Verenium SC TO-I/A Issuer tender offer statement (amended)

Exhibit (a)(5)(4)

The accompanying unaudited pro forma consolidated statements of operations and financial ratios for the year ended December 31, 2011 and the nine months ended September 30, 2011 give effect to our repurchase of the Notes as if the Notes were repurchased at the end of all periods presented. The accompanying unaudited pro forma consolidated balance sheet as of December 31, 2011 gives effect to our repurchase of the Notes as if the Notes were repurchased as of December 31, 2011.

The historical financial information on which the pro forma information is based is included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2011, which was filed on March 5, 2012, and our Quarterly Report on Form 10-Q for the quarter ended September 30, 2011, which was filed on November 14, 2011. The pro forma information and the notes thereto should be read in conjunction with these historical consolidated financial statements.

The unaudited pro forma information are presented for illustrative purposes only and are subject to a number of assumptions which may not be indicative of the results of operations that would have occurred had the Notes been repurchased at the dates indicated or what the results will be for any future periods.

VERENIUM CORPORATION

UNAUDITED PRO FORMA CONSOLIDATED BALANCE SHEET

AS OF DECEMBER 31, 2011

(in thousands, except per share data)

	Historical			Pro Forma Adjustments			Pro Forma
ASSETS
Current assets:
Cash and cash equivalents	$	28,759			(35,330	)(c)	$	(6,571	)
Restricted cash		5,000						5,000
Accounts receivable, net of allowance for doubtful accounts of $0.1 million		11,371						11,371
Inventories, net		6,323						6,323
Prepaid expenses and other current assets		2,396						2,396
Total current assets		53,849						18,519
Property and equipment, net		7,806						7,806
Restricted cash		3,200						3,200
Other long term assets		482			(73	)(d)		409
Total assets	$	65,337					$	29,934
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	8,543					$	8,543
Accrued expenses		6,123			(479	)(e)		5,644
Deferred revenue		4,137						4,137
Accrued restructuring		396						396
Convertible debt, at carrying value (face value of $34.9 million)		34,851			(34,851	)(f)		—
Current liabilities of discontinued operations		436						436
Total current liabilities		54,486						19,156
Other long term liabilities		889						889
Long term liabilities of discontinued operations		17						17
Total liabilities		55,392						20,062
Stockholders’ equity:
Preferred stock—$0.001 par value; 5,000 shares authorized, no shares issued and outstanding		—						—
Common Stock—$0.001 par value; 245,000 shares authorized; 12,611 shares issued and outstanding		12						12
Additional paid-in capital		610,781						610,781
Accumulated deficit		(600,848	)		(73	)(d)		(600,921	)
Total stockholders’ equity		9,945						9,872
Total liabilities and stockholders’ equity	$	65,337					$	29,934

(c) Adjustment to remove cash paid for principal of $34.9 million and accrued and unpaid interest of $0.5 million as if the Notes were repurchased as of December 31, 2011.

(d) Adjustment to remove the capatilized debt issuance cost balance as if the Notes were repurchased as of December 31, 2011.

(e) Adjustment to remove the accrued and unpaid interest balance as if the Notes were repurchased as of December 31, 2011.

(f) Adjustment to remove the Notes principal balance as if the Notes were repurchased as of December 31, 2011.

VERENIUM CORPORATION

UNAUDITED PRO FORMA CONSOLIDATED STATEMENT OF OPERATIONS

FOR THE YEAR ENDED DECEMBER 31, 2011

(in thousands, except per share data)

	Historical			Pro Forma Adjustments			Pro Forma
Revenue:
Product	$	55,995					$	55,995
Collaborative and license		5,272						5,272
Total revenue		61,267						61,267
Operating expenses:
Cost of product revenue		34,481						34,481
Research and development		10,986						10,986
Selling, general and administrative		19,365						19,365
Restructuring charges		2,943						2,943
Total operating expenses		67,775						67,775
Loss from operations		(6,508	)					(6,508	)
Other income and expenses:
Interest and other income, net		56						56
Interest expense		(3,062	)					(3,062	)
Gain on debt extinguishment upon repurchase of convertible notes		15,349			(73	)(d)		15,276
Loss on net change in fair value of derivative assets and liabilities		(964	)					(964	)
Total other income and (expenses), net		11,379						11,306
Net income from continuing operations before income taxes		4,871						4,798
Income tax benefit		368						368
Net income from continuing operations		5,239						5,166
Net loss from discontinued operations		(112	)					(112	)
Net income attributed to Verenium Corporation	$	5,127					$	5,054
Net income (loss) per share, basic and diluted:
Continuing operations	$	0.42					$	0.40
Discontinued operations	$	(0.01	)				$	(0.01	)
Attributed to Verenium Corporation	$	0.41					$	0.40
Weighted average shares used in calculating basic and diluted net income (loss) per share		12,608						12,608

(d) Adjustment to show the loss on debt extinguishment related to the write off of the capitalized debt issuance cost balance as if the Notes were repurchased as of December 31, 2011.

VERENIUM CORPORATION

UNAUDITED PRO FORMA CONSOLIDATED STATEMENT OF OPERATIONS

FOR THE NINE MONTHS ENDED SEPTEMBER 30, 2011

(in thousands, except per share data)

	Historical			Pro Forma Adjustments			Pro Forma
Revenue:
Product	$	42,252					$	42,252
Collaborative and license		4,694						4,694
Total revenue		46,946						46,946
Operating expenses:
Cost of product revenue		26,174						26,174
Research and development		7,593						7,593
Selling, general and administrative		14,106						14,106
Restructuring charges		2,940						2,940
Total operating expenses		50,813						50,813
Loss from operations		(3,867	)					(3,867	)
Other income and expenses:
Interest and other income, net		50						50
Interest expense		(2,421	)					(2,421	)
Gain on debt extinguishment upon repurchase of convertible notes		15,349			(147	)(g)		15,202
Loss on net change in fair value of derivative assets and liabilities		(1,005	)					(1,005	)
Total other income and (expenses), net		11,973						11,826
Net income from continuing operations before income taxes		8,106						7,959
Income tax benefit		—						—
Net income from continuing operations		8,106						7,959
Net income from discontinued operations		37						37
Net income attributed to Verenium Corporation	$	8,143					$	7,996
Net income per share, basic and diluted:
Continuing operations	$	0.64					$	0.63
Discontinued operations	$	0.00					$	0.00
Attributed to Verenium Corporation	$	0.65					$	0.63
Weighted average shares used in calculating basic and diluted net income (loss) per share		12,607						12,607

(g) Adjustment to show the loss on debt extinguishment related to the write off of the capitalized debt issuance cost balance as if the Notes were repurchased as of September 30, 2011.

VERENIUM CORPORATION

UNAUDITED PRO FORMA RATIO OF EARNINGS TO FIXED CHARGES

(in thousands, except ratio data)

	For the Year Ended December 31, 2011		For the Nine Months Ended September 30, 2011
Earnings:
Pre-tax income from continuing operations	$	4,798	$	7,959
Add: Total fixed charges (see details below)		2,945		2,392
Total income before provision for income taxes plus fixed charges	$	7,743	$	10,351
Fixed Charges:
Sum of:
Interest expense(a)	$	2,718	$	2,239
Amortized premiums, discounts and capitalized expenes related to indebtedness (b)		227		153
Total fixed charges	$	2,945	$	2,392
Ratio of earnings to fixed charges		2.63		4.33

VERENIUM CORPORATION

UNAUDITED PRO FORMA BOOK VALUE PER SHARE

AS OF DECEMBER 31, 2011

(in thousands, except per share data)

	Pro Forma
Stockholders’ Equity	$	9,872
Outstanding Shares		12,611
Book Value per Share	$	0.78