SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549


                                  SCHEDULE 13G
                                 (RULE 13d-102)

             INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
           TO RULES 13D-1(b) (c) AND (d) AND AMENDMENTS THERETO FILED
                              PURSUANT TO 13d-2(b)
                               (AMENDMENT NO. 2)1

                            GENOME THERAPEUTICS CORP.
                            -------------------------
                                (Name of Issuer)

                                  COMMON STOCK
                          -----------------------------
                         (Title of Class of Securities)

                                   372430 10 8
                                   -----------
                                 (CUSIP Number)

                                  JUNE 11, 2001
                                  -------------
             (Date of Event Which Requires Filing of this Statement)


Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

                  |_|      Rule 13d-1(b)
                  |X|      Rule 13d-1(c)
                  |_|      Rule 13d-1(d)





------------------
(1)   The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 or otherwise subject to the liabilities of that section of the Act but
shall be subject to all other provisions of the Act (however, SEE the NOTES).



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 2 OF 9
----------------------------                        ----------------------------

--------- ----------------------------------------------------------------------
   1      NAME OF REPORTING PERSON:
                   BIOTECHNOLOGY VALUE FUND, L.P.
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

--------- ----------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) |X|  (b) |_|
--------- ----------------------------------------------------------------------
   3      SEC USE ONLY

--------- ----------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
-------------------------- ----- -----------------------------------------------
         NUMBER              5   SOLE VOTING POWER
           OF                            0
         SHARES            ----- -----------------------------------------------
      BENEFICIALLY           6   SHARED VOTING POWER
      OWNED BY EACH                      263,000
        REPORTING          ----- -----------------------------------------------
         PERSON              7   SOLE DISPOSITIVE POWER
          WITH                           0
                           ----- -----------------------------------------------
                             8   SHARED DISPOSITIVE POWER
                                         263,000
--------- ----------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                   263,000
--------- ----------------------------------------------------------------------
   10     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
          CERTAIN SHARES*                                                    |_|
--------- ----------------------------------------------------------------------
   11     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                   1.2%
--------- ----------------------------------------------------------------------
   12     TYPE OF REPORTING PERSON*
                   PN
--------- ----------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 3 OF 9
----------------------------                        ----------------------------

--------- ----------------------------------------------------------------------
   1      NAME OF REPORTING PERSON:
                   BIOTECHNOLOGY VALUE FUND II, L.P.
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

--------- ----------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) |X|  (b) |_|
--------- ----------------------------------------------------------------------
   3      SEC USE ONLY

--------- ----------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
-------------------------- ----- -----------------------------------------------
         NUMBER              5   SOLE VOTING POWER
           OF                            0
         SHARES            ----- -----------------------------------------------
      BENEFICIALLY           6   SHARED VOTING POWER
      OWNED BY EACH                      118,124
        REPORTING          ----- -----------------------------------------------
         PERSON              7   SOLE DISPOSITIVE POWER
          WITH                           0
                           ----- -----------------------------------------------
                             8   SHARED DISPOSITIVE POWER
                                         118,124
--------- ----------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                   118,124
--------- ----------------------------------------------------------------------
   10     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
          CERTAIN SHARES*                                                    |_|
--------- ----------------------------------------------------------------------
   11     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                   0.8%
--------- ----------------------------------------------------------------------
   12     TYPE OF REPORTING PERSON*
                   PN
--------- ----------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 4 OF 9
----------------------------                        ----------------------------

--------- ----------------------------------------------------------------------
   1      NAME OF REPORTING PERSON:
                   BVF INVESTMENTS, L.L.C.
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

--------- ----------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) |X|  (b) |_|
--------- ----------------------------------------------------------------------
   3      SEC USE ONLY

--------- ----------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
-------------------------- ----- -----------------------------------------------
         NUMBER              5   SOLE VOTING POWER
           OF                            0
         SHARES            ----- -----------------------------------------------
      BENEFICIALLY           6   SHARED VOTING POWER
      OWNED BY EACH                      94,576
        REPORTING          ----- -----------------------------------------------
         PERSON              7   SOLE DISPOSITIVE POWER
          WITH                           0
                           ----- -----------------------------------------------
                             8   SHARED DISPOSITIVE POWER
                                         94,576
--------- ----------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                   94,576
--------- ----------------------------------------------------------------------
   10     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
          CERTAIN SHARES*                                                    |_|
--------- ----------------------------------------------------------------------
   11     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                   0.4%
--------- ----------------------------------------------------------------------
   12     TYPE OF REPORTING PERSON*
                   OO
--------- ----------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 5 OF 9
----------------------------                        ----------------------------

--------- ----------------------------------------------------------------------
   1      NAME OF REPORTING PERSON:
                   BVF PARTNERS L.P.
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

--------- ----------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) |X|  (b) |_|
--------- ----------------------------------------------------------------------
   3      SEC USE ONLY

--------- ----------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
-------------------------- ----- -----------------------------------------------
         NUMBER              5   SOLE VOTING POWER
           OF                            0
         SHARES            ----- -----------------------------------------------
      BENEFICIALLY           6   SHARED VOTING POWER
      OWNED BY EACH                      587,800
        REPORTING          ----- -----------------------------------------------
         PERSON              7   SOLE DISPOSITIVE POWER
          WITH                           0
                           ----- -----------------------------------------------
                             8   SHARED DISPOSITIVE POWER
                                         587,800
--------- ----------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                   587,800
--------- ----------------------------------------------------------------------
   10     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
          CERTAIN SHARES*                                                    |_|
--------- ----------------------------------------------------------------------
   11     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                   2.6%
--------- ----------------------------------------------------------------------
   12     TYPE OF REPORTING PERSON*
                   PN
--------- ----------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 6 OF 9
----------------------------                        ----------------------------

--------- ----------------------------------------------------------------------
   1      NAME OF REPORTING PERSON:
                   BVF INC.
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

--------- ----------------------------------------------------------------------
   2      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) |X|  (b) |_|
--------- ----------------------------------------------------------------------
   3      SEC USE ONLY

--------- ----------------------------------------------------------------------
   4      CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
-------------------------- ----- -----------------------------------------------
         NUMBER              5   SOLE VOTING POWER
           OF                            0
         SHARES            ----- -----------------------------------------------
      BENEFICIALLY           6   SHARED VOTING POWER
      OWNED BY EACH                      587,800
        REPORTING          ----- -----------------------------------------------
         PERSON              7   SOLE DISPOSITIVE POWER
          WITH                           0
                           ----- -----------------------------------------------
                             8   SHARED DISPOSITIVE POWER
                                         587,800
--------- ----------------------------------------------------------------------
   9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                   587,800
--------- ----------------------------------------------------------------------
   10     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
          CERTAIN SHARES*                                                    |_|
--------- ----------------------------------------------------------------------
   11     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                   2.6%
--------- ----------------------------------------------------------------------
   12     TYPE OF REPORTING PERSON*
                   IA, CO
--------- ----------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 7 OF 9
----------------------------                        ----------------------------

ITEM 1(a).        NAME OF ISSUER:
                  Genome Therapeutics Corp. ("Genome")

ITEM 1(b).        ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:

                  100 Beaver Street
                  Waltham, Massachusetts 02154


ITEM 2(a).        NAME OF PERSON FILING:

                  This Amendment to Schedule 13G is being filed on behalf of the
                  following persons* (the "Reporting Persons"):

                  (i)      Biotechnology Value Fund, L.P. ("BVF")
                  (ii)     Biotechnology Value Fund II, L.P. ("BVF2")
                  (iii)    BVF Investments, L.L.C. ("Investments")
                  (iv)     BVF Partners L.P.  ("Partners")
                  (v)      BVF Inc. ("BVF Inc.")

                  *        Attached as Exhibit 1 is a copy of an agreement among
                           the Reporting Persons filing (as specified
                           hereinabove) that this Amendment to Schedule 13G is
                           being filed on behalf of each of them.

ITEM 2(b).        ADDRESS OF PRINCIPAL BUSINESS OFFICE:

                  The principal business office of the Reporting Persons
comprising the group filing this Amendment to Schedule 13G is located at 227
West Monroe Street, Suite 4800, Chicago, Illinois, 60606.

ITEM 2(c).        CITIZENSHIP:

                  BVF:                  a Delaware limited partnership
                  BVF2:                 a Delaware limited partnership
                  Investments:          a Delaware limited liability company
                  Partners:             a Delaware limited partnership
                  BVF Inc.:             a Delaware corporation

ITEM 2(d).        TITLE OF CLASS OF SECURITIES:

                  Common Stock, $0.10 par value.

ITEM 2(e).        CUSIP NUMBER:

                  372430 10 8


----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 8 OF 9
----------------------------                        ----------------------------

ITEM 3.           IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(b), OR
                  13d-2(b) OR (c) CHECK WHETHER THE PERSON FILING IS: ONE OF
                  THE FOLLOWING

                  Not applicable as this Amendment to Schedule 13G is filed
pursuant to Rule 13d 1(c).

ITEM 4.           OWNERSHIP:

                  The information in items 1 and 5 through 11 on the cover pages
(pp. 2-6) on this Amendment to Schedule 13G is hereby incorporated by reference.

ITEM 5.           OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS:

                  If this statement is being filed to report the fact that as of
the date hereof the Reporting Persons have ceased to be the beneficial owner of
more than five percent of the class of securities check the following. |X|

ITEM 6.           OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER
                  PERSON:

                  BVF shares voting and dispositive power over the shares of the
common stock it beneficially owns with Partners. BVF2 also shares voting and
dispositive power over the shares of the common stock it beneficially owns with
Partners. Investments also shares voting and dispositive power over the shares
of the common stock it beneficially owns with Partners. Partners and BVF Inc.
share voting and dispositive power over the shares of the common stock they
beneficially own with, in addition to BVF, BVF2 and Investments, certain managed
accounts on whose behalf Partners, as investment manager, purchased such shares.
None of the managed accounts individually owns more than 5% of the common stock
of Genome.

ITEM 7.           IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
                  ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING
                  COMPANY:

                  Not applicable.

ITEM 8.           IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A GROUP:

                  Not applicable.

ITEM 9.           NOTICE OF DISSOLUTION OF GROUP:

                  Not applicable.


----------------------------                        ----------------------------
  CUISP NO. 372430 10 8               13G             PAGE 9 OF 9
----------------------------                        ----------------------------

ITEM 10.          CERTIFICATION

                  By signing below I certify that, to the best of my knowledge
and belief, the securities referred to above were not acquired and are not held
for the purpose of or with the effect of changing or influencing the control of
the issuer of the securities and were not acquired and are not held in
connection with or as a participant in any transaction having that purpose or
effect.

                  After reasonable inquiry and to the best of my knowledge and
belief, I certify that the information set forth in this statement is true,
complete and correct.

Dated: June 15, 2001

                  BIOTECHNOLOGY VALUE FUND, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner

                                    By:     /s/  MARK N. LAMPERT
                                            ------------------------------------
                                            Mark N. Lampert
                                            President

                  BIOTECHNOLOGY VALUE FUND II, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner

                                    By:     /s/  MARK N. LAMPERT
                                            ------------------------------------
                                            Mark N. Lampert
                                            President

                  BVF INVESTMETNS L.L.C.

                  By:      BVF Partners L.P., its manager

                           By:      BVF Inc., its general partner

                                    By:     /s/  MARK N. LAMPERT
                                            ------------------------------------
                                            Mark N. Lampert
                                            President

                  BVF PARTNERS L.P.

                  By:      BVF Inc., its general partner

                           By:      /s/  MARK N. LAMPERT
                                    ------------------------------------
                                    Mark N. Lampert
                                    President

                  BVF INC.

                  By:      /s/  MARK N. LAMPERT
                           ------------------------------------
                           Mark N. Lampert
                           President