Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Significant components of the Company's deferred tax assets

	December 31,

(in thousands)	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	411,000		$	359,000
Deferred revenues		4,000			56,000
Capitalized research and development expenditures		35,000			35,000
Research and development tax credit carryforwards		38,000			37,000
Other		33,000			31,000
Valuation allowance		(521,000	)		(518,000	)

Net deferred tax assets	$	—		$	—

Schedule of the differences between the U.S. federal statutory income tax rate to the Company's effective tax rate

	Year Ended December 31,

	2012			2011			2010
U.S. federal statutory income tax rate		34.00	%		34.00	%		34.00	%
State income taxes, net of federal benefit		—			—			5.83
Federal and state research credits		(4.21	)		1.67			2.91
Non-deductible executive compensation		(13.24	)		—			—
Stock-based compensation		(1.36	)		(0.32	)		2.29
Expiration of net operating loss		(1.81	)		(0.42	)		—
Other		(2.09	)		0.75			(0.05	)
Change in valuation allowance		(11.29	)		(35.68	)		(44.98	)

Effective tax rate		(0.00	)%		(0.00	)%		(0.00	)%

Reconciliation of gross unrecognized tax benefits

A reconciliation of the beginning and ending balances of the total amounts of unrecognized tax benefits are as follows (in thousands):


Unrecognized tax benefits as of December 31, 2009	$	39,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		3,000

Unrecognized tax benefits as of December 31, 2010		42,600
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		4,300

Unrecognized tax benefits as of December 31, 2011		46,900
Gross decrease for tax positions for prior years		—
Gross increase in tax positions for current year		5,600

Unrecognized tax benefits as of December 31, 2012	$	52,500

- Definition

Tabular disclosure of tax positions taken in the tax returns filed or to be filed for which it is more likely than not that the tax position will not be sustained upon examination by taxing authorities (i.e., uncertain tax positions) and other types of income tax contingencies, including: (1) the policy on classification of interest and penalties; (2) a tabular reconciliation of the total amounts of unrecognized tax benefits at the beginning and end of the period; the total amount(s) of: (3) unrecognized tax benefits that, if recognized, would affect the effective tax rate, and (4) interest and penalties recognized in each of the income statement and balance sheet; (5) for positions for which it is reasonably possible that the total amounts unrecognized will significantly change within 12 months of the reporting date the: (i) nature of the uncertainty, (ii) nature of the event that could occur that would cause the change, and (iii) an estimate of the range of the reasonably possible change or a statement that an estimate of the range cannot be made; and (6) a description of tax years that remain subject to examination by major tax jurisdictions.

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