%		(0.03	%)		10.04	%

Schedule of Company's Deferred Tax Assets

Significant components of the Company’s deferred tax assets for Federal and state income taxes are follows:

	December 31,
	2013			2012
Deferred tax assets:
Deferred revenue	$	6,073		$	15,491
Net operating loss carry forward		80,620			72,232
Stock-based compensation		21,257			12,721
Research and development credits		22,616			13,897
Depreciation, amortization and other		—			109
Accruals and reserves		10,544			6,530
Total deferred tax assets		141,110			120,980
Less: valuation allowance		(120,807	)		(98,671	)
Total net deferred tax assets		20,303			22,309
Deferred tax liabilities
Depreciation, amortization, and other		(2,674	)		—
Convertible Notes		(17,629	)		(22,309	)
Total deferred tax liabilities		(20,303	)		(22,309	)
Net deferred tax assets	$	—		$	—
Recorded as:
Net current deferred tax assets (included in “Prepaid expenses and other current assets”)	$	5,541		$	3,800
Net non-current deferred tax assets		—			—
Net current deferred tax liabilities		—			—
Net non-current deferred tax liabilities (included in “Other non-current liabilities”)		(5,541	)		(3,800	)
Net deferred tax assets	$	—		$	—

Schedule of Gross Unrecognized Tax Positions

The following table summarizes activity related to the Company’s gross unrecognized tax positions:

	December 31,
	2013			2012			2011
Balance as of beginning of year	$	4,602		$	3,936		$	4,128
Additions based on tax positions related to the current year		702			400			500
Additions based on tax position related to prior year		660			270			109
Decreases based on tax positions related to prior year		(9	)		(4	)		(801	)
Balance as of end of year	$	5,955		$	4,602		$	3,936