Document and Entity Information	6 Months Ended
Document and Entity Information	Jun. 30, 2012	Jul. 31, 2012
Document and Entity Information
Entity Registrant Name	MERRIMACK PHARMACEUTICALS INC
Entity Central Index Key	0001274792
Document Type	10-Q
Document Period End Date	Jun. 30, 2012
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Non-accelerated Filer
Entity Common Stock, Shares Outstanding		93,718,994
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q2

Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 32,043	$ 50,454
Available-for-sale securities	74,669
Restricted cash	100
Accounts receivable	6,940	7,426
Deferred financing costs		1,946
Prepaid expenses and other current assets	6,570	5,763
Total current assets	120,322	65,589
Restricted cash	381	381
Property and equipment, net	5,040	6,206
Other assets	23	23
Intangible assets, net	2,325	2,485
In-process research and development	7,010	7,010
Goodwill	3,605	3,605
Total assets	138,706	85,299
Current liabilities:
Accounts payable	2,745	4,656
Accrued expenses and other	14,113	12,855
Dividends payable	261
Capital lease obligations		48
Deferred revenues	8,562	7,712
Deferred lease benefits	115	125
Deferred tax incentives	876	755
Total current liabilities	26,672	26,151
Deferred revenues	77,736	78,033
Deferred lease benefits	202	23
Deferred tax incentives	1,011	1,267
Convertible preferred stock warrants		1,516
Total liabilities	105,621	106,990
Commitments and contingencies (Note 10)
Convertible preferred stock		268,225
Non-controlling interest	343	574
Stockholders' (deficit) equity:
Preferred stock, $0.01 par value: no shares and 10,000 shares authorized at December 31, 2011 and June 30, 2012, respectively; no shares issued or outstanding at December 31, 2011 and June 30, 2012, respectively
Common stock, $0.01 par value: 138,500 and 200,000 shares authorized at December 31, 2011 and June 30, 2012, respectively; 11,834 and 93,540 shares issued and outstanding at December 31, 2011 and June 30, 2012, respectively	935	118
Additional paid-in capital	426,005	60,231
Accumulated other comprehensive loss	(49)
Accumulated deficit	(394,149)	(350,839)
Total stockholders' (deficit) equity	32,742	(290,490)
Total liabilities, convertible preferred stock, non-controlling interest and stockholders' (deficit) equity	$ 138,706	$ 85,299

Condensed Consolidated Balance Sheets (Parenthetical) (USD $) In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Condensed Consolidated Balance Sheets
Preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, authorized shares	10,000	0
Preferred stock, issued shares	0	0
Preferred stock, outstanding shares	0	0
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, authorized shares	200,000	138,500
Common stock, issued shares	93,540	11,834
Common stock, outstanding shares	93,540	11,834

Number of shares of common stock outstanding. Common stock represent the ownership interest in a corporation.

+ References+ Details

- Definition

Face amount or stated value per share of nonredeemable preferred stock (or preferred stock redeemable solely at the option of the issuer); generally not indicative of the fair market value per share.

+ References+ Details

Condensed Consolidated Statements of Comprehensive Income (Loss) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Collaboration revenues	$ 12,063	$ 6,595	$ 23,407	$ 13,056
Operating expenses
Research and development	28,758	31,187	60,409	49,188
General and administrative	3,610	4,832	7,338	7,933
Total operating expenses	32,368	36,019	67,747	57,121
Loss from operations	(20,305)	(29,424)	(44,340)	(44,065)
Other income and expenses
Interest income	54	29	63	43
Interest expense		(4)		(10)
Other, net	112	203	736	1,301
Net loss	(20,139)	(29,196)	(43,541)	(42,731)
Less net loss attributable to non-controlling interest	(113)	(145)	(231)	(223)
Net loss attributable to Merrimack Pharmaceuticals, Inc.	(20,026)	(29,051)	(43,310)	(42,508)
Other comprehensive loss:
Unrealized loss on available-for-sale securities	(49)		(49)
Other comprehensive loss	(49)		(49)
Comprehensive loss	$ (20,075)	$ (29,051)	$ (43,359)	$ (42,508)
Net loss per share available to common stockholders-basic and diluted (in dollars per share)	$ (0.22)	$ (2.76)	$ (0.89)	$ (4.14)
Weighted-average common shares used in computing net loss per share available to common stockholders-basic and diluted	90,581	11,282	51,214	11,158

Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011
Cash flows from operating activities
Net loss	$ (43,541)	$ (42,731)
Adjustments to reconcile net loss to net cash used in operating activities
Remeasurement of convertible preferred stock warrants	(587)	576
Amortization of premium on available-for-sale securities	341
Amortization of deferred lease benefits and tax incentives	(295)	(385)
Depreciation and amortization	2,217	2,670
Stock-based compensation	2,749	3,784
Changes in operating assets and liabilities
Purchased premiums and interest on available-for-sale securities	(1,760)
Accounts receivable	486	(1,027)
Prepaid expenses and other current assets	(281)	(1,184)
Accounts payable	(1,911)	1,355
Accrued expenses and other	1,258	1,455
Deferred revenues	553	3,916
Deferred lease benefits and tax incentives	329	1,212
Other assets and liabilities, net		14
Net cash used in operating activities	(40,442)	(30,345)
Cash flows from investing activities
Purchase of available-for-sale securities	(73,825)
Purchase of property and equipment	(891)	(1,833)
Other investing activities, net	(100)	1
Net cash used in investing activities	(74,816)	(1,832)
Cash flows from financing activities
Proceeds from initial public offering, net of offering costs	100,025
Proceeds from issuance of convertible preferred stock, net of offering costs		76,949
Proceeds from exercise of stock options	847	457
Proceeds from exercise of stock warrants	26
Principal payments on capital lease obligations	(48)	(307)
Payment of dividends on Series B convertible preferred stock	(4,003)
Net cash provided by financing activities	96,847	77,099
Net increase (decrease) in cash and cash equivalents	(18,411)	44,922
Cash and cash equivalents, beginning of period	50,454	30,713
Cash and cash equivalents, end of period	32,043	75,635
Non-cash investing and financing activities
Conversion of convertible preferred stock to common stock	268,225
Conversion of convertible preferred stock warrants to common stock warrants	929
Reclassification of deferred financing costs to stockholders' equity	2,748
Dividends on Series B convertible preferred stock declared but not paid	261
Supplemental disclosure of cash flows
Cash paid for interest		$ 10

Nature of the Business

6 Months Ended

Jun. 30, 2012

Nature of the Business

Nature of the Business

1. Nature of the Business

Merrimack Pharmaceuticals, Inc. (the “Company”) is a biopharmaceutical company discovering, developing and preparing to commercialize innovative medicines consisting of novel therapeutics paired with companion diagnostics. The Company has five targeted therapeutic oncology candidates in clinical development (MM-398, MM-121, MM-111, MM-302 and MM-151), multiple product candidates in preclinical development and a discovery effort advancing additional candidate medicines. The Company uses its interdisciplinary Network Biology approach in drug discovery and development.

The Company is subject to risks and uncertainties common to companies in the biopharmaceutical industry, including, but not limited to, its ability to secure additional capital to fund operations, development by competitors of new technological innovations, dependence on collaborative arrangements, protection of proprietary technology, compliance with government regulations and dependence on key personnel. Product candidates currently under development will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel, infrastructure and extensive compliance reporting capabilities.

The Company has incurred significant losses and does not have commercial operations underway. The accompanying condensed consolidated financial statements have been prepared on a basis which assumes that the Company will continue as a going concern and which contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business. In April 2012, the Company closed the initial public offering of its common stock pursuant to a registration statement on Form S-1, as amended. The Company sold an aggregate of 15,042,459 shares of common stock under the registration statement at a public offering price of $7.00 per share, including 742,459 shares pursuant to the exercise by the underwriters of an over-allotment option. Net proceeds were approximately $98.1 million, after deducting underwriting discounts and commissions and other offering expenses but prior to the payment of dividends on the Company’s Series B convertible preferred stock. As of June 30, 2012, the Company had unrestricted cash and cash equivalents and available-for-sale securities of $106.7 million. The Company expects its existing unrestricted cash and cash equivalents and available-for-sale securities on hand as of June 30, 2012 to be sufficient to fund operations into the second half of 2013.

The Company may seek additional funding through public or private debt or equity financings, or through existing or new collaboration arrangements. The Company may not be able to obtain financing on acceptable terms, or at all, and the Company may not be able to enter into additional collaborative arrangements. The terms of any financing may adversely affect the holdings or the rights of the Company’s stockholders. Arrangements with collaborators or others may require the Company to relinquish rights to certain of its technologies or product candidates. If the Company is unable to obtain funding, the Company could be forced to delay, reduce or eliminate its research and development programs or commercialization efforts, which could adversely affect its business prospects.

Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Significant accounting policies followed by the Company in the preparation of its condensed consolidated financial statements are as follows:

Basis of Presentation

The accompanying condensed consolidated financial statements as of June 30, 2012, and for the three and six months ended June 30, 2011 and 2012, have been prepared in accordance with the rules and regulations of the Securities and Exchange Commission (the “SEC”) and generally accepted accounting principles in the United States of America (“GAAP”) for condensed consolidated financial information. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. In the opinion of management, these condensed consolidated financial statements reflect all adjustments which are necessary for a fair statement of the Company’s financial position and results of its operations, as of and for the periods presented. These condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Current Report on Form 8-K filed with the SEC on April 27, 2012.

The information presented in the condensed consolidated financial statements and related notes as of June 30, 2012, and for the three and six months ended June 30, 2011 and 2012, is unaudited. The December 31, 2011 condensed consolidated balance sheet included herein was derived from the audited financial statements as of that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements.

Interim results for the three and six months ended June 30, 2012 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2012, or any future period.

Principles of Consolidation

These condensed consolidated financial statements include the accounts of the Company, its wholly owned subsidiary Hermes BioSciences, Inc., which was merged with and into the Company during 2011, its wholly owned subsidiary Merrimack Pharmaceuticals (Bermuda) Ltd., which was incorporated during 2011, and its 74% majority owned subsidiary Silver Creek Pharmaceuticals, Inc. (“Silver Creek”). All intercompany transactions and balances have been eliminated in consolidation.

There were no changes to the Company’s ownership of Silver Creek during the six months ended June 30, 2011 and 2012. The Company’s consolidated financial statement activity related to Silver Creek during these periods was as follows:

(in thousands)	Non-Controlling Interest
Balance at December 31, 2010	$	1,027
Net loss attributable to Silver Creek	(223		)
Balance at June 30, 2011	$	804

	Non-Controlling Interest
Balance at December 31, 2011	$	574
Net loss attributable to Silver Creek	(231		)
Balance at June 30, 2012	$	343

Use of Estimates

GAAP requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets, liabilities, revenues, expenses and related disclosures. The Company bases estimates and judgments on historical experience and on various other factors that it believes to be reasonable under the circumstances. The significant estimates in these condensed consolidated financial statements include revenue recognition, useful lives with respect to long-lived assets and intangibles and the valuation of stock options, convertible preferred stock warrants, contingencies, accrued expenses, intangible assets, goodwill, in-process research and development and tax valuation reserves. The Company’s actual results may differ from these estimates under different assumptions or conditions. The Company evaluates its estimates on an ongoing basis. Changes in estimates are reflected in reported results in the period in which they become known by the Company’s management.

Cash, Cash Equivalents and Restricted Cash

Cash and cash equivalents are short-term, highly liquid investments with original maturities of three months or less at the date of purchase. Investments qualifying as cash equivalents primarily consist of money market funds and commercial paper.

Cash accounts with any type of restriction are classified as restricted cash. If restrictions are expected to be lifted in the next twelve months, the restricted cash account is classified as current. As of December 31, 2011 and June 30, 2012, the Company recorded restricted cash of $381,000 and $481,000, respectively.

Marketable Securities

Marketable securities as of June 30, 2012 consisted of U.S. government agencies securities and corporate debt securities, including commercial paper, which were maintained by an investment manager and had expected average maturity dates in excess of three months, but not longer than twelve months. The Company classified these investments as available-for-sale. Available-for-sale securities are carried at fair value, with the unrealized gains and losses included in other comprehensive income (loss) as a component of stockholders’ equity until realized. Realized gains and losses are recognized in interest income. There were no realized gains or losses recognized on the sale or maturity of securities during the three and six months ended June 30, 2012.

Available-for-sale securities, all of which have maturities of twelve months or less, as of June 30, 2012 consisted of the following:

	Amortized Cost		Unrealized Gains		Unrealized Losses			Fair Value
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	1,000	$	—	$	(1	)	$	999
Corporate debt securities	73,718		1		(49		)	73,670
Total	$	74,718	$	1	$	(50	)	$	74,669

The aggregate fair value of securities held by the Company in an unrealized loss position for less than 12 months as of June 30, 2012 was $66.2 million, representing 22 securities. To determine whether an other-than-temporary impairment exists, the Company performs an analysis to assess whether it intends to sell, or whether it would more likely than not be required to sell, the security before the expected recovery of the amortized cost basis. Where the Company intends to sell a security, or may be required to do so, the security’s decline in fair value is deemed to be other-than-temporary and the full amount of the unrealized loss is recognized on the statement of comprehensive income (loss) as an other-than-temporary impairment charge. When this is not the case, the Company performs additional analysis on all securities with unrealized losses to evaluate losses associated with the creditworthiness of the security. Credit losses are identified where the Company does not expect to receive cash flows, based on using a single best estimate, sufficient to recover the amortized cost basis of a security and amount of the loss recognized in other income (expense).

Marketable securities in an unrealized loss position as of June 30, 2012 consisted of the following:

	Aggregate Fair Value		Unrealized Losses
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	999	$	(1	)
Corporate debt securities	65,172		(49		)
Total	$	66,171	$	(50	)

The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. There was no material change in the credit risk of the investments. The Company determined it did not hold any investments with an other-than-temporary-impairment as of June 30, 2012.

Concentrations of Credit Risk

Financial instruments that subject the Company to credit risk consist primarily of cash and cash equivalents, available-for-sale securities and accounts receivable. The Company places its cash deposits in accredited financial institutions and, therefore, the Company’s management believes these funds are subject to minimal credit risk. The Company invests cash equivalents and available-for-sale securities in money market funds, U.S. government agencies securities and corporate debt securities. Credit risk in these securities is reduced as a result of the Company’s investment policy to limit the amount invested in any one issue or any single issuer and to only invest in high credit quality securities.

Revenue Recognition

The Company enters into biopharmaceutical product development agreements with collaborative partners for the research and development of therapeutic and diagnostic products. The terms of the agreements may include nonrefundable signing and licensing fees, funding for research, development and manufacturing, milestone payments and royalties on any product sales derived from collaborations. These multiple element arrangements are analyzed to determine whether the deliverables can be separated or whether they must be accounted for as a single unit of accounting.

In January 2011, the Company adopted new authoritative guidance on revenue recognition for multiple element arrangements. This guidance, which applies to multiple element arrangements entered into or materially modified on or after January 1, 2011, amends the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a best estimate of selling price if vendor specific objective evidence and third-party evidence are not available. Deliverables under the arrangement will be separate units of accounting provided that a delivered item has value to the customer on a stand-alone basis and if the arrangement does not include a general right of return relative to the delivered item and delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The Company also adopted guidance that permits the recognition of revenue contingent upon the achievement of a milestone in its entirety, in the period in which the milestone is achieved, only if the milestone meets certain criteria and is considered to be substantive. The Company did not enter into any significant multiple element arrangements or materially modify any of its existing multiple element arrangements during the year ended December 31, 2011 or the three and six months ended June 30, 2012. The Company’s existing license and collaboration agreements continue to be accounted for under previously issued revenue recognition guidance for multiple element arrangements and milestone revenue recognition, as described below.

The Company recognized upfront license payments as revenue upon delivery of the license only if the license had stand-alone value and the fair value of the undelivered performance obligations could be determined. If the fair value of the undelivered performance obligations could be determined, such obligations were accounted for separately as the obligations were fulfilled. If the license was considered to either not have stand-alone value or have stand-alone value but the fair value of any of the undelivered performance obligations could not be determined, the arrangement was accounted for as a single unit of accounting and the license payments and payments for performance obligations were recognized as revenue over the estimated period of when the performance obligations would be performed.

Whenever the Company determined that an arrangement should be accounted for as a single unit of accounting, it determined the period over which the performance obligations would be performed and revenue would be recognized. If the Company could not reasonably estimate the timing and the level of effort to complete its performance obligations under the arrangement, then revenue under the arrangement was recognized on a straight-line basis over the period the Company expected to complete its performance obligations, which is reassessed at each subsequent reporting period.

The Company’s collaboration agreements may include additional payments upon the achievement of performance-based milestones. As milestones are achieved, a portion of the milestone payment, equal to the percentage of the total time that the Company has performed the performance obligations to date over the total estimated time to complete the performance obligations, multiplied by the amount of the milestone payment, will be recognized as revenue upon achievement of such milestone. The remaining portion of the milestone will be recognized over the remaining performance period. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in the Company’s revenue model until the performance conditions are met.

Royalty revenue will be recognized upon the sale of the related products provided the Company has no remaining performance obligations under the arrangement.

Convertible Preferred Stock and Convertible Preferred Stock Warrants

Convertible preferred stock is initially recorded at the proceeds received, net of issuance costs and warrants, where applicable. As described in Note 3, in April 2012, the Company closed the initial public offering of its common stock. Upon closing, all outstanding shares of the Company’s convertible preferred stock were converted into 66,255,529 shares of common stock. Also upon closing, the Company’s restated certificate of incorporation became effective and authorized 10.0 million shares of $0.01 par value undesignated preferred stock.

The Company accounts for freestanding warrants as liabilities at their fair value. The Company measures the fair value of the convertible preferred stock warrants at the end of each reporting period and records the change in fair value to other income (expense). For the three months ended June 30, 2011 and 2012, the Company recorded other income related to this re-measurement of $141,000 and $29,000, respectively, and for the six months ended June 30, 2011 and 2012, the Company recorded other income (expense) related to this re-measurement of $(576,000) and $587,000, respectively. As described in Note 3, in April 2012, the Company closed the initial public offering of its common stock. Upon closing, all outstanding warrants to purchase shares of convertible preferred stock were converted into warrants to purchase shares of common stock and reclassified to stockholders’ equity.

Comprehensive Income (Loss)

Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions, and other events and circumstances, from non-owner sources and currently consists of net loss and changes in unrealized gains and losses on available-for-sale securities. Comprehensive loss from operations was calculated as follows:

	Three Months Ended June 30,						Six Months Ended June 30,
(in thousands)	2011			2012			2011			2012
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$	(29,051	)	$	(20,026	)	$	(42,508	)	$	(43,310	)
Unrealized loss on available-for-sale securities	—			(49		)	—			(49		)
Comprehensive loss	$	(29,051	)	$	(20,075	)	$	(42,508	)	$	(43,359	)

Other Income (Expense)

The Company records gains and losses on the remeasurement of fair value of convertible preferred stock warrants, the recognition of federal and state sponsored tax incentives and other one-time income or expense-related items in other income (expense) on the Company’s condensed consolidated statement of comprehensive income (loss). Additionally, other income recognized during the six months ended June 30, 2011 included the impact of a cash settlement of $1.8 million from a former service provider.

Deferred Financing Costs

The Company capitalizes certain legal, accounting and other fees that are directly associated with in-process equity financings as current assets until such financings occur. After occurrence, these costs are recorded in equity, in the case of a common stock financing, or mezzanine equity, in the case of a convertible preferred stock financing, net of proceeds received.

As of December 31, 2011, the Company recorded deferred financing costs of $1,946,000 on the accompanying condensed consolidated balance sheet in contemplation of an initial public offering. As discussed in Note 3, in April 2012, the Company closed the initial public offering of its common stock. Upon closing, $2,748,000 of deferred financing costs were netted against the equity proceeds within stockholders’ equity.

Recent Accounting Pronouncements

In July 2012, the Financial Accounting Standards Board issued ASU No. 2012-02, Testing Indefinite-Lived Intangible Assets for Impairment (“ASU 2012-02”). ASU 2012-02 is intended to reduce the cost and complexity of testing indefinite-lived intangible assets other than goodwill for impairment. It allows companies to perform a “qualitative” assessment to determine whether further impairment testing of indefinite-lived intangible assets is necessary, similar in approach to the goodwill impairment test. ASU 2012-02 is effective for annual and interim impairment tests performed for fiscal years beginning after September 15, 2012. Early adoption is permitted, and the Company expects to adopt ASU 2012-02 in the third quarter of 2012 upon its annual impairment testing of indefinite-lived intangible assets. The Company is currently evaluating the impact, if any, that its adoption of ASU 2012-02 will have on its consolidated financial statements.

Initial Public Offering

6 Months Ended

Jun. 30, 2012

Initial Public Offering

Initial Public Offering

3. Initial Public Offering

In April 2012, the Company closed the initial public offering of its common stock pursuant to a registration statement on Form S-1, as amended. The Company sold an aggregate of 15,042,459 shares of common stock under the registration statement at a public offering price of $7.00 per share, including 742,459 shares pursuant to the exercise by the underwriters of an over-allotment option. Net proceeds were approximately $98.1 million, after deducting underwriting discounts and commissions and other offering expenses but prior to the payment of dividends on the Company’s Series B convertible preferred stock.

Upon closing the initial public offering, all outstanding shares of the Company’s convertible preferred stock were converted into 66,255,529 shares of common stock, all outstanding warrants to purchase shares of convertible preferred stock were converted into warrants to purchase shares of common stock and approximately $4.3 million of cash dividends became payable to the holders of Series B convertible preferred stock.

Net Loss Per Common Share

6 Months Ended

Jun. 30, 2012

Net Loss Per Common Share

Net Loss Per Common Share

4. Net Loss Per Common Share

Basic net loss per share is calculated by dividing the net loss attributable to common stockholders by the weighted-average number of common shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method. For purposes of this calculation, convertible preferred stock, stock options and warrants are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive.

The following table presents the computation of basic and diluted net loss per share available to common stockholders for the three and six months ended June 30, 2011 and 2012:

	Three months ended June 30,						Six months ended June 30,
(in thousands, except per share amount)	2011			2012			2011			2012

Net Loss Per Share:
Numerator:
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$	(29,051	)	$	(20,026	)	$	(42,508	)	$	(43,310	)
Plus: Unaccreted dividends on convertible preferred stock	(2,129		)	(67		)	(3,666		)	(2,107		)
Net loss available to common stockholders—basic and diluted	(31,180		)	(20,093		)	(46,174		)	(45,417		)
Denominator:
Weighted-average common shares—basic and diluted	11,282			90,581			11,158			51,214
Net loss per share available to common stockholders—basic and diluted	$	(2.76	)	$	(0.22	)	$	(4.14	)	$	(0.89	)

The following common stock equivalents of potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding as of June 30, 2011 and 2012, as the Company recorded a net loss in all periods and, therefore, they would be anti-dilutive:

	As of June 30,
(in thousands)	2011	2012

Convertible preferred stock	66,256	—
Options to purchase common stock	17,728	17,455
Convertible preferred stock warrants	303	—
Common stock warrants	2,937	2,905

- Definition

The entire disclosure for earnings per share.

+ References+ Details

License and Collaboration Agreements

6 Months Ended

Jun. 30, 2012

License and Collaboration Agreements

License and Collaboration Agreements

5. License and Collaboration Agreements

Sanofi

On September 30, 2009, the Company entered into a license and collaboration agreement with Sanofi for the development and commercialization of a drug candidate being developed by the Company under the name MM-121. The agreement became effective on November 10, 2009 and Sanofi paid the Company a nonrefundable, noncreditable upfront license fee of $60.0 million. During the third quarter of 2010 and the fourth quarter of 2011, the Company received a total of $20.0 million in milestone payments associated with dosing the first patients in Phase 2 clinical trials in breast cancer and non-small cell lung cancer. During the first quarter of 2012, the Company received an additional milestone payment of $5.0 million associated with dosing the first patient in a Phase 2 clinical trial in ovarian cancer. The Company is eligible to receive additional future development, regulatory and sales milestone payments as well as future royalty payments depending on the success of MM-121.

Under the agreement, Sanofi is responsible for all MM-121 development and manufacturing costs. The Company retained the right to participate in the development of MM-121 through Phase 2 proof of concept trials. The Company also has the right, but not the obligation, to co-promote MM-121 in the United States. Sanofi reimburses the Company for direct costs incurred in development and compensates the Company for its internal development efforts based on a full time equivalent (“FTE”) rate. Also as part of the agreement, the Company was required to manufacture certain quantities of MM-121 and, at Sanofi’s and the Company’s option, may continue to manufacture additional quantities of MM-121 in the future. Sanofi reimburses the Company for direct costs incurred in manufacturing and compensates the Company for its internal manufacturing efforts based on an FTE rate. The Company satisfied its manufacturing obligations during 2010 and has elected to continue to manufacture quantities of MM-121.

The Company applied revenue recognition guidance to determine whether the performance obligations under this collaboration, including the license, the right to future technology, back-up compounds, participation on steering committees, development services and manufacturing services, could be accounted for separately or as a single unit of accounting. The Company determined that its development services performance obligation is considered a separate unit of accounting, as it is set at the Company’s option, has stand-alone value and the FTE rate is considered fair value. Therefore, the Company recognizes cost reimbursements for MM-121 development services as incurred. The Company determined that the license, the right to future technology, back-up compounds, participation on steering committees and manufacturing services performance obligations represented a single unit of accounting. As the Company cannot reasonably estimate its level of effort over the collaboration, the Company recognizes revenue from the upfront payment, milestone payment and manufacturing services payments using the contingency-adjusted performance model over the expected development period, which is currently estimated to be 12 years from the effective date of the agreement. Under this model, when a milestone is earned or manufacturing services are rendered and product is delivered, revenue is immediately recognized on a pro-rata basis in the period the milestone was achieved or product was delivered based on the time elapsed from the effective date of the agreement. Thereafter, the remaining portion is recognized on a straight-line basis over the remaining development period.

During the three and six months ended June 30, 2011 and 2012, the Company recognized revenue based on the following components of the Sanofi agreement:

	Three months ended June 30,				Six months ended June 30,
(in thousands)	2011		2012		2011		2012
Upfront payment	$	1,250	$	1,250	$	2,500	$	2,500
Milestone payment	209		521		417		1,933
Development services	4,687		9,160		9,392		17,302
Manufacturing services and other	439		1,106		694		1,627
Total	$	6,585	$	12,037	$	13,003	$	23,362

As of December 31, 2011 and June 30, 2012, the Company maintained the following assets and liabilities related to the Sanofi agreement:

(in thousands)	December 31, 2011		June 30, 2012

Accounts receivable, billed	$	4,478	$	2,013
Accounts receivable, unbilled	2,925		4,909
Deferred revenue	84,466		85,057

PharmaEngine, Inc.

On May 5, 2011, the Company entered into an assignment, sublicense and collaboration agreement with PharmaEngine, Inc. (“PharmaEngine”) under which the Company reacquired rights in Europe and certain countries in Asia to a drug being developed under the name MM-398. In exchange, the Company agreed to pay PharmaEngine a nonrefundable, noncreditable upfront payment of $10.0 million and will be required to make up to an aggregate of $80.0 million in development and regulatory milestone payments and $130.0 million in sales milestone payments upon the achievement of specified development, regulatory and annual net sales milestones. During the first quarter of 2012, the Company paid a milestone of $5.0 million under the collaboration agreement with PharmaEngine in connection with dosing the first patient in a Phase 3 clinical trial of MM-398 in pancreatic cancer. PharmaEngine is also entitled to tiered royalties on net sales of MM-398 in Europe and certain countries in Asia. The Company is responsible for all future development costs of MM-398 except those required specifically for regulatory approval in Taiwan. The Company determined that PharmaEngine is a variable interest entity based on an analysis of PharmaEngine’s capitalization. However, the Company determined that the Company cannot control the activities of PharmaEngine, and therefore, the Company is not the primary beneficiary and should not consolidate the financial results of PharmaEngine.

During the three and six months ended June 30, 2012, the Company recognized research and development expenses of $0.3 million and $5.6 million, respectively, related to the agreement with PharmaEngine. During the three and six months ended June 30, 2011, the Company recognized research and development expenses of $10.5 million related to the agreement with PharmaEngine. These amounts included a $5.0 million milestone payment recognized in the first quarter of 2012 and a $10.0 million upfront payment recognized in the second quarter of 2011.

Fair Value of Financial Instruments

6 Months Ended

Jun. 30, 2012

Fair Value of Financial Instruments

Fair Value of Financial Instruments

6. Fair Value of Financial Instruments

The carrying amounts of cash and cash equivalents, available-for-sale securities, prepaid expenses, accounts receivable, accounts payable and accrued expenses and other short-term assets and liabilities approximate fair value due to the short-term nature of these instruments. Capital lease obligations and convertible preferred stock warrants are also carried at fair value.

Fair value is an exit price, representing the amount that would be received from the sale of an asset or paid to transfer a liability in an orderly transaction between market participants. Fair value is determined based on observable and unobservable inputs. Observable inputs reflect readily obtainable data from independent sources, while unobservable inputs reflect certain market assumptions. As a basis for considering such assumptions, GAAP establishes a three-tier value hierarchy, which prioritizes the inputs used to develop the assumptions and for measuring fair value as follows: (Level 1) observable inputs such as quoted prices in active markets for identical assets; (Level 2) inputs other than the quoted prices in active markets that are observable either directly or indirectly; and (Level 3) unobservable inputs in which there is little or no market data, which requires the Company to develop its own assumptions. This hierarchy requires the Company to use observable market data, when available, and to minimize the use of unobservable inputs when determining fair value.

The following tables show assets and liabilities measured at fair value on a recurring basis as of December 31, 2011 and June 30, 2012 and the input categories associated with those assets and liabilities:

As of December 31, 2011 (in thousands)	Level 1		Level 2		Level 3

Assets:
Cash equivalents — U.S. treasury securities	$	35,076	$	—	$	—
Liabilities:
Convertible preferred stock warrants	—		—		1,516

As of June 30, 2012 (in thousands)	Level 1		Level 2		Level 3

Assets:
Cash equivalents — money market funds	$	23,794	$	—	$	—
Cash equivalents — corporate debt securities	—		6,000		—
Investments — U.S. government agencies securities	—		999		—
Investments — corporate debt securities	—		73,670		—

The Company’s investment portfolio consists of investments classified as cash equivalents and available-for-sale securities. All highly liquid investments with an original maturity of three months or less when purchased are considered to be cash equivalents. The Company’s cash and cash equivalents are invested in U.S. treasury and corporate debt securities that approximate their face value. All marketable securities with an original maturity when purchased of greater than three months are classified as available-for-sale. Available-for-sale securities are carried at fair value, with the unrealized gains and losses reported in other comprehensive income (loss). The amortized cost of securities in this category is adjusted for amortization of premiums and accretion of discounts to maturity. The fair value of the convertible preferred stock warrants as of December 31, 2011 was determined using the Black-Scholes option valuation model.

The following table provides a roll-forward of the fair value of the convertible preferred stock warrants categorized as Level 3 instruments, for the six months ended June 30, 2012:

(in thousands)	Convertible preferred stock warrants

Balance, December 31, 2011	$	1,516
Unrealized gain included in other income (expense)	(587		)
Reclassification to common stock warrants	(929		)

Balance, June 30, 2012	$	—

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef

-Publisher FASB

-Name Statement of Financial Accounting Standard (FAS)

-Number 107

-Paragraph 3, 10, 14, 15

-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

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+ Details

Accrued Expenses and Other

6 Months Ended

Jun. 30, 2012

Accrued Expenses and Other

Accrued Expenses and Other

7. Accrued Expenses and Other

Accrued expenses and other as of December 31, 2011 and June 30, 2012 consisted of the following:

(in thousands)	December 31, 2011		June 30, 2012

Goods and services	$	9,189	$	8,708
Payroll and related benefits	3,666		4,313
Contractual liability (Note 10)	—		1,092
Total accrued expenses and other	$	12,855	$	14,113

Common Stock

6 Months Ended

Jun. 30, 2012

Common Stock

Common Stock

8. Common Stock

During the first quarter of 2012, the Company amended its certificate of incorporation to increase the number of authorized shares of common stock to 200.0 million shares of $0.01 par value common stock. As of December 31, 2011 and June 30, 2012, the Company had 138.5 million shares and 200.0 million shares, respectively, of $0.01 par value common stock authorized. There were 11,834,000 and 93,540,000 shares of common stock issued and outstanding as of December 31, 2011 and June 30, 2012, respectively. The shares reserved for future issuance as of December 31, 2011 and June 30, 2012 consisted of the following:

(in thousands)	December 31, 2011	June 30, 2012

Conversion of Series B, Series C, Series D, Series E, Series F and Series G convertible preferred stock	66,256	—
Convertible preferred stock warrants	302	—
Common stock warrants	2,640	2,905
Equity compensation plans	17,617	17,455

	86,815	20,360

Stock-Based Compensation

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation

Stock-Based Compensation

9. Stock-Based Compensation

As of December 31, 2011, there were 830,000 shares of common stock available to be issued under the 2008 Stock Incentive Plan, as amended (the “2008 Plan”). The 2011 Stock Incentive Plan (the “2011 Plan”) became effective upon closing of the Company’s initial public offering in April 2012. Upon effectiveness of the 2011 Plan, no further awards were available to be issued under the 2008 Plan. The 2011 Plan is administered by the Board of Directors of the Company and permits the Company to grant incentive and non-qualified stock options, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards. The 2011 Plan increased the total number of shares of common stock available to be issued by 3.5 million.

During the six months ended June 30, 2011 and 2012, the Company issued options to purchase 1.9 million and 0.3 million shares of common stock, respectively. These options generally vest over a three-year period for employees and immediately for directors. After the closing of the Company’s initial public offering in April 2012, options granted to directors will be issued with a one-year vesting period. During the six months ended June 30, 2011, the Company also issued options to purchase 0.1 million shares of common stock to non-employees. The assumptions used to determine the fair value of options granted to non-employees were consistent with those used for employee grants.

The weighted-average assumptions used to estimate the fair value of options at the date of grant for the three and six months ended June 30, 2011 and 2012 were as follows:

	Three months ended June 30,		Six months ended June 30,
	2011	2012	2011	2012
Risk-free interest rate	2.5%	0.89-1.11%	2.5%	0.89-1.11%
Expected dividend yield	0%	0%	0%	0%
Expected term	5.0-5.9 years	5.8-5.9 years	5.0-5.9 years	5.8-5.9 years
Expected volatility	73%	71-72%	73%	71-72%

The Company recognized stock-based compensation expense as follows for the three and six months ended June 30, 2011 and 2012:

	Three months ended June 30,				Six months ended June 30,
(in thousands)	2011		2012		2011		2012
Employee awards:
Research and development	$	933	$	945	$	1,633	$	1,853
General and administrative	1,775		432		2,048		862
Stock-based compensation for employee awards	2,708		1,377		3,681		2,715
Stock-based compensation for non-employee awards	56		33		103		34
Total stock-based compensation	$	2,764	$	1,410	$	3,784	$	2,749

The following table summarizes stock option activity during the six months ended June 30, 2012:

(in thousands, except per share amounts)	Number of shares		Weighted average exercise price		Aggregate intrinsic value

Outstanding, December 31, 2011	17,617		$	2.56	$	74,329
Granted	294		$	6.73
Exercised	(378	)	$	2.24
Forfeited	(78	)	$	3.42

Outstanding, June 30, 2012	17,455		$	2.63	$	81,093

Exercisable, June 30, 2012	14,529		$	2.27	$	72,740
Vested and expected to vest, June 30, 2012	17,304		$	2.61	$	80,782

The aggregate intrinsic value was calculated as the difference between the exercise price of the stock options and the fair value of the underlying common stock as of the respective balance sheet date.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef

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+ Details

Commitments and Contingencies

6 Months Ended

Jun. 30, 2012

Commitments and Contingencies

Commitments and Contingencies

10. Commitments and Contingencies

Operating leases

The Company leases its office, laboratory and manufacturing space under non-cancellable operating leases. Total rent expense under these operating leases was $797,000 and $1,089,000 for the three months ended June 30, 2011 and 2012, respectively, and $1,497,000 and $1,981,000 for the six months ended June 30, 2011 and 2012, respectively.

During March 2012, the Company entered into a lease amendment to further expand its office, laboratory and manufacturing space. The amendment leases additional space for a seven year term effective March 2012. The aggregate rent due over the seven year term of the lease amendment is approximately $2.7 million. As part of this agreement, the landlord agreed to reimburse the Company for a portion of tenant improvements made to the facility, up to a total of $464,000. Tenant improvements are recorded in deferred lease benefits on the accompanying condensed consolidated balance sheets and amortized over the term of the lease as reductions to rent expense.

Contingencies

Contractual matter

The Company manufactures MM-121 under a license and collaboration agreement with Sanofi. Under this agreement, Sanofi reimburses the Company for direct costs incurred in manufacturing. During 2009 and 2010, the Company utilized a third party contractor to perform fill-finish manufacturing services. This third party contractor experienced U.S. Food and Drug Administration (“FDA”) inspection issues with its quality control process that resulted in a formal warning letter from the FDA. Following a review by Sanofi and the Company, some MM-121 was pulled from clinical trial sites and replaced with MM-121 that was filled by a different contractor. Sanofi had requested that the Company assume financial responsibility for the MM-121 material that was pulled from clinical trial sites. The Company and Sanofi have since agreed that, beginning in April 2012 and throughout 2013, the Company will reimburse Sanofi approximately $1.2 million of previously billed amounts. The Company’s revenue recognition model for manufacturing services performed under the license and collaboration agreement with Sanofi is to recognize these services over the period of performance, which is currently estimated to be 12 years from the effective date of the agreement. Removal of these previously billed amounts from the revenue recognition model and establishing this contractual liability resulted in an earnings reduction of $0.2 million for the three months ended March 31, 2012 in the accompanying condensed consolidated statement of comprehensive income (loss).

- Definition

The entire disclosure for commitments and contingencies.

+ References

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-Name FASB Interpretation (FIN)

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+ Details

Related Party Transactions

6 Months Ended

Jun. 30, 2012

Related Party Transactions

Related Party Transactions

11. Related Party Transactions

In connection with the initial public offering of the Company’s common stock, Sanofi purchased 5,217,391 shares of the Company’s common stock in April 2012.

In June 2012, the Company entered into a Right of Review Agreement (the “Agreement”) with Sanofi pursuant to which, if the Company determines to enter into negotiations with a third party regarding any license, option, collaboration, joint venture or similar transaction involving any therapeutic or companion diagnostic product candidate in the Company’s pipeline (an “Opportunity”), the Company will notify Sanofi of such Opportunity. Following such notice, Sanofi will have a specified period of time to determine whether to exercise an additional right to exclusively negotiate an agreement with the Company with respect to such Opportunity for a specified period of time. The Agreement terminates on April 1, 2017.

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

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+ Details

Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Basis of Presentation

Basis of Presentation

Interim results for the three and six months ended June 30, 2012 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2012, or any future period.

Principles of Consolidation

Principles of Consolidation

(in thousands)	Non-Controlling Interest
Balance at December 31, 2010	$	1,027
Net loss attributable to Silver Creek	(223		)
Balance at June 30, 2011	$	804

	Non-Controlling Interest
Balance at December 31, 2011	$	574
Net loss attributable to Silver Creek	(231		)
Balance at June 30, 2012	$	343

Use of Estimates

Use of Estimates

Cash, Cash Equivalents and Restricted Cash

Cash, Cash Equivalents and Restricted Cash

Marketable Securities

Marketable Securities

Available-for-sale securities, all of which have maturities of twelve months or less, as of June 30, 2012 consisted of the following:

	Amortized Cost		Unrealized Gains		Unrealized Losses			Fair Value
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	1,000	$	—	$	(1	)	$	999
Corporate debt securities	73,718		1		(49		)	73,670
Total	$	74,718	$	1	$	(50	)	$	74,669

Marketable securities in an unrealized loss position as of June 30, 2012 consisted of the following:

	Aggregate Fair Value		Unrealized Losses
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	999	$	(1	)
Corporate debt securities	65,172		(49		)
Total	$	66,171	$	(50	)

Concentrations of Credit Risk

Concentrations of Credit Risk

Revenue Recognition

Revenue Recognition

Royalty revenue will be recognized upon the sale of the related products provided the Company has no remaining performance obligations under the arrangement.

Convertible Preferred Stock and Convertible Preferred Stock Warrants

Convertible Preferred Stock and Convertible Preferred Stock Warrants

Comprehensive Income (Loss)

Comprehensive Income (Loss)

	Three Months Ended June 30,						Six Months Ended June 30,
(in thousands)	2011			2012			2011			2012
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$	(29,051	)	$	(20,026	)	$	(42,508	)	$	(43,310	)
Unrealized loss on available-for-sale securities	—			(49		)	—			(49		)
Comprehensive loss	$	(29,051	)	$	(20,075	)	$	(42,508	)	$	(43,359	)

Other Income (Expense)

Other Income (Expense)

Deferred Financing Costs

Deferred Financing Costs

Recent Accounting Pronouncements

Recent Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies

Schedule of non-controlling interest in subsidiary

(in thousands)	Non-Controlling Interest
Balance at December 31, 2010	$	1,027
Net loss attributable to Silver Creek	(223		)
Balance at June 30, 2011	$	804

	Non-Controlling Interest
Balance at December 31, 2011	$	574
Net loss attributable to Silver Creek	(231		)
Balance at June 30, 2012	$	343

Schedule of available-for-sale securities

	Amortized Cost		Unrealized Gains		Unrealized Losses			Fair Value
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	1,000	$	—	$	(1	)	$	999
Corporate debt securities	73,718		1		(49		)	73,670
Total	$	74,718	$	1	$	(50	)	$	74,669

Schedule of marketable securities in an unrealized loss position

	Aggregate Fair Value		Unrealized Losses
	(in thousands)
June 30, 2012:
U.S. government agencies securities	$	999	$	(1	)
Corporate debt securities	65,172		(49		)
Total	$	66,171	$	(50	)

Schedule of comprehensive loss from operations

	Three Months Ended June 30,						Six Months Ended June 30,
(in thousands)	2011			2012			2011			2012
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$	(29,051	)	$	(20,026	)	$	(42,508	)	$	(43,310	)
Unrealized loss on available-for-sale securities	—			(49		)	—			(49		)
Comprehensive loss	$	(29,051	)	$	(20,075	)	$	(42,508	)	$	(43,359	)

- Definition

Tabular disclosure of components of comprehensive income (loss) including, but not limited to: (a) foreign currency translation adjustments; (b) gains (losses) on foreign currency transactions that are designated as, and are effective as, economic hedges of a net investment in a foreign entity; (c) gains (losses) on intercompany foreign currency transactions that are of a long-term-investment nature, when the entities to the transaction are consolidated, combined, or accounted for by the equity method in the reporting enterprise's financial statements; (d) change in the market value of a futures contract that qualifies as a hedge of an asset reported at fair value; (e) unrealized holding gains (losses) on available-for-sale securities and that resulting from transfers of debt securities from the held-to-maturity category to the available-for-sale category; (f) a net loss recognized as an additional pension liability not yet recognized as net periodic pension cost; and (g) the net gain (loss) and net prior service cost or credit for pension plans and other postretirement benefit plans.

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Net Loss Per Common Share (Tables)

6 Months Ended

Jun. 30, 2012

Net Loss Per Common Share

Schedule of computation of basic and diluted net loss per share available to common stockholders

	Three months ended June 30,						Six months ended June 30,
(in thousands, except per share amount)	2011			2012			2011			2012

Net Loss Per Share:
Numerator:
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$	(29,051	)	$	(20,026	)	$	(42,508	)	$	(43,310	)
Plus: Unaccreted dividends on convertible preferred stock	(2,129		)	(67		)	(3,666		)	(2,107		)
Net loss available to common stockholders—basic and diluted	(31,180		)	(20,093		)	(46,174		)	(45,417		)
Denominator:
Weighted-average common shares—basic and diluted	11,282			90,581			11,158			51,214
Net loss per share available to common stockholders—basic and diluted	$	(2.76	)	$	(0.22	)	$	(4.14	)	$	(0.89	)

Schedule of potentially dilutive securities excluded from computation of diluted weighted average shares

	As of June 30,
(in thousands)	2011	2012

Convertible preferred stock	66,256	—
Options to purchase common stock	17,728	17,455
Convertible preferred stock warrants	303	—
Common stock warrants	2,937	2,905

License and Collaboration Agreements (Tables)

6 Months Ended

Jun. 30, 2012

License and Collaboration Agreements

Schedule of revenue recognized and assets and liabilities under collaborative arrangements

During the three and six months ended June 30, 2011 and 2012, the Company recognized revenue based on the following components of the Sanofi agreement:

	Three months ended June 30,				Six months ended June 30,
(in thousands)	2011		2012		2011		2012
Upfront payment	$	1,250	$	1,250	$	2,500	$	2,500
Milestone payment	209		521		417		1,933
Development services	4,687		9,160		9,392		17,302
Manufacturing services and other	439		1,106		694		1,627
Total	$	6,585	$	12,037	$	13,003	$	23,362

As of December 31, 2011 and June 30, 2012, the Company maintained the following assets and liabilities related to the Sanofi agreement:

(in thousands)	December 31, 2011		June 30, 2012

Accounts receivable, billed	$	4,478	$	2,013
Accounts receivable, unbilled	2,925		4,909
Deferred revenue	84,466		85,057

Fair Value of Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2012

Fair Value of Financial Instruments

Schedule of assets and liabilities measured at fair value on a recurring basis

As of December 31, 2011 (in thousands)	Level 1		Level 2		Level 3

Assets:
Cash equivalents — U.S. treasury securities	$	35,076	$	—	$	—
Liabilities:
Convertible preferred stock warrants	—		—		1,516

As of June 30, 2012 (in thousands)	Level 1		Level 2		Level 3

Assets:
Cash equivalents — money market funds	$	23,794	$	—	$	—
Cash equivalents — corporate debt securities	—		6,000		—
Investments — U.S. government agencies securities	—		999		—
Investments — corporate debt securities	—		73,670		—

Schedule of fair value of convertible preferred stock warrants categorized as Level 3 instruments

(in thousands)	Convertible preferred stock warrants

Balance, December 31, 2011	$	1,516
Unrealized gain included in other income (expense)	(587		)
Reclassification to common stock warrants	(929		)

Balance, June 30, 2012	$	—

- Definition

Tabular disclosure of the fair value measurement of liabilities using significant unobservable inputs (Level 3), a reconciliation of the beginning and ending balances, separately presenting changes attributable to the following: (1) total gains or losses for the period (realized and unrealized), segregating those gains or losses included in earnings (or changes in net assets), and gains or losses recognized in other comprehensive income (loss) and a description of where those gains or losses included in earnings (or changes in net assets) are reported in the statement of income (or activities); (2) purchases, sales, issues, and settlements (each type disclosed separately); and (3) transfers in and transfers out of Level 3 (for example, transfers due to changes in the observability of significant inputs) by class of liability.

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Accrued Expenses and Other (Tables)

6 Months Ended

Jun. 30, 2012

Accrued Expenses and Other

Schedule of accrued expenses and other

(in thousands)	December 31, 2011		June 30, 2012

Goods and services	$	9,189	$	8,708
Payroll and related benefits	3,666		4,313
Contractual liability (Note 10)	—		1,092
Total accrued expenses and other	$	12,855	$	14,113

Common Stock (Tables)

6 Months Ended

Jun. 30, 2012

Common Stock

Schedule of shares reserved for future issuance

(in thousands)	December 31, 2011	June 30, 2012

Conversion of Series B, Series C, Series D, Series E, Series F and Series G convertible preferred stock	66,256	—
Convertible preferred stock warrants	302	—
Common stock warrants	2,640	2,905
Equity compensation plans	17,617	17,455

	86,815	20,360

Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2012

Stock-Based Compensation

Schedule of assumptions used to calculate fair value of options granted

	Three months ended June 30,		Six months ended June 30,
	2011	2012	2011	2012
Risk-free interest rate	2.5%	0.89-1.11%	2.5%	0.89-1.11%
Expected dividend yield	0%	0%	0%	0%
Expected term	5.0-5.9 years	5.8-5.9 years	5.0-5.9 years	5.8-5.9 years
Expected volatility	73%	71-72%	73%	71-72%

Schedule of recognized stock-based compensation expense

	Three months ended June 30,				Six months ended June 30,
(in thousands)	2011		2012		2011		2012
Employee awards:
Research and development	$	933	$	945	$	1,633	$	1,853
General and administrative	1,775		432		2,048		862
Stock-based compensation for employee awards	2,708		1,377		3,681		2,715
Stock-based compensation for non-employee awards	56		33		103		34
Total stock-based compensation	$	2,764	$	1,410	$	3,784	$	2,749

Schedule of stock option activity

(in thousands, except per share amounts)	Number of shares		Weighted average exercise price		Aggregate intrinsic value

Outstanding, December 31, 2011	17,617		$	2.56	$	74,329
Granted	294		$	6.73
Exercised	(378	)	$	2.24
Forfeited	(78	)	$	3.42

Outstanding, June 30, 2012	17,455		$	2.63	$	81,093

Exercisable, June 30, 2012	14,529		$	2.27	$	72,740
Vested and expected to vest, June 30, 2012	17,304		$	2.61	$	80,782

Nature of the Business (Details) (USD $) In Millions, except Share data, unless otherwise specified	6 Months Ended	1 Months Ended
	Jun. 30, 2012 item	Apr. 30, 2012 Initial public offering Common stock
Nature of the Business
Number of targeted therapeutic oncology candidates	5
Unrestricted cash and cash equivalents and available-for-sale securities	$ 106.7
Public Offering
Aggregate shares of common stock sold in connection with initial public offering		15,042,459
Public offering price (in dollars per share)		$ 7.00
Common stock issued to underwriters under an over-allotment option (in shares)		742,459
Net proceeds from initial public offering		$ 98.1

- Definition

Cash includes currency on hand as well as demand deposits with banks or financial institutions. It also includes other kinds of accounts that have the general characteristics of demand deposits in that the customer may deposit additional funds at any time and effectively may withdraw funds at any time without prior notice or penalty. Cash equivalents, excluding items classified as marketable securities, include short-term, highly liquid Investments that are both readily convertible to known amounts of cash, and so near their maturity that they present minimal risk of changes in value because of changes in interest rates. Generally, only investments with original maturities of three months or less qualify under that definition. Original maturity means original maturity to the entity holding the investment. For example, both a three-month US Treasury bill and a three-year Treasury note purchased three months from maturity qualify as cash equivalents. However, a Treasury note purchased three years ago does not become a cash equivalent when its remaining maturity is three months. Short-term investments, exclusive of cash equivalents, generally consist of marketable securities intended to be sold within one year (or the normal operating cycle if longer) and may include trading securities, available-for-sale securities, or held-to-maturity securities (if maturing within one year), as applicable.

+ References+ Details

- Definition

Number of new stock issued during the period.

+ References+ Details

Summary of Significant Accounting Policies (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011
Activity related to Non-Controlling Interest
Net loss attributable to Silver Creek	$ (113)	$ (145)	$ (231)	$ (223)
Cash, Cash Equivalents and Restricted Cash
Restricted cash	481		481		381
Silver Creek
Non-Controlling Interest
Ownership interest (as a percent)	74.00%		74.00%
Activity related to Non-Controlling Interest
Balance at the beginning of the period			574	1,027
Net loss attributable to Silver Creek			(231)	(223)
Balance at the end of the period	$ 343	$ 804	$ 343	$ 804

- Definition

Total of all stockholders' equity (deficit) items, net of receivables from officers, directors, owners, and affiliates of the entity which is directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent (that is, noncontrolling interest, previously referred to as minority interest).

+ References+ Details

- Definition

Amount of Net Income (Loss) attributable to noncontrolling interest.

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- Definition

The carrying amounts of cash and cash equivalent items which are restricted as to withdrawal or usage. Restrictions may include legally restricted deposits held as compensating balances against borrowing arrangements, contracts entered into with others, or entity statements of intention with regard to particular deposits; however, time deposits and short-term certificates of deposit are not generally included in legally restricted deposits. Excludes compensating balance arrangements that are not agreements which legally restrict the use of cash amounts shown on the balance sheet. This element is for unclassified presentations; for classified presentations there is a separate and distinct element.

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Summary of Significant Accounting Policies (Details 2) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2012
Amortized Cost
Amortized Cost	$ 74,718
Unrealized Gains
Unrealized Gains	1
Unrealized Losses
Unrealized Losses	(50)
Fair Value
Fair Value	74,669
Number of securities in unrealized loss position for less than 12 months	22
Aggregate fair value of marketable securities in unrealized loss position
Aggregate Fair Value	66,171
Unrealized loss position
Unrealized Losses	(50)
Corporate debt securities
Amortized Cost
Amortized Cost	73,718
Unrealized Gains
Unrealized Gains	1
Unrealized Losses
Unrealized Losses	(49)
Fair Value
Fair Value	73,670
Aggregate fair value of marketable securities in unrealized loss position
Aggregate Fair Value	65,172
Unrealized loss position
Unrealized Losses	(49)
U.S. Government agencies securities
Amortized Cost
Amortized Cost	1,000
Unrealized Losses
Unrealized Losses	(1)
Fair Value
Fair Value	999
Aggregate fair value of marketable securities in unrealized loss position
Aggregate Fair Value	999
Unrealized loss position
Unrealized Losses	$ (1)
Minimum
Available-for-sale securities
Expected average maturities period of marketable securities classified as available-for-sale	3 months
Maximum
Available-for-sale securities
Expected average maturities period of marketable securities classified as available-for-sale	12 months

Summary of Significant Accounting Policies (Details 3) (USD $)	3 Months Ended		6 Months Ended			1 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011	Apr. 30, 2012 Initial public offering
Public Offering
Convertible preferred stock converted into common stock (in shares)						66,255,529
Convertible Preferred Stock and Convertible Preferred Stock Warrants
Change in fair value of convertible preferred stock warrants	$ 29,000	$ 141,000	$ 587,000	$ (576,000)
Preferred stock
Authorized undesignated preferred stock (in shares)	10,000,000		10,000,000		0
Preferred stock, par value (in dollars per share)	$ 0.01		$ 0.01		$ 0.01
Comprehensive Income (Loss)
Net loss attributable to Merrimack Pharmaceuticals, Inc.	(20,026,000)	(29,051,000)	(43,310,000)	(42,508,000)
Unrealized loss on available-for-sale securities	(49,000)		(49,000)
Comprehensive loss	(20,075,000)	(29,051,000)	(43,359,000)	(42,508,000)
Other Income (Expense)
Settlement from former service provider				1,800,000
Deferred Financing Costs
Deferred financing costs					1,946,000
Deferred financing costs netted against the equity proceeds within stockholders' equity			$ 2,748,000

Initial Public Offering (Details) (Initial public offering, USD $) In Millions, except Share data, unless otherwise specified	1 Months Ended
	Apr. 30, 2012
Public Offering
Convertible preferred stock converted into common stock (in shares)	66,255,529
Cash dividends payable to Series B convertible preferred stock holders	$ 4.3
Common stock
Public Offering
Aggregate shares of common stock sold in connection with initial public offering	15,042,459
Public offering price (in dollars per share)	$ 7.00
Common stock issued to underwriters under an over-allotment option (in shares)	742,459
Net proceeds from initial public offering	$ 98.1

- Definition

The number of new shares issued in the conversion of stock in a noncash (or part noncash) transaction. Noncash is defined as transactions during a period that do not result in cash receipts or cash payments in the period. "Part noncash" refers to that portion of the transaction not resulting in cash receipts or cash payments in the period.

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- Definition

Equity impact of preferred stock cash dividends declared by an entity during the period. This element includes paid and unpaid dividends declared during the period.

+ References+ Details

- Definition

Number of new stock issued during the period.

+ References+ Details

Net Loss Per Common Share (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Numerator - basic:
Net loss attributable to Merrimack Pharmaceuticals, Inc.	$ (20,026)	$ (29,051)	$ (43,310)	$ (42,508)
Plus: Unaccreted dividends on convertible preferred stock	(67)	(2,129)	(2,107)	(3,666)
Net loss available to common stockholders - basic	(20,093)	(31,180)	(45,417)	(46,174)
Numerator - diluted:
Net loss attributable to Merrimack Pharmaceuticals, Inc.	(20,026)	(29,051)	(43,310)	(42,508)
Plus: Unaccreted dividends on convertible preferred stock	(67)	(2,129)	(2,107)	(3,666)
Net loss available to common stockholders - diluted	$ (20,093)	$ (31,180)	$ (45,417)	$ (46,174)
Denominator:
Weighted-average common shares-basic and diluted	90,581	11,282	51,214	11,158
Net loss per share available to common stock holders-basic and diluted	$ (0.22)	$ (2.76)	$ (0.89)	$ (4.14)
Convertible preferred stock
Potentially dilutive securities excluded from computation of diluted weighted average shares
Potentially dilutive securities (in shares)				66,256
Options to purchase common stock
Potentially dilutive securities excluded from computation of diluted weighted average shares
Potentially dilutive securities (in shares)			17,455	17,728
Convertible preferred stock warrants
Potentially dilutive securities excluded from computation of diluted weighted average shares
Potentially dilutive securities (in shares)				303
Common stock warrants
Potentially dilutive securities excluded from computation of diluted weighted average shares
Potentially dilutive securities (in shares)			2,905	2,937

License and Collaboration Agreements (Details) (USD $)	3 Months Ended		6 Months Ended		1 Months Ended	3 Months Ended		6 Months Ended			18 Months Ended	3 Months Ended	1 Months Ended	3 Months Ended		6 Months Ended		1 Months Ended		3 Months Ended
License and Collaboration Agreements (Details) (USD $)	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Nov. 30, 2009 License and Collaboration Agreements Sanofi	Jun. 30, 2012 License and Collaboration Agreements Sanofi	Jun. 30, 2011 License and Collaboration Agreements Sanofi	Jun. 30, 2012 License and Collaboration Agreements Sanofi	Jun. 30, 2011 License and Collaboration Agreements Sanofi	Dec. 31, 2011 License and Collaboration Agreements Sanofi	Dec. 31, 2011 License and Collaboration Agreements Sanofi Phase 2 clinical trials in breast cancer and non-small cell lung cancer	Mar. 31, 2012 License and Collaboration Agreements Sanofi Phase 2 clinical trial in ovarian cancer	May 31, 2011 License and Collaboration Agreements PharmaEngine	Jun. 30, 2012 License and Collaboration Agreements PharmaEngine	Jun. 30, 2011 License and Collaboration Agreements PharmaEngine	Jun. 30, 2012 License and Collaboration Agreements PharmaEngine	Jun. 30, 2011 License and Collaboration Agreements PharmaEngine	May 31, 2011 License and Collaboration Agreements PharmaEngine Development and regulatory milestone	May 31, 2011 License and Collaboration Agreements PharmaEngine Sales milestone	Mar. 31, 2012 License and Collaboration Agreements PharmaEngine Phase 3 clinical trial in pancreatic cancer
License and collaboration agreements
Upfront license fee received					$ 60,000,000
Milestone payments received											20,000,000	5,000,000
Expected development period from the effective date of agreement					12 years
Recognized revenue under collaboration agreements
Upfront payment						1,250,000	1,250,000	2,500,000	2,500,000
Milestone payment						521,000	209,000	1,933,000	417,000
Development services						9,160,000	4,687,000	17,302,000	9,392,000
Manufacturing services and other						1,106,000	439,000	1,627,000	694,000
Total						12,037,000	6,585,000	23,362,000	13,003,000
Assets and liabilities related to collaboration agreement
Accounts receivable, billed						2,013,000		2,013,000		4,478,000
Accounts receivable, unbilled						4,909,000		4,909,000		2,925,000
Deferred revenue						85,057,000		85,057,000		84,466,000
Collaborative arrangement additional information
Upfront license feess paid													10,000,000		10,000,000
Maximum milestone payment obligation																		80,000,000	130,000,000
Milestone payment																				5,000,000
Research and development expenses	$ 28,758,000	$ 31,187,000	$ 60,409,000	$ 49,188,000										$ 300,000	$ 10,500,000	$ 5,600,000	$ 10,500,000

Fair Value of Financial Instruments (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Assets
Investments	$ 74,669
Liabilities
Convertible preferred stock warrants		1,516
Corporate debt securities
Assets
Investments	73,670
U.S. Government agencies securities
Assets
Investments	999
Recurring basis \| Level 1
Assets
Cash equivalents - money market funds	23,794
Recurring basis \| Level 1 \| U.S. treasury securities
Assets
Cash equivalents		35,076
Recurring basis \| Level 2 \| Corporate debt securities
Assets
Cash equivalents	6,000
Investments	73,670
Recurring basis \| Level 2 \| U.S. Government agencies securities
Assets
Investments	999
Recurring basis \| Level 3
Liabilities
Convertible preferred stock warrants		$ 1,516

- Definition

This element represents the portion of the balance sheet assertion valued at fair value by the entity whether such amount is presented as a separate caption or as a parenthetical disclosure. Additionally, this element may be used in connection with the fair value disclosures required in the footnote disclosures to the financial statements. The element may be used in both the balance sheet and disclosure in the same submission. This item represents Available-for-sale Securities which consist of all investments in certain debt and equity securities neither classified as trading or held-to-maturity securities. A debt security represents a creditor relationship with an enterprise. Debt securities include, among other items, US Treasury securities, US government securities, municipal securities, corporate bonds, convertible debt, commercial paper, and all securitized debt instruments. An equity security represents an ownership interest in an enterprise or the right to acquire or dispose of an ownership interest in an enterprise at fixed or determinable prices. Equity securities include, among other things, common stock, certain preferred stock, warrant rights, call options, and put options, but do not include convertible debt. An entity may opt to provide the reader with additional narrative text to better understand the nature of investments in debt and equity securities which are categorized as Available-for-sale.

+ References+ Details

- Definition

Amount of short-term, highly liquid investments that are both readily convertible to known amounts of cash and so near their maturity that they present insignificant risk of changes in value because of changes in interest rates. Excludes cash and cash equivalents within disposal group and discontinued operation.

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- Definition

Investment in short-term money-market instruments (such as commercial paper, banker's acceptances, repurchase agreements, government securities, certificates of deposit, and so forth) which are highly liquid (that is, readily convertible to known amounts of cash) and so near their maturity that they present an insignificant risk of changes in value because of changes in interest rates. Generally, only investments with original maturities of three months or less qualify as cash equivalents by definition. Original maturity means an original maturity to the entity holding the investment. For example, both a three-month US Treasury bill and a three-year Treasury note purchased three months from maturity qualify as cash equivalents. However, a Treasury note purchased three-years ago does not become a cash equivalent when its remaining maturity is three months.

+ References+ Details

Fair Value of Financial Instruments (Details 2) (Convertible preferred stock warrants, USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2012
Convertible preferred stock warrants
Roll-forward of the fair value of the convertible preferred stock warrants categorized as Level 3 instruments
Balance at the beginning of the period	$ 1,516
Unrealized gain/loss included in other income (expense)	(587)
Reclassification to common stock warrants	$ (929)

Accrued Expenses and Other (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Accrued expenses and other
Goods and services	$ 8,708	$ 9,189
Payroll and related benefits	4,313	3,666
Contractual liability	1,092
Accrued expenses and other	$ 14,113	$ 12,855

- Definition

Aggregate carrying amount of current liabilities (due within one year or within the normal operating cycle if longer) not separately disclosed in the balance sheet. Includes costs that are statutory in nature, are incurred on contractual obligations, or accumulate over time and for which invoices have not yet been received or will not be rendered and of liabilities not separately disclosed.

+ References+ Details

Common Stock (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011
Common Stock
Common stock, authorized shares	200,000	200,000	138,500
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01	$ 0.01
Common stock, issued shares	93,540		11,834
Common stock, outstanding shares	93,540		11,834
Shares reserved for future issuance
Conversion of Series B, Series C, Series D, Series E, Series F and Series G convertible preferred stock			66,256
Convertible preferred stock warrants			302
Common stock warrants	2,905		2,640
Equity compensation plans	17,455		17,617
Shares reserved for future issuance	20,360		86,815

Stock-Based Compensation (Details)	3 Months Ended		6 Months Ended		3 Months Ended		6 Months Ended		3 Months Ended		6 Months Ended					6 Months Ended	1 Months Ended	6 Months Ended		1 Months Ended
Stock-Based Compensation (Details)	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012 Minimum	Jun. 30, 2011 Minimum	Jun. 30, 2012 Minimum	Jun. 30, 2011 Minimum	Jun. 30, 2012 Maximum	Jun. 30, 2011 Maximum	Jun. 30, 2012 Maximum	Jun. 30, 2011 Maximum	Jun. 30, 2012 Employee	Jun. 30, 2011 Employee	Dec. 31, 2011 2008 Plan	Jun. 30, 2012 2008 Plan Employee	Apr. 30, 2012 2011 Plan	Jun. 30, 2012 2011 Plan Employee	Jun. 30, 2011 2011 Plan Non-employee	Apr. 30, 2012 2011 Plan Director
Stock-based compensation
Common stock available for issuance (in shares)															830,000
Additional common stock available for issuance (in shares)																	3,500,000
Stock options issued (in shares)			294,000										300,000	1,900,000					100,000
Vesting period																3 years		3 years		1 year
Assumptions used to estimate grant date fair value of options granted
Risk-free interest rate (as a percent)		2.50%		2.50%	0.89%		0.89%		1.11%		1.11%
Expected dividend yield (as a percent)	0.00%	0.00%	0.00%	0.00%
Expected term					5 years 9 months 18 days	5 years	5 years 9 months 18 days	5 years	5 years 10 months 24 days	5 years 10 months 24 days	5 years 10 months 24 days	5 years 10 months 24 days
Expected volatility (as a percent)		73.00%		73.00%	71.00%		71.00%		72.00%		72.00%

Stock-Based Compensation (Details 2) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Stock-based compensation
Stock-based compensation expense for employee awards	$ 1,377	$ 2,708	$ 2,715	$ 3,681
Stock-based compensation expense for non-employee awards	33	56	34	103
Total stock-based compensation expense	1,410	2,764	2,749	3,784
Research and development
Stock-based compensation
Stock-based compensation expense for employee awards	945	933	1,853	1,633
General and administrative
Stock-based compensation
Stock-based compensation expense for employee awards	$ 432	$ 1,775	$ 862	$ 2,048

- Definition

Represents the expense recognized during the period arising from equity-based compensation arrangements (for example, shares of stock, unit, stock options or other equity instruments) with employees, directors and certain consultants qualifying for treatment as employees.

+ References+ Details

Stock-Based Compensation (Details 3) (USD $) In Thousands, except Per Share data, unless otherwise specified	6 Months Ended
	Jun. 30, 2012
Number of shares
Outstanding at the beginning of the period (in shares)	17,617
Granted (in shares)	294
Exercised (in shares)	(378)
Forfeited (in shares)	(78)
Outstanding at the end of the period (in shares)	17,455
Exercisable at the end of the period (in shares)	14,529
Vested and expected to vest at the end of the period (in shares)	17,304
Weighted average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 2.56
Granted (in dollars per share)	$ 6.73
Exercised (in dollars per share)	$ 2.24
Forfeited (in dollars per share)	$ 3.42
Outstanding at the end of the period (in dollars per share)	$ 2.63
Exercisable at the end of the period (in dollars per share)	$ 2.27
Vested and expected to vest at the end of the period (in dollars per share)	$ 2.61
Aggregate intrinsic value
Outstanding at the beginning of the period (in dollars)	$ 74,329
Outstanding at the end of the period (in dollars)	81,093
Exercisable at the end of the period (in dollars)	72,740
Vested and expected to vest at the end of the period (in dollars)	$ 80,782

Commitments and Contingencies (Details) (USD $)	1 Months Ended	3 Months Ended		6 Months Ended		1 Months Ended	3 Months Ended
Commitments and Contingencies (Details) (USD $)	Mar. 31, 2012	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011	Nov. 30, 2009 License and Collaboration Agreements Sanofi	Mar. 31, 2012 Quality control issues related to fill-finish manufacturing services License and Collaboration Agreements Sanofi	Jun. 30, 2012 Quality control issues related to fill-finish manufacturing services License and Collaboration Agreements Sanofi
Operating leases
Total rent expense		$ 1,089,000	$ 797,000	$ 1,981,000	$ 1,497,000
Lease term of additional space	7 years
Aggregate rent due over amended term of lease	2,700,000
Maximum reimbursement for tenant improvements agreed by landlord	464,000
Contractual matter
Previously billed amount the Company will reimburse								1,200,000
Expected development period from the effective date of agreement						12 years
Reduction in earnings due to reimbursement of previously billed amounts							$ 200,000

Related Party Transactions (Details) (Sanofi)	1 Months Ended
Related Party Transactions (Details) (Sanofi)	Apr. 30, 2012
Sanofi
Related Party Transactions
Shares of common stock purchased by related party in connection with initial public offering	5,217,391