Equity Plans and Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2013

Option Activity under Stock-Based Compensation Plans

Activity under our stock plans is set forth below:

	Shares Underlying Outstanding Options (in thousands)			Weighted-Average Exercise Price Per Share (in thousands)		Weighted-Average Remaining Contractual Term (years)		Aggregate Intrinsic Value
Balance at December 31, 2012		13,806		$	3.38
Options granted		5,614			2.69
Options exercised		(131	)		1.43
Options cancelled:
Options forfeited (unvested)		(2,555	)		3.31
Options cancelled (vested)		(969	)		3.34
Balance at December 31, 2013		15,765			3.17		5.26	$	1,427
Vested and expected to vest at December 31, 2013		15,765			3.17		5.26	$	1,427
Exercisable at December 31, 2013		10,628			3.36		3.61	$	1,289

Summary of Restricted Stock Units Activity

Our non-vested stock awards are comprised of restricted stock units granted with performance-based vesting criteria. A summary of the status of non-vested restricted stock units as of December 31, 2013, and activities during 2013 is summarized as follows:

	Number of Shares (In thousands)			Weighted-Average Grant-Date Fair Value
Non-vested as of December 31, 2012		1,755		$	4.23
Granted		250		$	1.23
Vested		(115	)	$	1.10
Forfeited or expired		(615	)	$	4.23
Non-vested as of December 31, 2013		1,275		$	3.93

Fair Value-Based Measurements and Weighted-Average Assumptions

Under our stock-based compensation plans, option awards generally vest over a four-year period contingent upon continuous service and expire ten years from the date of grant (or earlier upon termination of continuous service). The Company has also granted performance-based equity awards to certain of our employees under the 2011 Plan, the 2004 Plan and the Inducement Plan. As of December 31, 2013, 2,047,466 shares were outstanding related to options and restricted stock units subject to these performance-based vesting criteria. The fair value of each option is estimated on the date of grant using the Black-Scholes option valuation model and the following weighted-average assumptions:

	Stock Options									Employee Stock Purchase Plan
	Year Ended December 31,									Year Ended December 31,
	2013			2012			2011			2013			2012			2011
Weighted-average fair value	$	2.41		$	3.30		$	2.76		$	0.93		$	3.54		$	2.09
Risk-free interest rate		1.1	%		0.5	%		1.3	%		0.2	%		0.2	%		0.3	%
Expected life (in years)		5.9			4.2			4.0			1.3			1.1			1.2
Volatility		1.4			1.6			1.6			0.8			1.6			1.6

Stock-Based Compensation Expense

We recognized the following amounts of stock-based compensation expense (in thousands):

	Year Ended December 31,
	2013		2012		2011
Employees and directors stock-based compensation expense	$	11,828	$	10,439	$	5,185
Non-employees stock-based compensation expense		512		-		4
Total	$	12,340	$	10,439	$	5,189

	Year Ended December 31,
	2013		2012		2011
Research and development	$	4,228	$	3,514	$	2,103
General and administrative		8,112		6,925		3,086
Total	$	12,340	$	10,439	$	5,189