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Basic and Diluted Net Loss Per Share
 9 Months Ended
Sep. 30, 2014
Earnings Per Share [Abstract]  
Basic and Diluted Net Loss Per Share
BASIC AND DILUTED NET LOSS PER SHARE
Basic net loss per share is computed by dividing the Company’s net loss by the weighted-average number of common shares outstanding during the period. Diluted net loss per share is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units and common stock warrants. Basic and diluted net loss per share was the same for all periods presented as the inclusion of all potentially dilutive securities outstanding was anti-dilutive.
The following table summarizes the Company’s calculation of basic and diluted net loss per share (in thousands, except share and per share amounts):
 
Three Months Ended September 30,
 
Nine Months Ended September 30,
 
2014
 
2013
 
2014
 
2013
Numerator
 
 
 
 
 
 
 
Net loss
$
(39,677
)
 
$
(30,703
)
 
$
(117,275
)
 
$
(83,053
)
Denominator
 
 
 
 
 
 
 
Weighted-average number of common shares used in net loss per share calculation
78,866,597

 
64,823,095

 
74,716,970

 
62,802,684

Less: Weighted-average shares subject to repurchase
—

 
(11,463
)
 
(686
)
 
(20,016
)
Denominator: basic and diluted
78,866,597

 
64,811,632

 
74,716,284

 
62,782,668

Net loss per share, basic and diluted
$
(0.50
)
 
$
(0.47
)
 
$
(1.57
)
 
$
(1.32
)


The following outstanding shares of potentially dilutive securities were excluded from the calculation of diluted net loss per share for the three and nine months ended September 30, 2014 and 2013, as their effect was anti-dilutive:
 
September 30,
 
2014
 
2013
Options to purchase common stock
11,363,128

 
10,202,053

Common stock subject to repurchase
—

 
8,623

Restricted stock units
2,028,289

 
1,909,224

Warrants to purchase common stock
1,250,000

 
1,500,000

Shares of common stock to be issued upon conversion of convertible debt ("Notes")
18,790,996

 
9,905,521

Total
33,432,413

 
23,525,421

This table does not reflect (1) the series of warrants issued to Archer-Daniels-Midland Company (“ADM”) in March 2013 for payment in stock or cash, at the Company’s election, of future annual fees for use and operation of a portion of the ADM fermentation facility in Clinton, Iowa (the “Clinton Facility”) under the Strategic Collaboration Agreement (the "Collaboration Agreement") (Note 10) and (2) early conversion payment features of the Notes (see Notes 5 and 11) that may be settled, at the Company’s election, in cash or, subject to satisfaction of certain conditions, in shares of the Company’s common stock.