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FORM 10-Q SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549
 (Mark One)þ
    
    Quarterly Report Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934 for the quarterly period ended
March 31, 2005, oro
    
    Transition Period Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934 for the Transition Period From
to
..
 Commission file number 0-19591 EPIMMUNE INC.  Delaware
    
    33-0245076(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification No.)
 5820 Nancy Ridge Drive
San Diego, California 92121 
  (858) 860-2500 
  Indicate by check mark whether the registrant (1) has filed all reports required to be filed by
Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for
such shorter period that the registrant was required to file such reports), and (2) has been
subject to such filing requirements for the past 90 days. Yes þ No o Indicate by check mark whether the Registrant is an accelerated filer as defined in Rule 12b-2 of
the Securities Exchange Act of 1934. Yes o No þ Indicate the number of shares outstanding of each of the issuers classes of common stock, as of
the latest practicable date. Common Stock: $.01 par value 16,023,786 shares outstanding as of May 13, 2005.




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EPIMMUNE INC.
QUARTERLY REPORT
FORM 10-Q COVER PAGE
    
    
    1TABLE OF CONTENTS
    
    
    2PART I. FINANCIAL INFORMATIONITEM 1.
    
    Financial StatementsCondensed Balance Sheets as of March 31, 2005 (unaudited) and December 31, 2004
    
    
    3Condensed Statements of Operations (unaudited) for the Three Months Ended March 31, 2005 and 2004
    
    
    4Condensed Statements of Cash Flows (unaudited) for Three Months Ended March 31, 2005 and 2004
    
    
    5Notes to Condensed Financial Statements (unaudited)
    
    
    6ITEM 2.
    
    Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    10ITEM 3.
    
    Quantitative and Qualitative Disclosures about Market Risk
    
    
    15Risk Factors
    
    
    16ITEM 4.
    
    Controls and Procedures
    
    
    29PART II. OTHER INFORMATIONITEM 1.
    
    Legal Proceedings
    
    
    30ITEM 2.
    
    Unregistered Sales of Equity Securities and Use of Proceeds
    
    
    *ITEM 3.
    
    Defaults upon Senior Securities
    
    
    *ITEM 4.
    
    Submission of Matters to a Vote of Security Holders
    
    
    *ITEM 5.
    
    Other Information
    
    
    *ITEM 6.
    
    Exhibits
    
    
    30SIGNATURE
    
    
    
    
    33EXHIBIT 31.1EXHIBIT 31.2EXHIBIT 32.1
    *
    No information provided due to inapplicability of item. 2




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PART I. FINANCIAL
INFORMATION 
 ITEM I. FINANCIAL
STATEMENTS
 
 EPIMMUNE INC
CONDENSED BALANCE SHEETS
(in thousands, except share and per share data) March 31,
    
    
    December 31,2005
    
    
    2004(unaudited)ASSETSCurrent assets:Cash and cash equivalents
    
    $
    5,673
    
    
    $
    7,006Accounts receivable
    
    
    1,110
    
    
    
    2,667Prepaids and other current assets
    
    
    334
    
    
    
    221Total current assets
    
    
    7,117
    
    
    
    9,894Restricted long-term cash
    
    
    354
    
    
    
    354Property and equipment, net
    
    
    962
    
    
    
    1,032Patents and other assets
    
    
    3,447
    
    
    
    3,527TOTAL ASSETS
    
    $
    11,880
    
    
    $
    14,807LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable, trade
    
    $
    1,213
    
    
    $
    1,013Accrued liabilities
    
    
    1,008
    
    
    
    1,700Deferred contract revenues
    
    
    493
    
    
    
    607Accrued payroll and related expenses
    
    
    192
    
    
    
    161Total current liabilities
    
    
    2,906
    
    
    
    3,481Deferred rent
    
    
    208
    
    
    
    210Stockholders equity:Preferred stock, $.01 par value, 10,000,000 shares authorized,
1,409,288 shares issued and outstanding of Series S and S-1 convertible
preferred stock at March 31, 2005 and December 31, 2004. Liquidation
preference of $10,000,000 at March 31, 2005 and December 31, 2004.
    
    
    14
    
    
    
    14Common stock, $.01 par value, 40,000,000 shares authorized,
16,023,786 shares and 16,011,655 shares issued and outstanding
at March 31, 2005 and December 31, 2004, respectively.
    
    
    160
    
    
    
    160Additional paid-in capital
    
    
    172,942
    
    
    
    172,933Deferred compensation
    
    
    (165
    )
    
    
    (184
    )Accumulated deficit
    
    
    (164,185
    )
    
    
    (161,807
    )Total stockholders equity
    
    
    8,766
    
    
    
    11,116TOTAL LIABILITIES AND STOCKHOLDERS EQUITY
    
    $
    11,880
    
    
    $
    14,807
 See accompanying notes. 3




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EPIMMUNE INC.
CONDENSED STATEMENTS OF OPERATIONS
(unaudited)
(in thousands, except per share data) Three months ended March 31,2005
    
    
    2004RevenuesLicense fees and milestones
    
    $
    114
    
    
    $
    97Research grants and contract revenue
    
    
    1,719
    
    
    
    1,454Related party revenue
    
    
    
    
    
    
    1,026Total revenues
    
    
    1,833
    
    
    
    2,577Costs and expenses:Research and development
    
    
    2,686
    
    
    
    2,407General and administrative
    
    
    467
    
    
    
    658Business combination transaction costs
    
    
    1,089
    
    
    
    Total costs and expenses
    
    
    4,242
    
    
    
    3,065Loss from operations
    
    
    (2,409
    )
    
    
    (488
    )Interest income, net
    
    
    36
    
    
    
    4Other expense, net
    
    
    (5
    )
    
    
    (1
    )Net loss
    
    $
    (2,378
    )
    
    $
    (485
    )Net loss per
share - basic and diluted
    
    $
    (0.15
    )
    
    $
    (0.04
    )Shares used in computing net loss per share
    
    
    16,015
    
    
    
    13,456
 See accompanying notes. 4




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EPIMMUNE INC. 
 CONDENSED STATEMENTS OF CASH FLOWS
(unaudited)
(in thousands)
 Three months ended March 31,2005
    
    
    2004OPERATING ACTIVITIESNet loss
    
    $
    (2,378
    )
    
    $
    (485
    )Adjustments to reconcile net loss to net cash used in operating
activities:Depreciation and amortization
    
    
    215
    
    
    
    220Stock-based compensation
    
    
    17
    
    
    
    12Deferred rent
    
    
    (2
    )
    
    
    3Deferred revenue
    
    
    (114
    )
    
    
    (229
    )Write-off of abandoned patents
    
    
    102
    
    
    
    Change in operating assets and liabilities:Accounts receivable
    
    
    1,557
    
    
    
    (559
    )Prepaids and other current assets
    
    
    (113
    )
    
    
    (179
    )Accounts payable, trade
    
    
    200
    
    
    
    290Accrued liabilities
    
    
    (685
    )
    
    
    (184
    )Accrued payroll and related expenses
    
    
    31
    
    
    
    152Net cash used in operating activities
    
    
    (1,170
    )
    
    
    (959
    )INVESTING ACTIVITIESPurchase of property and equipment
    
    
    (3
    )
    
    
    (17
    )Patents and other assets
    
    
    (163
    )
    
    
    (244
    )Net cash used in investing activities
    
    
    (166
    )
    
    
    (261
    )FINANCING ACTIVITIESNet proceeds from issuance of common stock
    
    
    3
    
    
    
    5Net cash provided by financing activities
    
    
    3
    
    
    
    5Decrease in cash and cash equivalents
    
    
    (1,333
    )
    
    
    (1,215
    )Cash and cash equivalents at beginning of year
    
    
    7,006
    
    
    
    6,416Cash and cash equivalents at end of period
    
    $
    5,673
    
    
    $
    5,201SUPPLEMENTAL DISCLOSURE OF CASH FLOW
INFORMATIONInterest paid
    
    $
    1
    
    
    $
    2Reclassification of unvested common shares from liabilities to equity
    
    $
    7
    
    
    $
    44
 See accompanying notes. 5




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EPIMMUNE INC.
NOTES TO CONDENSED FINANCIAL STATEMENTS
(unaudited)
March 31, 2005 1. Basis of Presentation The interim unaudited condensed financial statements contained herein have been prepared in
accordance with U.S. generally accepted accounting principles for interim financial information.
Accordingly, they do not include all of the information and disclosures required by U.S. generally
accepted accounting principles for complete financial statements. In managements opinion, the
unaudited information includes all adjustments, consisting only of normal recurring adjustments,
necessary for a fair presentation of the financial position, results of operations and cash flows
for the periods presented. Interim results are not necessarily indicative of results to be
expected for the full year. The financial statements should be read in conjunction with the
audited financial statements and disclosures thereto included in the Companys Form 10-K, as
amended, for the year ended December 31, 2004. The preparation of financial statements in conformity with accounting principles generally accepted
in the United States requires management to make estimates and assumptions that affect the reported
amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the
date of the financial statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates. The Company has an accumulated deficit of $164.2 million as of March 31, 2005. The Companys
ability to attain profitable operations is dependent upon obtaining sufficient working capital to
complete the successful development of its products, regulatory approval of its products, achieving
market acceptance of such products and achievement of sufficient levels of revenue to support the
Companys cost structure. In March 2005 the Company agreed to combine its business with IDM S.A. (Immuno-Designed Molecules),
or IDM. If the planned combination is successful the Company expects to be able to maintain its
current level of operations through 2005, based on anticipated expenditures. If the planned
combination is unsuccessful, management intends to take the appropriate steps, including the delay
or discontinuation of certain of its research and development programs and operational activities,
to ensure that the Company will have sufficient funds to support its operations through at least
December 31, 2005. The Company would also anticipate seeking additional equity financing if the
planned combination with IDM is unsuccessful. While the Company has been successful in raising
equity financing in the past, there can be no assurance that the Company will be able to raise
additional funds in the future, and it will likely be even more difficult to raise additional
funding on satisfactory terms, if at all, if the IDM transaction is not completed. Earnings per share (EPS) is computed in accordance with Statement of Financial Accounting
Standards (SFAS) No. 128, Earnings per Share. SFAS No. 128 requires dual presentation of basic and
diluted earnings per share. Basic EPS includes no dilution and is computed by dividing net income
by the weighted average number of common shares outstanding for the period, excluding owned but
unvested shares. There were 0 and 56,511 owned but unvested shares as of March 31, 2005 and 2004,
respectively, which were excluded from the earnings per share calculation. Diluted EPS reflects
the potential dilution of securities that could share in the Companys earnings, such as common
stock equivalents that may be issuable upon exercise of outstanding common stock options or
warrants as well as all shares of preferred stock, which may be converted into common stock. Prior
to the application of the treasury stock method, common stock equivalents of 6,459,314 and 4,278,439 for the three months
ended March 31, 2005 and 2004, respectively, have been excluded from EPS as the effect is
antidilutive. 6




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The following table shows total shares outstanding as of March 31, 2005 and 2004, respectively, on
a fully diluted basis, assuming full vesting and conversion of all common stock equivalents upon
exercise of outstanding common stock options and warrants as well as conversion of all shares of
preferred stock: 2005
    
    
    2004Common stock outstanding
    
    
    16,023,786
    
    
    
    13,525,622Preferred shares, as converted
    
    
    1,787,572
    
    
    
    1,703,298Options outstanding
    
    
    2,396,316
    
    
    
    1,777,943Warrants outstanding
    
    
    2,275,426
    
    
    
    797,198Fully diluted shares
    
    
    22,483,100
    
    
    
    17,804,061
 As permitted by SFAS No. 123, Accounting for Stock-based Compensation, the Company elected to
follow Accounting Principles Board (APB) Opinion No. 25, Accounting for Stock Issued to Employees,
and related interpretations in accounting for its employee stock options. Under APB Opinion No. 25,
among other things, when the exercise price of its employee stock options is not less than the
market price of the underlying stock on the date of grant, no compensation expense is recognized. As required under SFAS No. 123 and SFAS No. 148, Accounting for Stock-Based Compensation -
Transition and Disclosure, the pro forma effects of stock-based compensation on net income and net
earnings per common share have been estimated at the date of grant using the Black-Scholes option
pricing model based on the following weighted average assumptions for March 31, 2005 and March 31,
2004: risk-free interest rates of 4% and 4.5%, respectively; dividend yield of zero for both
periods; and a weighted average expected life for all options of six years. The volatility factor
assumptions of the expected market price of the Companys common stock were 59% and 107% for March
31, 2005 and 2004, respectively. For purposes of adjusted pro forma disclosures, the estimated fair value of the options is
amortized to expense over the options vesting period. The effect of applying SFAS No. 123 for
purposes of providing pro forma disclosures is not likely to be representative of the effects on
the Companys operating results for future years because changes in the subjective input
assumptions can materially affect future value estimates. Pro forma information for the three
months ended March 31, 2005 and 2004 is as follows: Three months ended March 31,2004
    
    
    2003Net loss as reported
    
    $
    (2,378,000
    )
    
    $
    (485,000
    )Add: stock-based employee compensation expense
included in reported net loss
    
    
    15,000
    
    
    
    Deduct: total stock-based employee compensation expense
determined under fair value based method for all awards
    
    
    (288,000
    )
    
    
    (216,000
    )Pro forma net loss
    
    $
    (2,651,000
    )
    
    $
    (701,000
    )Net loss per share:Basic and diluted  as reported
    
    $
    (0.15
    )
    
    $
    (0.04
    )Basic and diluted  pro forma
    
    $
    (0.17
    )
    
    $
    (0.05
    )
 In December 2004, the Financial Accounting Standards Board issued SFAS No. 123(R),
Share-Based Payments, which replaces SFAS No. 123 and supersedes APB Opinion No. 25. SFAS No.
123(R) will require all share-based payments to employees, including grants of employee stock
options, to be recognized in the statement of operations based on their fair values. SFAS No. 123(R) offers
alternative methods for determining the fair value. In April 2005, the SEC issued a new rule that
allows companies to implement SFAS No. 123(R) at the beginning of the next fiscal year, instead of
the next reporting 7




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period, that begins after June 15, 2005. As a result, we will implement SFAS No.
123(R) in the reporting period starting January 1, 2006. We expect that SFAS No. 123(R) will have a
significant impact on our financial statements. At the present time, we have not yet determined
which valuation method we will use. The impact of adoption of SFAS No. 123(R) cannot be accurately
predicted at this time because it will depend on levels of share-based payments granted in the
future. However, had the Company adopted Statement No. 123(R) in prior periods, the impact of that
standard would have approximated the impact of Statement No. 123 as described in the disclosure of
pro forma net income and earnings per share included elsewhere in this Note 1 to the financial
statements. 2. Proposed Business Combination with IDM S.A. On March 16, 2005, the Company announced that it had agreed to combine its business with IDM, a
privately held company based in France, pursuant to a Share Exchange Agreement, as amended, or the
Share Exchange Agreement. The all-stock transaction has been unanimously approved by the boards of
directors of both companies. In addition, as of May 9, 2005, IDM shareholders collectively owning
more than 95% of the IDM shares had thus far entered into the Share Exchange Agreement. Under Nasdaq National Market rules, the Company must obtain shareholder approval of the issuance of
shares of its common stock contemplated by the Share Exchange Agreement. On April 22, 2005, the
Company filed a preliminary proxy statement with the Securities and Exchange Commission, or SEC, to
seek approval from its shareholders of the issuance of shares of Epimmune common stock pursuant to
the Share Exchange Agreement and related transactions, as well as approval of certain related
actions including changing the Companys corporate name to IDM, Inc., increasing its authorized
shares of capital stock and effecting a reverse split of its outstanding common stock. The closing
of the transaction with IDM is subject to, among other things, approval by the Companys
shareholders of the foregoing actions and other customary closing conditions. Upon closing of the
transaction, the combined companys shares are expected to be traded on the Nasdaq National Market
under the symbol IDMI. The combined company will focus on immunotherapeutic products for cancer
and selected infectious diseases. Pursuant to the Share Exchange Agreement, the Company will acquire all of the outstanding shares of
IDM, except shares and a warrant held in French share savings plans, in exchange for shares of the
Companys common stock, and IDM will become a subsidiary of the Company. Each share of IDM will be
exchanged for approximately 3.771865 shares of the Companys common stock, and the former
shareholders of IDM will hold, in aggregate, approximately 78% of the Companys outstanding common
stock, on a fully diluted basis, immediately following the closing of the transaction. In
connection with the transaction, the Companys outstanding Series S and Series S-1 preferred stock
will be exchanged for a total of 1,949,278 shares of the Companys common stock, pursuant to an
Amended and Restated Preferred Exchange Agreement dated April 12, 2005 between the Company and G.D.
Searle, LLC, the holder of all of the outstanding shares of preferred stock of the Company. The
Share Exchange Agreement also sets forth the terms for treatment of outstanding options and
warrants to purchase IDM shares in the transaction. Subsequent to the transaction, the shareholders of IDM will effectively control the Company. As a
result, if approved and completed, the transaction will be accounted for as a reverse acquisition
in which, for financial reporting purposes, IDM is considered the acquiring company. Following the
closing of the transaction, the historical financial statements of IDM will become the historical
financial statements of the Company and include the results of operations of the Company only from
the acquisition date forward. The shares the Company will issue in the exchange will not be registered under U.S. securities laws
and may not be offered or sold in the U.S. absent registration or unless an applicable exemption
from the 8




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registration requirements is available. The Company has agreed to file a registration
statement covering the resale of the shares issued in the transaction following the closing of the
transaction. We have filed a proxy statement concerning our proposed combination with IDM with the SEC, which
explains the proposed transaction in greater detail, including the risks involved. Investors and
security holders are advised to read the proxy statement related to the proposed transaction
because it contains important information related to the transaction. The forgoing statements regarding the proposed transaction between Epimmune and IDM include forward
looking statements, which are subject to risks and uncertainties, including but not limited to the
possibility that the proposed transaction with IDM may not ultimately close for any of a number of
reasons, such as Epimmune not obtaining shareholder approval of the transaction or related matters;
the possibility that IDM shareholders who have not become parties to the definitive agreement make
an alternative bid regarding a transaction involving IDM to the IDM shareholders pursuant to rights
under the shareholders agreement among the IDM shareholders and, if so, that the IDM shareholders
accept that bid instead of the transaction with us; the possibility that Nasdaq will not approve
the listing of the combined companys shares for trading on the Nasdaq National Market; and the
possibility that, in the event the transaction is completed, the combination of Epimmune and IDM
may not result in a stronger company, that the technologies and clinical programs of the two
companies may not be compatible and that the parties may be unable to successfully execute their
integration strategies or realize the expected benefits of the transaction. 9




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ITEM 2.
    MANAGEMENTS DISCUSSION AND ANALYSIS OF
FINANCIAL CONDITION AND RESULTS OF OPERATIONS Except for the historical information contained herein, the following discussion contains
forward-looking statements that involve risks and uncertainties. Our actual results could differ
materially from those discussed here. Factors that could cause or contribute to such differences
include, without limitation, those discussed below and in the section entitled Risk Factors. Epimmune was incorporated in Delaware on July 10, 1987 as Cytel Corporation. On July 1, 1999,
Cytel merged with its majority-owned subsidiary, Epimmune Inc., and changed its name from Cytel
Corporation to Epimmune Inc. Epimmune(R) and PADRE(R) are our trademarks and
EIS(R) and ImmunoSense(R) are our service marks. Since 1997, we have devoted substantially all of our resources to the discovery and development of
potential therapeutic and prophylactic products. To date, we have not received any revenues from
the sale of products. We began a Phase I/II clinical trial targeting HIV in September 2002 and two
Phase I/II clinical trials targeting lung cancer and colorectal cancer in February 2003. Based on
the results we received from those clinical trials during the course of 2004, we began a Phase II
clinical trial in late-stage lung cancer patients at the end of 2004 and expect to initiate a
follow-on Phase I/II trial in HIV-infected patients in the fourth quarter of 2005 to evaluate
alternative vaccine delivery options. We have funded our research and development primarily from
equity-derived working capital and through strategic alliances and collaborations with other
companies. We have not been profitable since our inception and expect to incur substantial
operating losses for at least the next several years. As of March 31, 2005, our accumulated deficit
was approximately $164.2 million. In July 2001, we entered into a collaboration with Genencor International, Inc. to develop vaccines
to treat or prevent hepatitis B virus, hepatitis C virus and human papilloma virus. In February
2004, we announced that we had earned a milestone payment from Genencor as a result of Genencor
filing an Investigational New Drug Application, or IND, for a vaccine to treat hepatitis B, the
lead program in the collaboration. In March 2004, Genencor assigned its rights under our
collaboration agreement to Innogenetics NV. In connection with the assignment by Genencor, we
extended the collaboration term with Innogenetics through September 2005. Innogenetics has the
right to terminate the collaboration early, upon three months written notice. In April 2004, we completed a private placement of 2,466,379 shares of common stock and warrants to
purchase up to 1,233,188 shares of common stock to selected institutional and accredited investors,
including current shareholders, for a total purchase price of $5.5 million. We received net
proceeds of $5.0 million. The purchase price of each security, which is the combination of one
share of common stock and, for each two shares of common stock purchased, a warrant to purchase one
share of common stock, was priced at the market value of $2.2125, which was equal to or greater
than the sum of the closing bid price of our common stock as quoted on the Nasdaq National Market
on the date of execution of the purchase agreements, and $0.0625, the imputed value of a warrant to
purchase one share of common stock. In addition, we issued warrants to purchase an aggregate of
250,000 shares of our common stock to a placement agent for services rendered in connection with
the private placement. Each warrant, including the warrant issued to the placement agent, has a
three-year term and an exercise price equal to 120% of $2.2125 or $2.655 per share. Critical Accounting Policies Our discussion and analysis of our financial condition and results of operations are based upon our
financial statements, which have been prepared in accordance with U.S. generally accepted
accounting principles unless otherwise indicated. The preparation of these financial statements
requires us to make estimates and judgments that affect the reported amounts of assets,
liabilities, revenues and expenses, and 10




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related disclosure of contingent assets and liabilities. On an ongoing basis, we evaluate our
estimates on an ongoing basis, including those related to revenue recognition, patents and income
taxes. We base our estimates on historical experience and on various other assumptions that are
believed to be reasonable under the circumstances, the results of which form the basis for making
judgments about the carrying values of assets and liabilities that are not readily apparent from
other sources. Actual results may differ from these estimates under different assumptions or
conditions. We believe the following critical accounting policies affect the significant judgments
and estimates used in the preparation of our financial statements. Revenue Recognition We recognize revenues pursuant to Staff Accounting Bulletin No. 101, Revenue Recognition. License
fees are earned and recognized in accordance with the provisions of each agreement. Upfront
license fees for perpetual licenses where we have no performance obligations are recognized when
received. License fees under agreements in which we have ongoing involvement or performance
obligations are recognized over the term of the agreement. Milestone payments are recognized as
revenue upon the completion of the milestone as long as the milestone event was substantive, and
its achievability was not reasonably assured at inception and our performance obligations after
milestone achievement will continue to be funded at a comparable level before the milestone
achievement. Contract research and development funding is recognized as revenue in the same period
as reimbursable expenses under a contract are incurred and in an amount or at a rate billable under
each contracts terms. Revenues from grants are recognized on a percentage-of-completion basis as
related costs are incurred. We defer revenue recognition until performance obligations have been
completed and collectibility is reasonably assured. Patents We capitalize the costs incurred to file patent applications when we believe there is a high
likelihood that the patent will issue and there will be future economic benefit associated with the
patent. These costs are amortized over a ten-year life from the date of patent filing. We expense
all costs related to abandoned patent applications. In addition, we review the carrying value of
patents for indicators of impairment on a periodic basis. If we elect to abandon any of our
currently issued or unissued patents or we determine that the carrying value is impaired, the
related expense could be material to our results of operations for the period of the abandonment. Investment Policy The primary objective of our investment activities is to preserve principal while at the same time
achieving competitive yields, without significantly increasing risk. To achieve this objective, we
primarily invest in cash and money market accounts as well as A1 or P1 or higher rated debt
securities with maturities of less than two years, with the weighted average maturity not to exceed
eighteen months. We also attempt to minimize our portfolio risk by placing constraints on how much
of our portfolio may be held in a specific type of investment such as asset-backed securities or
collateralized mortgage obligations as well as limiting our holdings in any one issuer. At March
31, 2005, our investment portfolio included only cash and money market accounts and had no
fixed-income securities. Results of Operations Three months ended March 31, 2005, as compared with three months ended March 31, 2004. In the three months ended March 31, 2005, we had total revenues of $1.8 million, as compared to
$2.6 million in revenues in the three months ended March 31, 2004. The decrease in the three
months ended March 31, 2005 resulted primarily from a $1.0 million decrease in related party
revenue offset by a $0.3 million increase in research grant and contract revenue. Related party
revenue includes milestone 11




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payments, amortization of license fees and contract research and development funding, as a result
of our previous collaboration with Genencor, which owns an equity position in Epimmune. In March
2004, Genencor assigned its rights under our collaboration agreement to Innogenetics. Innogenetics
does not own an equity position in Epimmune and, therefore, is not a related party, and
reimbursements under our collaboration agreement with them are now recorded as contract revenue.
The decrease in related party revenue during the three months ended March 31, 2005, compared to the
three months ended March 31, 2004, was a result of the assignment of the collaboration agreement.
During the first quarter of 2004, we received a milestone payment from Genencor in connection with
an Investigational New Drug (IND) application filed by Genencor for a Hepatitis B vaccine candidate
on which we collaborated. In connection with the assignment by Genencor, we extended the
collaboration term with Innogenetics through September 2005. Innogenetics has the right to
terminate the collaboration early, upon three months written notice, if we breach our obligations
under the collaboration agreement or upon certain force majeure events. The increase in research
grant and contract revenue in the three months ended March 31, 2005 as compared to the three months
ended March 31, 2004 was also a result of the assignment by Genencor to Innogenetics and the
corresponding change in revenue accounts, offset by a decrease in reimbursements under grants and
contracts from the National Institutes of Health (NIH) due to the timing of costs to be reimbursed.
Licensing and milestone revenue was $0.1 million in the three months ended March 31, 2005 and in
the three months ended March 31, 2004. Research and development expenses increased to $2.7 million in the three months ended March 31,
2005 from $2.4 million in the three months ended March 31, 2004. The increase in the three months
ended March 31, 2005 primarily relates to a $0.2 million increase in subcontract and other outside
costs incurred under NIH grants and contracts, a $0.2 million increase in costs related to our
ongoing Phase II clinical trial in non-small cell lung cancer (NSCLC) which began in late December
2004, and a $0.1 million expense associated with abandoned patents in certain geographic locations.
These increases in research and development expenses were partially offset by a $0.2 million
decrease in costs related to product formulation and manufacturing of product for use in our
previous Phase I/II clinical trials in HIV and lung and colorectal cancer. General and administrative costs were approximately $0.5 million in the three months ended March
31, 2005 and $0.7 million in the three months ended March 31, 2004. The decrease in the three
months ended March 31, 2005 primarily relates to a decrease in non-cash, stock-based compensation
charges related to a lower stock price during the 2005 period for variable stock equity
instruments. We expect general and administrative expenses during 2005 to be relatively flat or
slightly lower than corresponding 2004 levels. In the three months ended March 31, 2005, we recorded $1.1 million in transaction costs associated
with our proposed business combination with IDM. These transaction costs included investment
banking advisory fees and accounting and legal fees. We expect to continue to incur transaction
costs for the next two quarters in connection with our proposed combination with IDM. Net interest income was negligible in both the three months ended March 31, 2005 and in the three
months ended March 31, 2004. We expect to incur significant operating losses over the next several years due to continuing
expenses associated with our research and development programs, including clinical trials,
preclinical testing and development activities, as well as transaction costs for our proposed
combination with IDM as described above. Operating losses may fluctuate from quarter to quarter as
a result of differences in the timing of revenues received and expenses incurred, and such
fluctuations may be substantial. Liquidity and Capital Resources We have financed operations since our inception primarily through private placements of equity
securities, two public common stock offerings, revenues under collaborative research and
development 12




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agreements, grant revenues, certain asset divestitures and interest income. Through March 31, 2005,
we had raised approximately $170.1 million from the sale of equity securities. As of March 31,
2005, we had 17,811,358 shares outstanding on an as-converted to common stock basis, assuming
conversion of all outstanding shares of our preferred stock. As of March 31, 2005, our cash and cash equivalents were $5.7 million compared to $7.0 million at
December 31, 2004. The decrease in cash and cash equivalents was due to cash used for operations,
primarily to fund our ongoing Phase II study in non-small cell lung cancer, or NSCLC, patients,
activities related to further clinical studies of our therapeutic HIV vaccine candidate, and
transaction related costs associated with our proposed business combination with IDM. Our
operating expenses were offset by license fees, milestone payments and grant and contract revenues
we received. We expect to continue to use our cash and cash equivalents to fund our ongoing and
future clinical trials, as well as drug research and development programs. Capital expenditures were negligible in the three months ended March 31, 2005 and in the three
months ended March 31, 2004. In the past, we have financed our laboratory equipment and research
and office facilities primarily through operating lease arrangements and a note payable. We fully
paid off our note payable as of the end of the first quarter of 2003. During 2005, we anticipate
that payments related to capital expenditures will continue to decrease compared to 2004 levels to
approximately $0.1 million. We will also pay approximately $0.6 million in rent on our lease
commitments during 2005. The future minimum rental commitment for the lease of our facility will
range from approximately $0.6 million to $0.7 million each year over five years, based upon
pre-established annual rent increases. Payments related to capitalized patent expenses were $0.2 million in the three months ended March
31, 2005 and in the three months ended March 31, 2004. We expect payments related to patents to be
relatively flat in 2005 compared to 2004 as we continue to pursue filings and claims in our
intellectual property portfolio. As funds are available, we expect our net cash burn to increase in 2005 compared to 2004 as we
incur costs related to ongoing clinical trials in connection with our ongoing drug research and
development programs, research and development activities on sponsored programs and contracts,
preclinical testing of product candidates and manufacturing of clinical supplies. We intend to seek
collaborative research and development relationships with suitable corporate partners and U.S.
government agencies. We have in the past and may in the future also license to third parties some
of our technology in markets that we are not pursuing ourselves or through our collaborations. Any
agreements that may result from these discussions may not successfully reduce our funding
requirements or, if entered into, may be terminated. We will continue to spend substantial amounts on research and development, including amounts spent
for manufacturing clinical supplies, conducting clinical trials for our product candidates and
advancing development of certain sponsored and partnered programs. Therefore, we will need to
secure additional funding. If we do not complete the proposed combination with IDM as planned, our
cash position will be further reduced, and it will likely be even more difficult to raise
additional funding on satisfactory terms, if at all. We do not have committed external sources of
funding and may not be able to obtain any additional funding, especially if volatile market
conditions persist for biotechnology companies. If we are unable to obtain additional funding, we
will be required to delay, further reduce the scope of or eliminate one or more of our research and
development projects, sell Epimmune or certain of its assets or technologies, or dissolve and
liquidate all of its assets. As of March 31, 2005, we had approximately $5.7 million in cash and
cash equivalents. We have incurred and will continue to incur investment banking advisory fees,
legal, accounting and other transaction costs in connection with our proposed combination with IDM.
Our future operational and capital requirements will depend on many factors, including: 13




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
    whether our proposed transaction with IDM is successfully completed;
    whether we are able to secure additional financing on favorable terms, or at all;
    the costs associated with our ongoing Phase I/II clinical trial for our vaccine
targeting HIV, which began in September 2002, including the status of our contract with the
NIH;
    the costs associated with our Phase II clinical trial for our vaccine targeting lung
cancer, which began in December 2004;
    progress with other preclinical testing and clinical trials in the future;
    our ability to establish and maintain collaboration and license agreements and any
government contracts and grants;
    the actual revenue we receive under our collaboration and license agreements;
    the actual costs we incur under our research collaboration with Bavarian Nordic;
    the time and costs involved in obtaining regulatory approvals;
    the costs involved in filing, prosecuting, enforcing and defending patent claims and any
other proprietary rights;
    competing technological and market developments;
    changes in our existing research relationships;
    continued scientific progress in our drug discovery programs; and
    the magnitude of our drug discovery and development programs. As is typical in the biotechnology industry, our commercial success will depend in part on not
infringing upon the patent or other proprietary rights of others and maintaining the technology
licenses upon which our products might be based. Our business is also subject to other significant
risks, including the uncertainties associated with our ability to enter into and maintain new
collaborations, the lengthy regulatory approval process, and potential competition from other
products. Even if our products appear promising at an early stage of development, they may not
reach the market for a number of reasons. Such reasons include, but are not limited to, our
inability to fund clinical development of such products, or the possibilities that the potential
products will be found ineffective during clinical trials, fail to receive necessary regulatory
approvals, be difficult to manufacture on a large scale or be uneconomical to market. 14




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ITEM 3.
    QUANTITATIVE AND
QUALITATIVE DISCLOSURE ABOUT MARKET RISK At March 31, 2005, our investment portfolio included only cash and money market accounts and had no
fixed-income securities. There would be no material impact to our investment portfolio, in the
short term, associated with any change in interest rates. Any decline in interest rates over time
will reduce our interest income, while increases in interest rates over time will increase our
interest income. 15




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RISK FACTORS We wish to caution readers that the following important factors, among others, in some cases have
affected our results and in the future could cause our actual results and needs to vary materially
from forward-looking statements made from time to time by us on the basis of managements
then-current expectations. The business in which we are engaged is rapidly changing and
competitive and involves a high degree of risk. Our substantial additional financing requirements and limited access to financing, which will
likely be even more limited in the absence of the proposed combination with IDM, may adversely
affect our ability to develop products and fund our operations. We will continue to spend substantial amounts on research and development, including amounts spent
for manufacturing clinical supplies, conducting clinical trials for our product candidates and
advancing development of certain sponsored and partnered programs. Therefore, we will need to
secure additional funding. If we do not complete the proposed combination with IDM as planned, our
cash position will be further reduced, and it will likely be even more difficult to raise
additional funding on satisfactory terms, if at all. We do not have committed external sources of
funding and may not be able to obtain any additional funding, especially if volatile market
conditions persist for biotechnology companies. If we are unable to obtain additional funding, we
will be required to delay, further reduce the scope of or eliminate one or more of our research and
development projects, sell Epimmune or certain of its assets or technologies, or dissolve and
liquidate all of its assets. As of March 31, 2005, we had approximately $5.7 million in cash and
cash equivalents. We have incurred and will continue to incur investment banking advisory fees,
legal, accounting and other transaction costs in connection with our proposed combination with IDM.
Our future operational and capital requirements will depend on many factors, including:  
    whether our proposed transaction with IDM is successfully completed;
    whether we are able to secure additional financing on favorable terms, or at all;
    the costs associated with our ongoing Phase I/II clinical trial for our vaccine
targeting HIV, which began in September 2002, including the status of our contract with the
NIH;
    the costs associated with our Phase II clinical trial for our vaccine targeting NSCLC,
which began in December 2004;
    progress with other preclinical testing and clinical trials in the future;
    our ability to establish and maintain collaboration and license agreements and any
government contracts and grants;
    the actual revenue we receive under our collaboration and license agreements;
    the actual costs we incur under our research collaboration with Bavarian Nordic;
    the time and costs involved in obtaining regulatory approvals;
    the costs involved in filing, prosecuting, enforcing and defending patent claims and any
other proprietary rights;
    competing technological and market developments;
    changes in our existing research relationships; 16




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
    continued scientific progress in our drug discovery programs; and
    the magnitude of our drug discovery and development programs. We intend to seek additional funding through collaboration and license agreements, government
research grants and contracts, or equity or debt financings. In the event we are able to obtain
financing, it may not be on favorable terms. In addition, we may not be able to enter into
additional collaborations to reduce our funding requirements. If we acquire funds by issuing
securities, dilution to existing stockholders will result, such as the dilution that occurred as a
result of our most recent financing in April 2004. If we raise funds through additional
collaborations and license agreements, we will likely have to relinquish some or all of the rights
to product candidates or technologies that we may have otherwise developed ourselves. If we are
unable to obtain funding, we may be required to engage in another restructuring, cease development
of some product candidates, further reduce the scope of our operations, sell the Company or certain
of its assets or technologies or cease operations. We presently do not meet all of The Nasdaq National Markets continued listing requirements and we
may be delisted, which could reduce the liquidity of our common stock and adversely affect our
ability to raise additional necessary capital. In order to continue trading on The Nasdaq National Market, we must comply with The Nasdaq National
Markets continued listing requirements, which require that we maintain a minimum stockholders
equity of $10.0 million and a minimum closing bid price of $1.00 per share. Our stockholders
equity was $8.8 million and $11.1 million as of March 31, 2005 and December 31, 2004, respectively.
We therefore did not satisfy the $10.0 million minimum stockholders equity continued listing
requirement as of the date of filing of this report. In addition, the closing bid price of our
common stock on the Nasdaq National Market has been below $1.00 since
April 14, 2005, and we will
not satisfy the $1.00 minimum closing bid price per share requirement if the closing bid price of
our common stock is less than $1.00 for a period of 30 consecutive business days. In the past, we
have been notified by Nasdaq National Market when we have failed to meet the minimum stockholders
equity continued listing requirement and have been asked to provide a plan to regain compliance.
The Nasdaq National Market has also continued to monitor our ongoing compliance with their
continued listing requirements. As a result of our failure to satisfy the continued listing
requirements at the time of filing of this quarterly report on Form 10-Q, our common stock may be
delisted from the Nasdaq National Market. We believe there is a significant risk that we will not
meet the stockholders equity requirement in the future if we do not complete the IDM transaction
and will not meet the closing bid price requirement if the reverse split of our common stock is not
approved by our stockholders. In connection with our proposed business combination with the IDM,
we believe we will satisfy both the minimum stockholders equity listing requirement and, as a
result of a planned reverse stock split, the minimum bid price listing requirement of the Nasdaq
National Market, although there can be no assurance we will do so. The delisting of our common
stock may result in the trading of the stock on the Nasdaq SmallCap Market or the OTC Bulletin
Board, which could reduce the liquidity of our common stock and adversely affect our ability to
raise additional capital. The process of developing therapeutic products requires significant research and development,
preclinical testing and clinical trials, all of which are extremely expensive and time-consuming
and may not result in a commercial product. Except for our HIV and NSCLC and colorectal cancer vaccine candidates, for which we began clinical
trials in September 2002 and February 2003 respectively, all of our potential vaccine products are
in research or preclinical development, the results of which do not necessarily predict or prove
safety or efficacy in humans. We must demonstrate for each vaccine, safety and efficacy in humans
through extensive clinical testing, which is very expensive, can take many years, and has an
uncertain outcome. We may experience numerous unforeseen events during or as a result of the
testing process that could delay or prevent testing or commercialization of our products, including
the following: 17




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
    the results of preclinical studies may be inconclusive, or they may not be indicative of
results that will be obtained in human clinical trials;
    after reviewing test results, we or our collaborators may abandon projects that we might
previously have believed to be promising;
    we, our collaborators or regulators may suspend or terminate clinical trials if the
participating subjects or patients are being exposed to unacceptable health risks;
    we may have to delay clinical trials as a result of scheduling conflicts with
participating clinicians and clinical institutions, or difficulties in identifying and
enrolling patients who meet trial eligibility criteria;
    safety and efficacy results attained in early human clinical trials may not be
indicative of results that are obtained in later clinical trials; and
    the effects our vaccine candidates have may not be the desired effects or may include
undesirable side effects or other characteristics that preclude regulatory approval or
limit their commercial use if ever approved. The data collected from clinical trials may not be sufficient to support regulatory approval of any
of our products, and the U.S. Food and Drug Administration, or FDA, may not ultimately approve any
of our therapeutic products for commercial sale, which will adversely affect our revenues and
prospects. If we fail to commence or complete, or experience delays in, any of our planned clinical
trials, our operating income, our stock price and our ability to conduct our business as currently
planned could be harmed. Some of our programs are funded by the U.S. government and the government may not allocate funds
for these programs in future fiscal years. We fund certain of our research and development related to our HIV, cancer and malaria programs
pursuant to multi-year grants and contracts from the U.S. government. The government is under no
obligation to and may not fund these programs over their full term which would have a significant
impact on our ability to continue development of our HIV, cancer and malaria programs. Our history of operating losses and our expectations of continuing losses may hurt our ability to
reach profitability or continue operations. We have experienced significant operating losses since our inception in 1987. As of March 31, 2005,
we had an accumulated deficit of $164.2 million. We expect to continue to incur substantial
operating expenses and net operating losses for the foreseeable future, which may hurt our ability
to continue operations. We have not generated revenues from the commercialization of any product.
All of our revenues to date have consisted of contract research and development revenues, license
and milestone payments, research grants, certain asset divestitures and interest income. We expect
that substantially all of our revenues for the foreseeable future will result from similar sources.
To achieve profitable operations, we, alone or with collaborators, must successfully identify,
develop, register and market proprietary products. We do not expect to generate revenues from the
commercialization of any product for at least six years (and this would assume approval of either
our HIV or lung cancer product candidates, which may not occur). We may not be able to generate
sufficient product revenue to become profitable. Even if we do achieve profitability, we may not be
able to sustain or increase our profitability on a quarterly or yearly basis. 18




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We are at an early stage of development, and we may experience delays and other problems in
entering clinical trials. We are an early stage research and development company, and only commenced our first Phase I/II
clinical trials for one of our vaccines within the past two years, and a Phase II trial for one of
our vaccines in December 2004. There are many factors outside of our control that may affect the
timing of completion of our current clinical trials, and any future clinical trials may not
commence when planned or be completed within any anticipated time frame. For example, in the past
we experienced unexpected delays in filing an IND for our therapeutic vaccine candidate targeting
HIV, due to additional time necessary to complete all of the animal safety studies that were
contemplated in our pre-IND discussions with the FDA. We may experience unexpected delays in our
research and development efforts that would require us to postpone the commencement or completion
of clinical trials of other vaccine candidates. The FDA may comment or raise concerns or questions
with respect to any IND that we file and, therefore, clinical trials may not begin when planned, if
at all. Unexpected side effects or other characteristics of our technology may delay or otherwise hurt the
development of our vaccine candidates. There may be side effects in our current or future clinical trials that we may discover, including
side effects that become apparent only after long-term exposure, even though our safety tests may
indicate favorable results. We may also encounter technological challenges relating to these
technologies and applications in our research and development programs that we may not be able to
resolve. Any such unexpected side effects or technological challenges may delay or otherwise
adversely affect the development, regulatory approval or commercialization of our drug candidates. There are no therapeutic vaccines that have been approved for use by the FDA and our vaccines may
not work, which would prevent us from ever becoming profitable. Because there are not yet any therapeutic vaccines that have undergone the complete clinical
development process and FDA review, there is still insufficient evidence that therapeutic vaccines
will become products. Our business is dependent upon the concept of therapeutic vaccines and,
therefore, if therapeutic vaccines were found not to be safe or effective, we would never
commercialize a product candidate and would never make a profit. Adverse publicity regarding the safety or side effects of the technology approach or products of
others could reduce our revenues and cause our stock price to fall. Despite any favorable safety tests that may be completed with respect to our product candidates,
adverse publicity regarding vaccines or products being developed or marketed by others could
negatively affect us. If other researchers studies raise or substantiate concerns over the safety
or side effects of vaccines or our technology approach or product development efforts generally,
our reputation and public support for our clinical trials or products could be harmed, which would
harm our business and could cause our stock price to fall. Our research and development programs may not yield effective product candidates, which could
prevent us from developing our products. We cannot guarantee that our research and development programs will be successful in identifying
vaccine candidates for clinical trials. Even if we do receive positive data during preclinical
testing and during Phase I/II clinical trials for our therapeutic vaccine candidate targeting HIV,
and Phase II clinical trials targeting lung cancer, or any other candidates we may develop, this
data cannot be relied upon as evidence that the clinical candidate will be safe and effective in
humans, and assuming we initiate any Phase III trials, data from Phase III or other pivotal
clinical trials may not be consistent with earlier data or be sufficient to support regulatory
approval. 19




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We may not identify the correct epitopes and, therefore, not develop a safe or effective vaccine. Our strategy involves identifying multiple epitopes in order to create our vaccines. If we are
unable to identify the correct epitopes, or if we are unable to combine them in the correct manner,
to stimulate desired immune responses we may never develop a vaccine that is safe or effective in
any of the indications that we are pursuing. Our business is based on a novel technology, which has not been used in any commercial drugs, and
may not work. Our vaccine candidates use epitopes to stimulate specific T cell immune responses, but we are not
aware of any commercial drugs that are based on this technology. Our technology related to T cell
stimulation is unproven and may not produce any commercial vaccines. Our failure to obtain issued patents and, consequently, to protect our proprietary technology,
could hurt our competitive position. Our success will depend in part on our ability to obtain and enforce claims in our patents directed
to our products, technologies and processes, both in the United States and other countries.
Although we have filed various patent applications, our patent position is highly uncertain and
involves complex legal and factual questions. Legal standards relating to patentability, validity
and scope of patent claims in epitope identification and other aspects of our technology field are
still evolving. Patents may not issue from any of the patent applications that we own or license
and, if patents do issue, claims issued in the patents may not be sufficiently broad to protect our
vaccines, technologies and processes. For example, even though our patent portfolio includes patent
applications with claims directed to peptide epitopes and methods of utilizing sequence motifs to
identify peptide epitopes, we cannot assure you of the breadth of claims that will be allowed or
that may issue in future patents. Other risks and uncertainties that we face with respect to our
patents and patent applications include the following:  
    the pending patent applications we have filed or to which we have exclusive rights may
not result in issued patents or may take longer than we expect to result in issued patents;
    the allowed claims of any patents that issue may not provide meaningful protection;
    we may be unable to develop additional proprietary technologies that are patentable;
    the patents licensed or issued to us may not provide a competitive advantage;
    other companies may challenge patents licensed or issued to us;
    disputes may arise regarding inventions and corresponding ownership rights in inventions
and know-how resulting from the joint creation or use of intellectual property by us, our
licensors, or collaborators; and
    other companies may design around our patented technologies. Our competitors may develop products that are more effective and that render our potential products
obsolete. The biotechnology industry continues to undergo rapid change, and competition is intense and is
expected to increase. Our competitors may succeed in developing technologies, vaccines or other
therapeutic products that are more effective than any of the products we are developing, which
would render our technology and products obsolete and noncompetitive. 20




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If we are unable to compete effectively in the highly competitive biotechnology industry, our
business will fail. Many companies and institutions compete with us in developing vaccines and other therapies to
activate the bodys immune system or to otherwise treat or more effectively manage infectious
diseases and cancer, including:  
    pharmaceutical companies;
    chemical companies;
    specialized biotechnology companies;
    academic institutions; and
    research organizations. Many of the companies developing competing technologies and products have significantly greater
financial resources and expertise in research and development, manufacturing, preclinical and
clinical development, obtaining regulatory approvals and marketing than we do, and we may not be
able to compete effectively against them. Our vaccines under development address a range of cancer and infectious disease markets. The
competition in these markets is extremely formidable. There are 27 drugs currently approved in the
United States for HIV and according to a PhRMA2003 report on pharmaceutical drug development,
there were 83 new product candidates in clinical development for HIV and related conditions,
including 15 HIV vaccines. In addition, according to the PhRMA2003 report, there were 395 new
product candidates in clinical development for the treatment of cancer, and at least 30 companies
were developing more than 50 vaccines against various cancers. An important factor in competition
may be the timing of market introduction of our vaccines and competitive products. Accordingly, the
relative speed with which we can develop vaccines, complete the clinical trials and approval
processes and supply commercial quantities of the vaccines to the market are expected to be
important competitive factors. We expect that competition among products approved for sale will be
based, among other things, on product effectiveness, safety, reliability, availability, price and
patent position. Litigation regarding intellectual property rights owned or used by us may be costly and
time-consuming. Litigation may be necessary to enforce the claims in any patents issued to us, to defend ourselves
against any patents owned by third parties that are asserted against us, or to determine the scope
and validity of others proprietary rights. In addition, we may have to participate in one or more
interference proceedings declared by the United States Patent and Trademark Office, which could
result in substantial costs to determine the priority of inventions. If we become involved in litigation or interference proceedings, we may incur substantial expense,
and the proceedings may divert the attention of our technical and management personnel, even if we
ultimately prevail. An adverse determination in proceedings of this type could subject us to
significant liabilities, allow our competitors to market competitive products without obtaining a
license from us, prohibit us from marketing vaccines or other products or require us to seek
licenses from third parties that may not be available on commercially reasonable terms, if at all.
If we cannot obtain such licenses, we may be restricted or prevented from developing and
commercializing our product candidates. The enforcement, defense and prosecution of intellectual property rights, United States Patent and
Trademark Office interference proceedings and related legal and administrative proceedings in the 21




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United States and elsewhere involve complex legal and factual questions. As a result, these
proceedings are costly and time-consuming, and their outcome is uncertain. Litigation may be
necessary to:  
    assert against others or defend ourselves against claims of infringement;
    enforce patents in our portfolio owned by us or licensed from another party;
    protect our trade secrets or know-how; or
    determine the enforceability, scope and validity of the proprietary rights of ours or others. If we cannot obtain and maintain strategic collaborations on acceptable terms in the future, we may
not be able to develop products in markets where it would be too costly or complex to do so on our
own. We will need to enter into and maintain collaborative arrangements with pharmaceutical and
biotechnology companies or other strategic partners both for development and commercialization of
potential vaccine products in markets where it would be too costly or complex to do so on our own.
Currently, our only collaborations are with Innogenetics and Bavarian Nordic. If we are not able
to enter into and maintain additional research and development collaborations or other
collaborations in the future on acceptable terms, we may be forced to abandon development and
commercialization of some vaccine product candidates. If our collaboration or license arrangements are unsuccessful, our revenues and product development
may be limited. Our collaborations and license arrangements generally pose the following risks:  
    collaborators and licensees may not pursue further development and commercialization of
potential products resulting from our collaborations or may elect not to renew research and
development programs;
    collaborators and licensees may delay clinical trials, under-fund a clinical trial
program, stop a clinical trial or abandon a product candidate, repeat or conduct new
clinical trials or require new formulation of a product candidate for clinical testing;
    expected revenue might not be generated because milestones may not be achieved and
product candidates may not be developed;
    collaborators and licensees could independently develop, or develop with third parties,
products that could compete with our future products;
    the terms of our contracts with our current or future collaborators and licensees may
not be favorable to us in the future;
    a collaborator or licensee with marketing and distribution rights to one or more of our
products may not commit enough resources to the marketing and distribution of our products,
limiting our potential revenues from the commercialization of a product;
    disputes may arise delaying or terminating the research, development or
commercialization of our product candidates, or result in significant and costly litigation
or arbitration; and
    collaborations and licensee arrangements may be terminated and we will experience
increased operating expenses and capital requirements if we elect to pursue further
development of the product candidate. 22




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We may not be able to obtain licenses to technology that is necessary for us to develop products. We may be required to enter into licenses or other collaborations with third parties in order to
access technology that is necessary to successfully develop certain of our products. We may not
successfully negotiate acceptable licenses or other collaborative arrangements that will allow us
to access such technologies. If we cannot obtain and maintain license rights on acceptable terms to
access necessary technologies, we may be prevented from developing some product candidates. In
addition, any technologies accessed through such licenses or other collaborations may not help us
achieve our product development goals. We may not be able to commercialize our products under development if they infringe claims in
existing patents or patents that have not yet issued, and this would materially harm our ability to
operate. As is typical in the biotechnology industry, our commercial success will depend in part on our
ability to avoid infringing patents issued to others or breaching the technology licenses upon
which we might base our vaccines or other products. We are aware of patents issued to others that
contain claims that may cover certain aspects of our or our collaborators technologies, including
cancer vaccine epitopes, HIV vaccine epitopes, and methods for delivering DNA vaccines to patients.
We do not believe that any of these known patents are likely to require us to obtain a license in
order to pursue the development or commercialization of our vaccine product candidates. However, we
may be required to take a license under one or more of these patents to practice certain aspects of
our vaccine technologies in the United States, and such a license may not be available on
commercially reasonable terms, if at all. If we fail to obtain a license on acceptable terms to any
technology that we need in order to develop or commercialize our vaccines or other products, or to
develop an alternative vaccine or other product that does not infringe on the patent rights of
others, we would be prevented from commercializing our vaccine, and our business would be harmed. If we, or our collaborators cannot cost-effectively manufacture vaccines in commercial quantities
and for clinical trials in compliance with regulatory requirements, we, or our collaborators may
not be able to successfully commercialize the products. We have not commercialized any products, and we do not have the experience, resources or facilities
to manufacture vaccines on a commercial scale. We will not be able to commercialize any vaccines
and earn product revenues unless we, or our collaborators, demonstrate that we can manufacture
commercial quantities of vaccines in accordance with regulatory requirements. Among the other
requirements for regulatory approval is the requirement that prospective manufacturers conform to
the FDAs Good Manufacturing Practices (GMP) requirements specifically for biological drugs, as
well as for other drugs. In complying with the FDAs GMP requirements, manufacturers must continue
to expend time, money and effort in production, record keeping and quality control to assure that
the product meets applicable specifications and other requirements. We currently rely and intend to continue to rely on third-party contract manufacturers to produce
materials needed for clinical trials and, ultimately, for product commercialization. Third-party
manufacturers may not be able to meet our needs with respect to timing, quantity or quality. If we
are unable to contract for a sufficient supply of needed materials on acceptable terms, or if we
encounter delays or difficulties in our relationships with manufacturers, it may delay clinical
trials, regulatory approvals and marketing efforts for our vaccines. Such delays could adversely
affect our ability to earn revenues and our chances of achieving profitability. We cannot be sure
that we can manufacture, either on our own our through contracts with outside parties, vaccines at
a cost or in quantities that are commercially viable. 23




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If we do not successfully develop and commercialize our products, we may never generate significant
revenues or become profitable. We have not completed the development of any product and, accordingly, have not begun to market or
generate revenues from the commercialization of any product. We do not expect to market any of our
therapeutic or prophylactic vaccines or any other products for at least six years (and this would
assume approval of either our HIV or lung cancer product candidate, which may not occur). If we do
not successfully develop and commercialize products, we will never generate revenues that would
allow us to become profitable. The lengthy approval process and uncertainty of government regulatory requirements may impair our
ability to develop, manufacture and sell any vaccines. We, and our collaborators, cannot commercialize our vaccines or other products if we do not receive
FDA or state regulatory approval to market our products. The regulatory process for new therapeutic
drug products, including the required preclinical studies and clinical testing, is lengthy,
uncertain and expensive. We, and our collaborators, may not receive necessary FDA clearances for
any of our vaccines or other potential products in a timely manner, or at all. Once approved, we
are subject to the continuing requirements of the FDA. Noncompliance with initial or continuing
requirements can result in, among other things:  
    fines and penalties;
    injunctions;
    seizure of products;
    total or partial suspension of product marketing;
    failure of the government to grant a new drug application;
    withdrawal of marketing approvals; and
    criminal prosecution. The length of the clinical trial process and the number of patients the FDA will require to be
enrolled in clinical trials in order to establish the safety and efficacy of our products is
uncertain. In addition, our clinical studies may not provide the FDA with sufficient clinical data
to permit approval of a new drug application, or NDA, or a biologic license application, or BLA,
even though we, or our collaborators, believe we are doing the right studies based on the protocol.
The FDA or we and our collaborators may decide to discontinue or suspend clinical trials at any
time if the subjects or patients who are participating in such trials are being exposed to
unacceptable health risks or if the results show no or limited benefit in patients treated with the
vaccine compared to patients in the control group. Regulatory requirements are evolving and uncertain. Future United States or state legislative or
administrative acts could also prevent or delay regulatory approval of our products. Even if we
obtain commercial regulatory approvals, the approvals may significantly limit the indicated uses
for which we may market our products. The approval process outside the United States is also uncertain and may limit our ability to
develop, manufacture and sell our products internationally. To market any drug products outside of the United States, we and our collaborators are also subject
to numerous and varying foreign regulatory requirements, implemented by foreign health authorities,
governing the design and conduct of human clinical trials and marketing approval for vaccines or
other 24




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drug products. The approval procedure varies among countries and can involve additional testing,
and the time required to obtain approval may differ from that required to obtain FDA approval. The
foreign regulatory approval process includes all of the risks associated with obtaining FDA
approval set forth above, and approval by the FDA does not ensure approval by the health
authorities of any other country, nor does the approval by foreign health authorities ensure
approval by the FDA. Even if we obtain regulatory approval, we may be required to perform additional clinical trials or
change the labeling of our products if we, or others identify side effects after our products are
on the market, which could harm sales of the affected products. If we, or others identify adverse side effects after any of our vaccines or other drug products are
on the market, or if manufacturing problems occur:  
    regulatory approval may be withdrawn;
    reformulation of our products, additional clinical trials, changes in labeling of our
products or changes to or re-approvals of our manufacturing facilities may be required;
    sales of the affected products may drop significantly;
    our reputation in the marketplace may suffer; and
    lawsuits, including costly and lengthy class action suits, may be brought against us. Any of the above occurrences could halt or reduce sales of the affected vaccines or other products
or could increase the costs and expenses of commercializing and marketing these vaccines or other
products. If we are unable to protect our trade secrets, we may be unable to protect from competitors our
interests in proprietary know-how that is not patentable or for which we have elected not to seek
patent protection. Our competitive position depends in part on our ability to protect trade secrets that are not
patentable or for which we have elected not to seek patent protection. To protect our trade
secrets, we rely primarily on confidentiality agreements with our collaborative partners, employees
and consultants. Nevertheless, our collaborative partners, employees and consultants may breach
these agreements and we may be unable to enforce these agreements. In addition, other companies may
develop similar or alternative technologies, methods or products or duplicate our technologies,
methods or vaccines that are not protected by our patents or otherwise obtain and use information
that we regard as proprietary, and we may not have adequate remedies in such event. Any material
leak of our confidential information into the public domain or to third parties could harm our
competitive position. If we lose our key scientific and management personnel or are unable to attract and retain
qualified personnel, it could delay or hurt our epitope identification and vaccine development
efforts. We are highly dependent on the principal members of our scientific and management staff. We do not
maintain key person life insurance on the life of any employee and, although we have an employment
contract with Dr. Emile Loria, he may terminate his employment at any time. Our ability to identify
epitopes, develop vaccines and achieve our other business objectives also will depend in part on
the continued service of our key scientific and management personnel and our ability to identify,
hire and retain additional qualified personnel. There is intense competition for qualified
personnel in biochemistry, molecular biology, immunology and other areas of our activities, and we
may not be able to continue to attract and retain such personnel necessary for the development of
our business. Because of the intense competition for qualified personnel among technology-based
businesses, particularly in the 25




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San Diego area, we may not be successful in adding technical personnel as needed to meet the
staffing requirements of additional collaborative relationships. Our failure to attract and retain
key personnel could delay or be significantly detrimental to our product development programs and
could cause our stock price to decline. We out-license technology outside of our core area of focus, and these licensees may not develop
any products using our technology, which may limit our revenue. We have licensed to third parties some of our technology in markets that we are not pursuing
ourselves or with our collaborators. If these licensees are not successful in developing and
commercializing products using our technology, our revenues would be limited. Our licensees may
pursue alternative technologies or develop alternative products either on their own or in
collaboration with others in competition with products developed under licenses or collaborations
with us. Some of our programs are funded by the U.S. government and, therefore, the government may have
rights to certain of our technology and could require us to grant licenses of our technology to
third parties. We fund certain of our research and development related to our HIV, cancer and malaria programs
pursuant to grants from the U.S. government. As a result of these grants, the government may have
rights in the technology and inventions developed with government funding. In addition, the
government may require us to grant to a third party an exclusive license to any inventions
resulting from the grant if the government determines that we have not taken adequate steps to
commercialize inventions, or for public health or safety needs. Adverse determinations concerning product pricing, reimbursement and related matters could prevent
us from successfully commercializing products and impair our ability to generate revenues. Our ability to successfully commercialize our vaccines or other products may depend in part on the
extent to which reimbursement for the cost of such products and related treatment will be available
from government health administration authorities, private health insurers and other organizations.
Third-party payors are increasingly challenging the price of medical products and services.
Significant uncertainty exists as to the reimbursement status of newly approved health care
products, and adequate third-party coverage may not be available to enable us to maintain price
levels sufficient to realize an appropriate return on our investment in product development. Product liability risks may expose us to significant liability that could cause us to incur
significant costs or cease developing our products. Our business exposes us to potential product liability risks that are inherent in the testing,
manufacturing and marketing of human therapeutic products. While we currently have product
liability insurance for an early stage clinical trial, we cannot be sure that we can maintain such
insurance on acceptable terms or obtain acceptable insurance as we progress through product
development and commercialization, or that our insurance will provide adequate coverage against
potential liabilities, either in human clinical trials or following commercialization of any
vaccines we may develop. Our use of hazardous materials could expose us to significant costs. Our research and development processes involve the controlled storage, use and disposal of
hazardous materials, chemicals and radioactive compounds. We are subject to federal, state and
local laws and regulations governing the use, manufacture, storage, handling and disposal of these
materials and some waste products. The risk of accidental contamination or injury from these
materials cannot be completely eliminated. In the event of an accident, we could be held liable for
any damages that result, and any liability could exceed our resources. We cannot be sure that
compliance with environmental laws and 26




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regulations in the future will not entail significant costs, or that our ability to conduct
research and development activities will not be harmed by current or future environmental laws or
regulations. The subordination of our common stock to our preferred stock could hurt common stockholders and,
upon conversion, our preferred stock will further dilute our holders of common stock. Our common stock is expressly subordinate to our series S and series S-1 preferred stock in the
event of our liquidation, dissolution or winding up. With respect to our series S preferred, any
merger or sale of substantially all of our assets shall be considered a deemed liquidation. If we
were to cease operations and liquidate our assets, we would first be required to pay $10 million to
our holders of preferred stock and there may not be any remaining value available for distribution
to the holders of common stock after providing for the series S and series S-1 preferred stock
liquidation preference. In addition, due to adjustments to the conversion price of our series S
preferred stock, in the event our series S preferred stock is converted to common stock, it will
further dilute our holders of common stock. The volatility of the price of our common stock may hurt our stockholders. The market prices for securities of biotechnology companies, including our common stock, have
historically been highly volatile, and the market from time to time has experienced significant
price and volume fluctuations that are not necessarily related to the operating performance of such
companies. From January 1, 2004 through March 31, 2005, our closing stock price has ranged from
$1.11 to $2.66 and has been and will continue to be influenced by general market and industry
conditions. In addition, the following factors may have a significant effect on the market price of
our common stock:  
    whether we are able to secure additional financing on favorable terms, or at all;
    announcements of technological innovations or new commercial vaccines or other
therapeutic products by us or others;
    governmental regulation that affects the biotechnology and pharmaceutical industries;
    developments in patent or other proprietary rights;
    receipt of funding under collaboration and license agreements and government grants;
    developments in, or termination of, our relationships with our collaborators and licensees;
    public concern as to the clinical results and/or the safety of drugs developed by us or
others; and
    announcements related to the sale of our stock. Fluctuations in our financial performance from period to period also may have a significant impact
on the market price of our common stock. Concentration of ownership among our existing officers, directors and principal stockholders may
prevent other stockholders from influencing significant corporate decisions and depress our stock
price. As of March 31, 2005, our officers, directors and those stockholders owning at least five percent
of our outstanding stock together control approximately 34.2% of our outstanding common stock as
converted and Pfizer, Inc., through G.D. Searle LLC, holds 100% of our preferred stock. If some or
all of these officers, directors and principal stockholders act together, they will be able to
exert a significant degree of influence over our management and affairs and over matters requiring
stockholder approval, including the election of directors and approval or disapproval of any
proposed merger or financing or other business combination transaction. The interests of this
concentration of ownership may not always 27




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coincide with our interests or the interests of other stockholders. For instance, officers,
directors and principal stockholders, acting together, could cause us to enter into transactions or
agreements that we would not otherwise consider. Similarly, this concentration of ownership may
have the effect of delaying or preventing a change in control of our company otherwise favored by
our other stockholders. This concentration of ownership also could depress our stock price. Compliance with the Sarbanes-Oxley Act of 2002 and other changing regulations of corporate
governance and public disclosure may result in additional expenses. Changing laws, regulations and standards relating to corporate governance and public disclosure,
including the Sarbanes-Oxley Act of 2002, new SEC regulations, Nasdaq Stock Market rules, and new
accounting pronouncements are creating uncertainty and additional complexities for companies such
as ours. In particular, the Section 404 internal control requirements under the Sarbanes-Oxley Act
will continue to add complexity and costs to our business and require a significant investment of
our time and resources to complete each year. We take these new requirements seriously and expect
to make every effort to ensure that we receive clean attestations on our internal controls each
year from our outside auditors. To maintain high standards of corporate governance and public
disclosure, we intend to invest all reasonably necessary resources to comply with all other
evolving standards. These investments may result in increased general and administrative expenses
and a diversion of management time and attention from strategic revenue generating and cost
management activities. 28




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ITEM 4. CONTROLS AND PROCEDURES (a) Evaluation of Disclosure Controls and Procedures Under the supervision and with the participation of our management, including our principal
executive officer and principal financial officer, we conducted an evaluation of the effectiveness
of the design and operation of our disclosure controls and procedures, as such term is defined
under Rules 13a-15(e) and 15d-15(e) promulgated under the Securities Exchange Act of 1934, as
amended (the Exchange Act), as of the end of the period covered by this report. Based on their
evaluation, our principal executive officer and principal financial officer concluded that our
disclosure controls and procedures are effective as of the evaluation date. (b) Changes in Internal Control Over Financial Reporting Our principal executive officer and principal financial officer also evaluated whether any change
in our internal control over financial reporting, as such term is defined under Rules 13a-15(f) and
15d-15(f) promulgated under the Exchange Act, occurred during our most recent fiscal quarter
covered by this report that has materially affected, or is likely to materially affect, our
internal control over financial reporting. Based on their evaluation, our principal executive
officer and principal financial officer concluded that there has been no change in our internal
control over financial reporting during our most recent fiscal quarter covered by this report that
has materially affected, or is likely to materially affect, our internal control over financial
reporting. 29




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PART II. OTHER INFORMATION 
 ITEM 1. LEGAL PROCEEDINGS From time to time we are involved in certain litigation arising out of our operations. We are not
currently engaged in any legal proceedings. 
 ITEM 6.
    
    EXHIBITSExhibit 3.1
    
    Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on December 2,
1991.(1)Exhibit 3.2
    
    Certificate of Designation of Series A Junior Participating Preferred
Stock filed with the Secretary of State of Delaware on April 2, 1993.(2)Exhibit 3.3
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 5, 1995.(3)Exhibit 3.4
    
    Certificate of Increase of Series A Junior Participating Preferred Stock
filed with the Secretary of State of Delaware on July 5, 1995.Exhibit 3.5
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 2, 1998.(4)Exhibit 3.6
    
    Certificate of Increase of Series A Junior Participating Preferred Stock
filed with the Secretary of State of Delaware on July 2, 1998.(4)Exhibit 3.7
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on November 12,
1998.(5)Exhibit 3.8
    
    Certificate of Designations of the Series S and Series S-1 Preferred
Stock filed with the Secretary of State of Delaware on June 29, 1999.(6)Exhibit 3.9
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on July 1, 1999.(7)Exhibit 3.10
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on September 23,
1999.(8)Exhibit 3.11
    
    Certificate of Decrease of Series A Junior Participating Preferred
Stock filed with the Secretary of State of Delaware on September 23, 1999.(8)Exhibit 3.12
    
    Certificate of Amendment of Amended and Restated Certificate of
Incorporation filed with the Secretary of State of Delaware on June 17,
2004.(9)Exhibit 3.13
    
    Amended and Restated Bylaws of the Registrant.(10)Exhibit 4.1
    
    Reference is made to Exhibits 3.1 through 3.13.Exhibit 4.2
    
    Specimen certificate of the common stock.(1)
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Exhibit 10.1
    
    Share Exchange Agreement dated March 15, 2005 among Epimmune Inc. and
certain shareholders of IDM S.A.(11)Exhibit 10.3
    
    Amendment No. 1 (to the Share Exchange Agreement) dated March 15, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(11)Exhibit 10.4
    
    Voting Agreement dated March 15, 2005 among Epimmune Inc., Hélène
Ploix, as the Shareholder Representative, and certain stockholders of Epimmune
Inc.(11)Exhibit 10.5
    
    Preferred Exchange Agreement dated March 15, 2005.(11)Exhibit 10.6
    
    Employment Agreement with Emile Loria, M.D. dated March 17, 2005.(11)Exhibit 10.7
    
    Employment Agreement with Mark Newman, Ph.D. dated March 17, 2005.(11)Exhibit 10.8
    
    Employment Agreement with Robert De Vaere dated March 17, 2005.(11)Exhibit 10.9
    
    Amended and Restated Preferred Exchange Agreement dated April 12,
2005.(12)Exhibit 10.10
    
    Amendment No. 2 (to the Share Exchange Agreement) dated April 21, 2005
among Epimmune Inc. and certain shareholders of IDM S.A.(13)Exhibit 31.1
    
    Certification of Principal Executive Officer pursuant to Rule 13a-14(a)
or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.Exhibit 31.2
    
    Certification of Principal Financial Officer pursuant to Rule 13a-14(a)
or Rule 15d-14(a) of the Securities Exchange Act of 1934, as amended.Exhibit 32.1
    
    Certification pursuant to Rule 13a-14(b) or Rule 15d-14(b) of the
Securities Exchange Act of 1934, as amended, and Section 1350 of Chapter 63 of
Title 18 of the United States Code (18 U.S.C. § 1350).
   (1)
    
    Incorporated by reference to the Companys Form S-1
Registration Statement and Amendments thereto filed with Securities and
Exchange Commission (the SEC) (File No. 33-43356).(2)
    
    Incorporated by reference to the Companys Form 8-K, filed with
the SEC on March 22, 1993.(3)
    
    Incorporated by reference to the Companys Annual Report on
Form 10-K for the fiscal year ended December 31, 1994, filed with the SEC on
March 31, 1995.(4)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended June 30, 1998, filed with the SEC on
August 14, 1998.(5)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended September 30, 1998, filed with the SEC
on November 16, 1998. 31




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(6)
    
    Incorporated by reference to the Companys Form 8-K, filed with
the SEC on July 16, 1999.(7)
    
    Incorporated by reference to the Companys Definitive Proxy
Statement, filed with the SEC on Form DEF 14A on July 28, 1999.(8)
    
    Incorporated by reference to the Companys Quarterly Report on
Form 10-Q for the quarterly period ended September 30, 1999, filed with the SEC
on November 15, 1999.(9)
    
    Incorporated by reference to the Companys Registration
Statement on Form S-8, filed with the SEC on July 2, 2004.(10)
    
    Incorporated by reference to the Companys Annual Report on
Form 10-K for the fiscal year ended December 31, 2001, filed with the SEC on
March 29, 2002.(11)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on March 18, 2005.(12)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on April 18, 2005.(13)
    
    Incorporated by reference to our Current Report on Form 8-K,
filed with the SEC on April 22, 2005. 32




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EPIMMUNE INC. 
 SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has
duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. EPIMMUNE INC.Dated: May 13, 2005
    
    By:
    
    /s/ Emile LoriaEmile Loria, M.D.President, Chief Executive Officer and Director(Principal Executive Officer)Dated: May 13, 2005
    
    By:
    
    /s/ Robert De VaereRobert De VaereVice President, Finance and Administration,Chief Financial Officer and Secretary(Principal Financial and Accounting Officer)
 33