<PAGE>   1

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                                UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549

                                  FORM 10-Q



(Mark One)

[X]      QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECIRITIES
         EXCHANGE ACT OF 1934
         FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2001


                                      OR


[ ]      TRANSITION REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES
         EXCHANGE ACT OF 1934
         FOR THE TRANSITION PERIOD FROM _______________ TO _______________.

                        COMMISSION FILE NUMBER 0-23317

-------------------------------------------------------------------------------

                               GENE LOGIC INC.

            (Exact name of registrant as specified in its charter)

-------------------------------------------------------------------------------

            DELAWARE                              06-1411336
(State or other jurisdiction of                (I.R.S. Employer
 incorporation or organization)              Identification No.)

                           708 QUINCE ORCHARD ROAD
                         GAITHERSBURG, MARYLAND 20878
                   (Address of principal executive offices)
                                (301) 987-1700
               (Registrant's phone number, including area code)

           --------------------------------------------------------

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 [X]  NO [ ]


The number of shares outstanding of the Registrant's Common Stock, $.01 par
value, was 26,409,628 as of April 30, 2001.

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<PAGE>   2


                               GENE LOGIC INC.


                              TABLE OF CONTENTS

<TABLE>
<S>                                                                                                         <C>
PART I            FINANCIAL INFORMATION

Item 1.  Financial Statements

Consolidated Balance Sheets at March 31, 2001 and December 31, 2000..............................................3
Consolidated Statements of Operations for the Three Months Ended
         March 31, 2001 and 2000.................................................................................4
Consolidated Statements of Cash Flows for the Three Months Ended
         March 31, 2001 and 2000.................................................................................5
Notes to Consolidated Financial Statements.......................................................................6

Item 2.  Management's Discussion and Analysis
         of Results of Operations and Financial Condition........................................................8

Item 3.  Quantitative and Qualitative Disclosure About Market Risk..............................................11

PART II           OTHER INFORMATION

Item 6.  Exhibits and Reports on Form 8-K.......................................................................12

Signatures......................................................................................................13
</TABLE>

                                      2.

<PAGE>   3


PART I            FINANCIAL INFORMATION

ITEM 1.    FINANCIAL STATEMENTS

                               GENE LOGIC INC.
                         CONSOLIDATED BALANCE SHEETS
                      (IN THOUSANDS, EXCEPT SHARE DATA)

<TABLE>
<CAPTION>
                                                                                        MARCH 31,        DECEMBER 31,
                                                                                           2001              2000
                                                                                      ---------------   --------------
                                                                                       (Unaudited)
<S>                                                                                    <C>               <C>
                                                        ASSETS
Current Assets:
     Cash and cash equivalents ...............................................         $     213,831     $    229,482
     Accounts receivable......................................................                 2,989            2,968
     Inventory................................................................                 3,240            2,295
     Prepaid expenses.........................................................                 3,022            2,537
     Other current assets.....................................................                 3,517            6,382
                                                                                      ---------------   --------------
         Total Current Assets.................................................               226,599          243,664
Property and Equipment, net ..................................................                19,241           15,994
Long-term Investments.........................................................                 7,727            9,081
Note Receivable from Employee.................................................                    75               75
Goodwill, net.................................................................                 3,820            4,201
Intangible and Other Assets, net .............................................                16,885           16,518
                                                                                      ---------------   --------------
         Total Assets ........................................................         $     274,347     $    289,533
                                                                                      ===============   ==============

                                         LIABILITIES AND STOCKHOLDERS' EQUITY

Current Liabilities:
      Accounts payable .......................................................         $      10,379     $      5,908
      Litigation settlement payable...........................................                    --            9,000
      Accrued expenses........................................................                 6,098            9,028
      Current portion of long-term debt.......................................                 1,284            1,335
      Deferred revenue........................................................                 7,600            7,093
                                                                                      ---------------   --------------
          Total Current Liabilities...........................................                25,361           32,364
Deferred Revenue..............................................................                   768            1,141
Long-Term Debt................................................................                 1,334            1,631
Other Noncurrent Liabilities..................................................                   918              682
                                                                                      ---------------   --------------
             Total Liabilities................................................                28,381           35,818
                                                                                      ---------------   --------------
Commitments and Contingencies
Stockholders' Equity:
      Preferred Stock, $.01 par value; 10,000,000 shares authorized; no shares
       issued and outstanding as of March 31, 2001 and December 31, 2000......                    --               --
      Common Stock, $.01 par value; 60,000,000 shares authorized; 26,372,678 and
       26,111,561 shares issued and outstanding as of March 31, 2001 and
       December 31, 2000, respectively........................................                   264              261
      Additional paid-in capital .............................................               358,921          356,347
      Deferred compensation on stock options, net ............................                  (459)            (738)
      Accumulated deficit ....................................................              (112,760)        (102,155)
                                                                                      ---------------   --------------
         Total Stockholders' Equity...........................................               245,966          253,715
                                                                                      ---------------   --------------
         Total Liabilities and Stockholders' Equity...........................         $     274,347     $    289,533
                                                                                      ===============   ==============
</TABLE>

                           See accompanying notes.

                                      3.


<PAGE>   4


                               GENE LOGIC INC.
                    CONSOLIDATED STATEMENTS OF OPERATIONS
                    (IN THOUSANDS, EXCEPT PER SHARE DATA)
                                 (UNAUDITED)


<TABLE>
<CAPTION>
                                                                          THREE MONTHS ENDED
                                                                              MARCH 31,
                                                                     ----------------------------
                                                                          2001           2000
                                                                     -------------  -------------
<S>                                                                  <C>            <C>
Revenues.........................................................    $       8,211  $       5,328
Expenses:
  Research and development.......................................           15,690          8,479
  Selling, general and administrative............................            4,793          3,379
  Amortization of goodwill.......................................              381            381
                                                                     -------------  -------------
          Total operating expenses...............................           20,864         12,239
                                                                     -------------  -------------
          Loss from operations...................................         (12,653)        (6,911)
Interest Income, net.............................................            3,286          2,357
Income Tax Expense...............................................               49            100
Equity in Net Loss of Unconsolidated Investee....................            1,189             --
                                                                     -------------  -------------
          Net loss before cumulative effect of change in accounting
             Principle...........................................         (10,605)        (4,654)
Cumulative Effect of Change in Accounting Principle..............               --          1,322
                                                                     -------------  -------------
          Net loss...............................................    $    (10,605)  $     (5,976)
                                                                     =============  =============

Basic and Diluted Net Loss Per Common Share:
  Net loss before cumulative effect of change in accounting
          principle..............................................    $      (0.40)  $      (0.20)
  Cumulative effect of change in accounting principle............               --         (0.06)
                                                                     -------------  -------------
          Net loss...............................................    $      (0.40)  $      (0.25)
                                                                     =============  =============

Shares Used in Computing Basic and Diluted Net Loss Per
     Common Share................................................           26,248         23,498
                                                                     =============  =============
</TABLE>

                           See accompanying notes.

                                      4.

<PAGE>   5


                               GENE LOGIC INC.
                    CONSOLIDATED STATEMENTS OF CASH FLOWS
                                (IN THOUSANDS)
                                 (UNAUDITED)

<TABLE>
<CAPTION>
                                                                            THREE MONTHS ENDED
                                                                                MARCH 31,
                                                                     ---------------  ---------------
                                                                           2001             2000
                                                                     ---------------  ---------------
<S>                                                                  <C>              <C>
  Cash Flows From Operating Activities:
  Net loss.....................................................        $   (10,605)     $    (5,976)
  Adjustments to reconcile net loss to net cash used in
     operating activities:
     Depreciation and amortization ............................              2,909            1,037
     Amortization of goodwill..................................                381              381
     Amortization of deferred compensation ....................                279              375
     Net loss from investment in unconsolidated investee.......              1,189               --
    Other non-cash expense.....................................                 --               73
  Changes in operating assets and liabilities:
     Accounts receivable.......................................                123           (1,847)
     Inventory.................................................               (945)             347
     Prepaid expenses..........................................               (485)            (202)
     Other current assets......................................              2,490               74
     Other assets..............................................               (152)              --
     Accounts payable .........................................              4,471           (1,700)
     Litigation settlement payable ............................             (9,000)              --
     Accrued expenses..........................................             (2,888)           1,074
     Deferred revenue .........................................                458            2,929
     Other noncurrent liabilities..............................                236               13
                                                                     ---------------  ---------------
          Net Cash Flows From Operating Activities ............            (11,539)          (3,422)
                                                                     ---------------  ---------------
  Cash Flows From Investing Activities:
     Purchases of property and equipment ......................             (4,677)          (1,152)
     Purchases of licenses and patent costs ...................               (315)            (128)
     Software and database development costs ..................             (1,349)            (770)
    Repayments of notes receivables from employees.............                 --              622
    Proceeds from sale and maturity of marketable securities
      available-for-sale.......................................                 --            7,155
                                                                     ---------------  ---------------
          Net Cash Flows From Investing Activities.............             (6,341)           5,727
                                                                     ---------------  ---------------
  Cash Flows From Financing Activities:
     Proceeds from issuance of common stock in public offering.                 --          262,080
     Issuance costs of public offering.........................                 --          (14,624)
     Proceeds from issuance of other common stock..............              2,043            2,713
     Proceeds from exercise of warrant.........................                534               --
     Repayments of capital lease obligations and
        equipment loans........................................               (348)            (272)
                                                                     ---------------  ---------------
          Net Cash Flows From Financing Activities.............              2,229          249,897
                                                                     ---------------  ---------------
  Net (Decrease) Increase in Cash and Cash Equivalents.........            (15,651)         252,202
  Cash and Cash Equivalents, beginning of period...............            229,482            5,294
                                                                     ---------------  ---------------
  Cash and Cash Equivalents, end of period.....................        $   213,831      $   257,496
                                                                     ===============  ===============

  Supplemental Disclosure:
     Interest paid.............................................        $        58      $        91
                                                                     ===============  ===============

  Non-Cash Transactions:
     Capital lease termination.................................        $        --      $       288
                                                                     ===============  ===============
</TABLE>

                           See accompanying notes.

                                      5.


<PAGE>   6



                               GENE LOGIC INC.
                  NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                MARCH 31, 2001
                                 (UNAUDITED)


NOTE 1.  SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

         The unaudited consolidated financial statements include the accounts
of Gene Logic Inc. and its wholly owned subsidiary (the "Company"). The
accompanying unaudited consolidated financial statements have been prepared in
accordance with generally accepted accounting principles for interim financial
information and with the instructions to Form 10-Q and Article 10 of
Regulation S-X. The consolidated balance sheet as of March 31, 2001,
consolidated statements of operations for the three months ended March 31,
2001 and 2000 and the consolidated statements of cash flows for the three
months ended March 31, 2001 and 2000 are unaudited, but include all
adjustments (consisting of normal recurring adjustments) which the Company
considers necessary for a fair presentation of the financial position,
operating results and cash flows for the periods presented. Although the
Company believes that the disclosures in these financial statements are
adequate to make the information presented not misleading, certain information
and footnote information normally included in financial statements prepared in
accordance with generally accepted accounting principles have been condensed
or omitted pursuant to the rules and regulations of the Securities and
Exchange Commission.

         Results for any interim period are not necessarily indicative of
results for any future interim period or for the entire year. The accompanying
unaudited consolidated financial statements should be read in conjunction with
the financial statements and notes thereto included in the Company's Annual
Report on Form 10-K for the year ended December 31, 2000.

Inventory

         Inventory is stated at the lower of cost or market. Cost is
determined using the first-in, first-out method. Inventory consists primarily
of Affymetrix, Inc. GeneChips(R) and tissue samples. All inventory at March
31, 2001 is classified as raw materials.

Goodwill

         Goodwill, from the acquisition of Oncormed, Inc. in September 1998,
represents the excess of the purchase price over the fair market value of the
net assets acquired. Goodwill is being amortized over five years at a rate of
approximately $1.5 million per year. Amortization expense was $0.4 million for
the three months ended March 31, 2001 and 2000. Accumulated amortization of
goodwill was $3.8 million and $3.4 million as of March 31, 2001 and December
31, 2000, respectively.

Change in Accounting Method

         Effective January 1, 2000, the Company changed its method of
accounting for revenue in accordance with Staff Accounting Bulletin No. 101,
"Revenue Recognition in Financial Statements." Prior to 2000, the Company
recognized as revenue certain nonrefundable up-front payments for the value of
data purchased, transfer of technology or other contractual rights that were
not contingent upon future performance under the terms of the agreement upon
signing of the agreement or when collected. Under the new accounting method
adopted retroactive to January 1, 2000, the Company now defers these
nonrefundable up-front payments and recognizes them as revenue systematically
over the life of the related collaboration agreements. The

                                      6.

<PAGE>   7

cumulative effect of the change on prior years resulted in a charge of $1.3
million, which is included in the net loss for the three months ended March
31, 2000. The effect of the change on the three months ended March 31, 2000,
was to increase revenue and decrease net loss before the cumulative effect of
the accounting change by $0.3 million. The impact for the three months ended
March 31, 2001 was an increase in revenue and a decrease in net loss of $0.1
million. The impact for the year ended December 31, 2001 will be an increase
in revenue and a decrease in net loss of $0.5 million.


Reclassifications

         Certain reclassifications have been made to the prior years'
financial statements to conform with the current year presentation.


NOTE 2.  LONG-TERM INVESTMENTS

         During 2000, the Company purchased Series A Convertible Preferred
Stock in Neuralstem, Inc., formerly NeuralStem BioPharmaceuticals, Ltd.
("Neuralstem"), an unconsolidated investee. At of the time of investment and
at March 31, 2001, the Company had a voting stock interest of 26.7% and 20.6%,
respectively, which is accounted for under the equity method of accounting.

         The Company recorded equity in losses of Neuralstem of $1.2 million
for the three months ended March 31, 2001. The Company had intercompany sales
and expenses with Neuralstem of $0.5 million and $0.3 million, respectively,
during the three months ended March 31, 2001. Intercompany transactions have
been eliminated in the accompanying financial statements based on the Company's
percentage of voting interest in Neuralstem.

NOTE 3.  SEGMENT INFORMATION

         Statement of Financial Accounting Standards No. 131, "Disclosure
about Segments of an Enterprise and Related Information" establishes standards
for reporting information about operating segments in annual and interim
financial statements and related disclosures about its products, services,
geographic areas and major customers. The Company's operations are treated as
one operating segment.

         The following is a breakdown of revenue by major customers exceeding
ten percent (10%) of such revenues and by geographic areas:


<TABLE>
<CAPTION>
                                                 MAJOR CUSTOMERS                     GEOGRAPHIC AREA
                                         -------------------------------        --------------------------
                                         A         B        C        D          JAPAN    EUROPE       US
                                         -------------------------------        --------------------------
<S>                                     <C>       <C>     <C>      <C>          <C>      <C>          <C>
    For the three months ended:
     March 31, 2001................        --      13%     --         --             --       --       13%
     March 31, 2000................       36%      23%     --        15%            36%      15%       23%
</TABLE>

                                      7.



<PAGE>   8


ITEM 2.    MANAGEMENT'S DISCUSSIONS AND ANALYSIS OF RESULTS OF OPERATIONS AND
           FINANCIAL CONDITION

      This Report on Form 10-Q contains forward-looking statements that
involve risks and uncertainties. We generally use words such as "anticipate,"
"estimate," "plan," "project," "continuing," "ongoing," "expect," "management
believes," "we believe," "we intend" and similar expressions to indicate when
we are making forward-looking statements. You should not place undue reliance
on these forward-looking statements. The forward-looking statements speak only
as of the date on which they are made, and we undertake no obligation to
update any forward-looking statement. Forward-looking statements include
statements about the performance and utility of our products, the timing and
availability of products under development, the ability of our customers to
develop products identified using our products, the adequacy of capital
resources and other expectations, plans, objectives, assumptions or future
events. These statements involve estimates, assumptions and uncertainties that
could cause actual results to differ materially from those expressed in this
Report on Form 10-Q. These risks and uncertainties include, but are not
limited to, the extent of utilization of genomic information by the
pharmaceutical and biotechnology industries in both research and development,
our ability to retain existing and obtain additional database customers, risks
relating to the development of genomic database products and their use by
existing and potential customers, the impact of technological advances and
competition, our ability to enforce our intellectual property rights, and the
impact of the intellectual property rights of others, as well as other risks
and uncertainties included in our Annual Report on Form 10-K for the year
ended December 31, 2000 filed with the Securities and Exchange Commission.

    Unless the context requires otherwise, references in this Report on Form
10-Q to "Gene Logic," the "Company," "we," "us," and "our" refer to Gene Logic
Inc. and its wholly owned subsidiary.

    GeneExpress(R) is a registered trademark of Gene Logic. READS(TM),
BioExpress(TM), ToxExpress(TM), PharmExpress(TM), CloneExpress(TM),
e-northern(TM), gene signature(TM) and Flow-thru Chip(TM) are trademarks of
Gene Logic. GeneChip(R) is a registered trademark of Affymetrix, Inc. Trade
names and trademarks of other companies appearing in this Report on Form 10-Q
are the property of their respective holders.

OVERVIEW

    We were incorporated in September 1994 and have devoted substantially all
of our resources to the development, marketing and sales of our genomics
technologies, bioinformatics systems and database products for use in
pharmaceutical, biotechnology, life sciences, diagnostic and agricultural
product research and development.

    Since 1997, we have developed custom gene expression databases designed
for our customers' internal research and development programs targeted to
specific therapeutic areas of interest, including heart failure, kidney
disease, osteoporosis, psychiatric disorders and other major illnesses.
Building on this know-how, in March 1999, we began developing the GeneExpress
Suite of databases, our large-scale reference database of gene expression
information. The GeneExpress Suite of databases contains information from a
broad range of normal and diseased human tissues, tissues from experimental
animals, human and animal cell lines and tissues that have been treated with
various drugs. We completed development of the first commercial version of the
GeneExpress Suite in November 1999. We currently market the GeneExpress Suite
through nonexclusive subscriptions to customers in the pharmaceutical,
biotechnology and diagnostic industries, and are developing versions of the
database suite to market to the academic and government life science research
community. We sold our first subscription to the GeneExpress Suite in December
1999.

    Typically, GeneExpress subscription agreement terms are for three years
with annual subscription fees ranging from $1.5 million to $4.0 million,
depending upon the level and type of information our customers obtain.
Customers for our custom discovery gene expression databases can provide us
with various combinations of recurring technology and database access fees,
research fees, additional payments upon the attainment of research and product
development milestones, royalty payments based


                                      8.

<PAGE>   9

on sales of any products resulting from their use of our products and
nonrefundable up-front payments. In addition, our business agreements can
provide the right for early termination without penalty to the customer.

    Subscription fees to the GeneExpress Suite are recognized systematically
over the term of the subscription. Technology and database access fees are
recognized systematically over the term of each customer agreement. We
recognize revenues from research and development support when they are earned,
which is ordinarily when the work is performed or costs are incurred.
Milestone payments and royalties are recognized when they are earned in
accordance with the applicable performance requirements and contractual terms.
Nonrefundable up-front payments received are recognized as revenue
systematically over the term of the agreement. Under collaboration agreements
in which we create research databases in exchange for fixed fees, revenues
from such collaborations are recognized on the percentage-of-completion
method.

    Payments to access the GeneExpress Suite are expected to be our primary
source of revenue for the foreseeable future. We have not received, and do not
expect to receive, significant royalty or other revenues from development and
commercialization of products by our customers using our databases and other
technology for several years, if at all. Revenues may be subject to
significant fluctuation in both timing and amount, and, therefore, our results
of operations for any period may not be comparable to the results of
operations for any other period.

    We have incurred operating losses in each year since our inception. At
March 31, 2001, we had accumulated losses of approximately $112.8 million. Our
losses have resulted principally from costs incurred in the development of our
gene expression databases, a $35.2 million non-recurring charge incurred in
connection with our acquisition of Oncormed and selling, general and
administrative costs associated with our operations. These costs have exceeded
our revenues which, to date, have been generated principally from agreements
for our custom databases and subscriptions to the GeneExpress Suite of
databases. We expect to incur additional operating losses in the future.

RESULTS OF OPERATIONS

Three Months Ended March 31, 2001 and March 31, 2000

    Revenues increased $2.9 million or 54% to $8.2 million during the three
months ended March 31, 2001 from $5.3 million for the same period in 2000. The
increase in revenues resulted primarily from additional customers for the
GeneExpress Suite of databases which was introduced in December of 1999.
Payments from Procter & Gamble accounted for 10% or more of revenue for the
three months ended March 31, 2001, and payments from each of Aventis
CropScience, Japan Tobacco and Procter & Gamble accounted for 10% or more of
revenue for the same period in 2000.

    Research and development expenses increased to $15.7 million for the three
months ended March 31, 2001 from $8.5 million for the same period in 2000. Of
the increase in research and development expenses for this period, $3.2
million was due to increased tissue acquisition and processing costs and
Affymetrix GeneChips usage and $1.5 million was due to research and consulting
agreement expenses. During the three months ended March 31, 2001, depreciation
and amortization expenses increased $1.9 million, of which $1.1 million was
due to amortization expense related to recent licenses of technology and
database development costs. Increased spending for research and development
will continue and is necessary to expand and enhance the content and
bioinformatic capabilities of the GeneExpress Suite of databases.

    Selling, general and administrative expenses increased to $4.8 million for
the three months ended March 31, 2001 from $3.4 million for the same period in
2000. These costs include the costs of corporate operations, finance and
accounting, human resources and other general operations. Of the increase in
selling, general and administrative expenses for this period, $0.9 million was
due to the establishment and

                                      9.

<PAGE>   10

further development of our sales and marketing efforts consisting primarily of
expenses related to increased personnel. Selling, general and administrative
expenses are expected to increase as we expand our product offerings and sales
and marketing efforts.

    Amortization of goodwill acquired as a result of the acquisition of
Oncormed in September 1998 was $0.4 million during the three months ended
March 31, 2001 and 2000.

    Net interest income increased to $3.3 million for the three months ended
March 31, 2001 from $2.4 million for the same period in 2000 primarily due to
investment of the proceeds of our public offering of common stock in February
2000.

    During the three months ended March 31, 2001, we recognized our
proportional share of losses for Neuralstem, an equity method investee. Such
non-cash losses amounted to $1.2 million for the quarter and in the future will
depend on a variety of factors including Neuralstem's results of operations and
the level of our ownership interest in Neuralstem.

    During the three months ended March 31, 2000, we recorded a cumulative
effect of an accounting change of $1.3 million related to the adoption of SAB
101.

LIQUIDITY AND CAPITAL RESOURCES

    From inception through March 31, 2001, we have financed our operations
through the sale of equity securities, payments from customers and equipment
and tenant improvement financing. In February 2000, we completed a public
offering of 4,680,000 shares of our common stock, generating net proceeds of
approximately $247.5 million. As of March 31, 2001, we had approximately
$213.8 million in cash and marketable securities, compared to $229.5 million
as of December 31, 2000.

    Net cash used in operating activities was $11.5 million for the three
months ended March 31, 2001 compared to $3.4 million during the same period in
2000. The net decrease in operating working capital for the three months ended
March 31, 2001 as compared to the same period in 2000 was primarily due to the
timing of payments for the Company's obligations, including the payment to
Incyte Genomics, Inc. of $9.0 million in connection with settlement of
outstanding litigation.

    During the three months ended March 31, 2001 and 2000, our investing
activities, other than sales, maturities and purchases of available-for-sale
securities, consisted primarily of capital expenditures and $1.3 million and
$0.8 million, respectively, for software and database development costs.
Capital expenditures for the three months ended March 31, 2001 amounted to $4.7
million and were primarily due to tenant improvements related to our new
production facility which was completed in March 2001. Capital expenditures for
the three months ended March 31, 2000 amounted to $1.2 million and were largely
due to purchases of laboratory equipment needed to expand the content of the
GeneExpress Suite of databases. We expect laboratory and computer equipment
purchases to increase as we continue to expand the content of the GeneExpress
Suite of databases.

    We have capitalized software costs of $1.3 million and $0.8 million for
the three months ended March 31, 2001 and 2000, respectively. These costs
relate to ongoing efforts to enhance GeneExpress 2000, the software platform
of the GeneExpress Suite of databases. Software and database development costs
are being amortized over their expected useful lives of three and two years,
respectively. Software development and database development costs are expected
to continue as a result of ongoing efforts to further enhance the GeneExpress
Suite of databases.

    Our financing activities, other than the repayment of capital lease
obligations and equipment loans, consisted of the issuance of common stock
primarily through our public offering in February 2000, the exercise of stock
options and the exercise of a warrant in February 2001.

    In January 1999, we entered into a three-year agreement with Affymetrix,
pursuant to which

                                     10.

<PAGE>   11

Affymetrix supplies its GeneChip probe arrays to us for the development of
gene expression databases. Under the terms of the agreement, we pay Affymetrix
subscription fees for access to the probe arrays, purchase the probe arrays
and related instrumentation and software, and will pay royalties to Affymetrix
on revenues generated from certain database subscription fees. Our commitments
under other research and license agreements do not represent significant
expenditures in relation to our total research and development expense.

    During January 2001, we paid Incyte Genomics, Inc. $9.0 million in
connection with settlement of outstanding litigation. As part of the
settlement agreement, we acquired a world-wide, nonexclusive license for the
terms of the relevant patents. A portion of the payment to Incyte has been
recorded as a license and is being amortized over its expected useful life of
five years.

    We believe that existing cash and cash equivalents and anticipated
payments from customers will be sufficient to support our operations and
repayment of equipment loans for the foreseeable future. These estimates are
forward-looking statements that involve risks and uncertainties. Our actual
future capital requirements and the adequacy of our available funds will
depend on many factors, including those discussed under "Risk Factors" in our
Annual Report on Form 10-K for the year ended December 31, 2000.

CHANGE IN ACCOUNTING PRINCIPLE

    Effective January 1, 2000, we changed our method of accounting for revenue
in accordance with Staff Accounting Bulletin No. 101, "Revenue Recognition in
Financial Statements." Prior to 2000, we recognized as revenue certain
nonrefundable up-front payments for the value of data purchased, transfer of
technology or other contractual rights that were not contingent upon future
performance under the terms of the agreement upon signing of the agreement or
when collected. Under the new accounting method adopted retroactive to January
1, 2000, we now defer these nonrefundable up-front payments and recognize them
as revenue systematically over the life of the related collaboration
agreements. The cumulative effect of the change on prior years resulted in a
charge of $1.3 million, which is included in the net loss for the three months
ended March 31, 2000. The effect of the change on the three months ended March
31, 2000, was to increase revenue and decrease net loss before the cumulative
effect of the accounting change by $0.3 million. The impact for the three
months ended March 31, 2001 was an increase in revenue and a decrease in net
loss of $0.1 million. The impact for the year ended December 31, 2001 will be
an increase in revenue and a decrease in net loss of $0.5 million.

ITEM 3.    QUANTITATIVE AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK

    We have limited exposure to financial market risks, including changes in
interest rates. At March 31, 2001, we had cash and cash equivalents of
approximately $213.8 million. Cash and cash equivalents consisted of money
market accounts and investment grade commercial paper. A 100 basis point
adverse movement in interest rates would increase net loss for the three
months ended March 31, 2001 by approximately $0.5 million. Actual changes in
rates may differ from the hypothetical assumptions used in computing this
exposure.

                                     11.

<PAGE>   12


PART II  OTHER INFORMATION


ITEM 6.    EXHIBITS AND REPORTS ON FORM 8-K

         A)       EXHIBITS:

                  *10.55     Executive Severance Plan, as amended February
                             2001.

----------

  * Indicates management compensatory plan, contract or arrangement.

         B)       REPORTS ON FORM 8-K:

                  No reports on Form 8-K were filed during the three months
                  ended March 31, 2001.

                                     12.

<PAGE>   13


                                  SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


                            GENE LOGIC INC.


Date:    May 11, 2001       By:  /s/ Philip L. Rohrer, Jr.
                                ---------------------------------------------
                               Philip L. Rohrer, Jr.
                               Chief Financial Officer
                               (Principal Financial and Accounting Officer)





                                     13.