ADVANCED MAGNETICS INC
SC 13D/A, 2000-01-11
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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<PAGE>

                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549

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

                                  SCHEDULE 13D
                                 (RULE 13d-101)

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

                            ADVANCED MAGNETICS, INC.
                            ------------------------
                                (Name of Issuer)

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

                                   00753P 10 3
                                   -----------
                                 (CUSIP Number)

                                   Hope Flack
                                BVF Partners L.P.
                       227 West Monroe Street, Suite 4800
                             Chicago, Illinois 60606
                                 (312) 263-7777
                       ----------------------------------
                  (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                DECEMBER 28, 1999
                                -----------------
             (Date of Event which Requires Filing of this Statement)

         If the filing person has previously filed a statement on Schedule
13G to report the acquisition which is the subject of this Schedule 13D, and
is filing this schedule because of Rule 13d-1(b)(3) or (4), check the
following box / /.

         NOTE: Six copies of this statement, including all exhibits, should
be filed with the Commission.  SEE Rule 13d-1(a) for other parties to whom
copies are to be sent.

                         (Continued on following pages)

                               (Page 1 of 9 Pages)



- -----------------------
    (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).

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 2 of 9 Pages
- -------------------------                                   ------------------

- --------------------------------------------------------------------------------
  1       NAME OF REPORTING PERSONS
          I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                   BIOTECHNOLOGY VALUE FUND, L.P.
- --------------------------------------------------------------------------------
  2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                (a) /X/ (b) / /
- --------------------------------------------------------------------------------
  3       SEC USE ONLY

- --------------------------------------------------------------------------------
  4       SOURCE OF FUNDS*
                   WC
- --------------------------------------------------------------------------------
  5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
          REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                        / /
- --------------------------------------------------------------------------------
  6       CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
- --------------------------------------------------------------------------------
                 NUMBER                      7      SOLE VOTING POWER
                   OF                                        -0-
                 SHARES                -----------------------------------------
              BENEFICIALLY                   8      SHARED VOTING POWER
              OWNED BY EACH                             385,413
                REPORTING              -----------------------------------------
                 PERSON                      9      SOLE DISPOSITIVE POWER
                  WITH                                    -0-
                                       -----------------------------------------
                                            10      SHARED DISPOSITIVE POWER
                                                        385,413
- --------------------------------------------------------------------------------
 11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
          REPORTING PERSON
                   385,413
- --------------------------------------------------------------------------------
 12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
          CERTAIN SHARES*                                                 / /
- --------------------------------------------------------------------------------
 13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                   5.7%
- --------------------------------------------------------------------------------
 14       TYPE OF REPORTING PERSON*
                   PN
- --------------------------------------------------------------------------------

                 * SEE INSTRUCTIONS BEFORE FILLING OUT!

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 3 of 9 Pages
- -------------------------                                   ------------------

- --------------------------------------------------------------------------------
   1       NAME OF REPORTING PERSONS
           I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                    BIOTECHNOLOGY VALUE FUND II, L.P.
- --------------------------------------------------------------------------------
   2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/  (b) / /
- --------------------------------------------------------------------------------
   3       SEC USE ONLY

- --------------------------------------------------------------------------------
   4       SOURCE OF FUNDS*
                    WC
- --------------------------------------------------------------------------------
   5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
           REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                       / /
- --------------------------------------------------------------------------------
   6       CITIZENSHIP OR PLACE OF ORGANIZATION
                    DELAWARE
- --------------------------------------------------------------------------------
                  NUMBER                      7      SOLE VOTING POWER
                    OF                                        -0-
                  SHARES               -----------------------------------------
               BENEFICIALLY                   8      SHARED VOTING POWER
               OWNED BY EACH                               394,257
                 REPORTING             -----------------------------------------
                  PERSON                      9      SOLE DISPOSITIVE POWER
                   WITH                                      -0-
                                       -----------------------------------------
                                             10      SHARED DISPOSITIVE POWER
                                                           394,257
- --------------------------------------------------------------------------------
  11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
           REPORTING PERSON
                    394,257
- --------------------------------------------------------------------------------
  12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
           CERTAIN SHARES*                                                / /
- --------------------------------------------------------------------------------
  13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                    5.8%
- --------------------------------------------------------------------------------
  14       TYPE OF REPORTING PERSON*
                    PN
- --------------------------------------------------------------------------------

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 4 of 9 Pages
- -------------------------                                   ------------------

- --------------------------------------------------------------------------------
  1       NAME OF REPORTING PERSONS
          I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                   BVF PARTNERS L.P.
- --------------------------------------------------------------------------------
  2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/  (b) / /
- --------------------------------------------------------------------------------
  3       SEC USE ONLY

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

  4       SOURCE OF FUNDS*
                   OO
- --------------------------------------------------------------------------------
  5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
          REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                        / /
- --------------------------------------------------------------------------------
  6       CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
- --------------------------------------------------------------------------------
                 NUMBER                      7      SOLE VOTING POWER
                   OF                                      -0-
                 SHARES                -----------------------------------------
              BENEFICIALLY                   8      SHARED VOTING POWER
              OWNED BY EACH                              796,050
                REPORTING              -----------------------------------------
                 PERSON                      9      SOLE DISPOSITIVE POWER
                  WITH                                     -0-
                                       -----------------------------------------
                                            10      SHARED DISPOSITIVE POWER
                                                         796,050
- --------------------------------------------------------------------------------
 11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
          REPORTING PERSON
                   796,050
- --------------------------------------------------------------------------------
 12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
          CERTAIN SHARES*                                                / /
- --------------------------------------------------------------------------------
 13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                   11.8%
- --------------------------------------------------------------------------------
 14       TYPE OF REPORTING PERSON*
                   PN
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!


<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 5 of 9 Pages
- -------------------------                                   ------------------

- --------------------------------------------------------------------------------
  1       NAME OF REPORTING PERSONS
          I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                   BVF INC.
- --------------------------------------------------------------------------------
  2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/  (b) / /
- --------------------------------------------------------------------------------
  3       SEC USE ONLY

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

  4       SOURCE OF FUNDS*
                   WC, OO
- --------------------------------------------------------------------------------
  5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
          REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                         / /
- --------------------------------------------------------------------------------
  6       CITIZENSHIP OR PLACE OF ORGANIZATION
                   DELAWARE
- --------------------------------------------------------------------------------
                 NUMBER                      7      SOLE VOTING POWER
                   OF                                      -0-
                 SHARES                -----------------------------------------
              BENEFICIALLY                   8      SHARED VOTING POWER
              OWNED BY EACH                               796,050
                REPORTING              -----------------------------------------
                 PERSON                      9      SOLE DISPOSITIVE POWER
                  WITH                                      -0-
                                       -----------------------------------------
                                            10      SHARED DISPOSITIVE POWER
                                                          796,050
- --------------------------------------------------------------------------------
 11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH
          REPORTING PERSON
                   796,050
- --------------------------------------------------------------------------------
 12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
          CERTAIN SHARES*                                                  / /
- --------------------------------------------------------------------------------
 13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                   11.8%
- --------------------------------------------------------------------------------
 14       TYPE OF REPORTING PERSON*
                   IA, CO
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!


<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 6 of 9 Pages
- -------------------------                                   ------------------

Amendment No. 1 (the "Amendment") to the Statement on Schedule 13D dated
September 8, 1998 (as so amended, the "Statement"), is filed with the
Securities and Exchange Commission on behalf of Biotechnology Value Fund,
L.P., a Delaware limited partnership ("BVF"), Biotechnology Value Fund II,
L.P., a Delaware limited partnership ("BVF2"), BVF Partners L.P., a Delaware
limited partnership ("Partners"), and BVF Inc., a Delaware corporation ("BVF
Inc." and, together with BVF and Partners, the "Reporting Persons") with
respect to the Common Stock, par value $0.01 per share (the "Stock"), of
Advanced Magnetics, Inc. ("Advanced Magnetics"). The principle office of
Advanced Magnetics is located at 61 Mooney Street, Cambridge, MA 02138-1038.

Item 2 is hereby amended to read in its entirety as follows:

ITEM 2.      IDENTITY AND BACKGROUND.

         The persons filing this Amendment, the persons enumerated in
Instruction C of Schedule 13D and, where applicable, their respective places
of organization, general partners, directors, executive officers and
controlling persons, and certain information regarding each of them, are as
follows:

         (a) Biotechnology Value Fund, L.P., a Delaware limited partnership
("BVF"), Biotechnology Value Fund II, L.P., a Delaware limited partnership
("BVF2"), BVF Partners L.P., a Delaware limited partnership ("Partners"), BVF
Inc., a Delaware corporation ("BVF Inc."), and Mark N. Lampert, an individual
("Lampert") (collectively, the "Reporting Persons").

         (b) The business address of BVF, BVF2 and Partners is 227 West
Monroe Street, Suite 4800, Chicago, Illinois 60606. The business address of
BVF Inc. and Lampert is One Sansome Street, 39th Floor, San Francisco,
California 94104.

         (c) Partners is the general partner of BVF, which is an investment
limited partnership. Similarly, Partners is the general partner of BVF2,
which also is an investment limited partnership. BVF Inc. is an investment
adviser to and general partner of Partners. Lampert is the sole shareholder,
sole director and an officer of BVF Inc.

         (d) During the last five years, none of such persons has been
convicted in a criminal proceeding (excluding traffic violations and similar
misdemeanors).

         (e) During the last five years, none of such persons was a party to
a civil proceeding of a judicial or administrative body of competent
jurisdiction and as a result of such proceeding was or is subject to a
judgment, decree or final order enjoining future violations of, or
prohibiting or mandating activities subject to, federal or state securities
laws or finding any violation with respect to such laws.

         (f) Lampert is a citizen of the United States of America.

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 7 of 9 Pages
- -------------------------                                   ------------------

Item 3 is hereby amended to read in its entirety as follows:

ITEM 3.      SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

         Since November 1, 1999, Partners, in its capacity as general partner
of BVF, has caused such limited partnership to purchase 7,000 shares of the
Stock for an aggregate consideration of $27,451.90, utilizing BVF's working
capital.

         BVF2, utilizing its working capital, has acquired 344,257 shares of
the Stock from BVF and certain of the managed accounts, for an aggregate
consideration of $1,157,994.49. In connection therewith, BVF transferred
111,287 shares of the Stock for consideration in the amount of $374,341.65,
and the managed account transferred 232,970 shares of the Stock for
consideration in the amount of $783,652.84. These transactions effected a
shift in the shares beneficially owned by BVF to BVF2, but the aggregate
number of shares beneficially owned by Partners and BVF Inc. was not
affected; nor did the transactions change the pecuniary interest of Partners
and BVF Inc. in the Stock.

In addition, Partners in its capacity as general partner of BVF2, has caused
such limited partnership to purchase an aggregate number of 50,000 shares of
the Stock for an aggregate consideration of $201,732.50, utilizing BVF2's
working capital.

Further, Partners, in its capacity as investment manager of a managed
account, has transferred directly to the beneficial owners of that managed
account or to a liquidating fund established for their benefit, 180,185
shares of the Stock for no consideration.

Item 5 is hereby amended to read in its entirety as follows:

ITEM 5.      INTEREST IN SECURITIES OF THE ISSUER.

         (a) BVF beneficially owns 385,413 shares of the Stock, BVF2
beneficially owns 394,257 shares of the Stock, Partners beneficially owns
796,050 shares of the Stock, and BVF Inc. beneficially owns 796,050 shares of
the Stock, approximately 5.7%, 5.8%, 11.8% and 11.8%, respectively, of the
aggregate number of shares outstanding as of December 7, 1999 (as reported in
Advanced Magnetics' most recent annual report on Form 10-K).

         (b) BVF shares voting and dispositive power over the 385,413 shares
of the Stock it beneficially owns with Partners. BVF2 shares voting and
dispositive power over the 394,257 shares of the Stock it beneficially owns
with Partners. Partners and BVF Inc. share voting and dispositive power over
the 796,050 shares of the Stock they beneficially own with, in addition to
BVF and BVF2, the managed accounts on whose behalf Partners, as investment
manager, acquired such shares. The managed accounts on whose behalf Partners
owns or has owned, shares of the Stock are Biotechnology Value Fund, Ltd., a
Cayman Islands Corporation ("BVF Ltd.") and Investment 10 L.L.C., an Illinois
limited liability company ("ILL10"). Together, BVF Ltd. and ILL10 are
referred to herein as the "Accounts." The Accounts specialize in holding
biotechnology stocks

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 8 of 9 Pages
- -------------------------                                   ------------------

for investment purposes and its business address is: BVF Partners L.P., 227
West Monroe Street, Suite 4800, Chicago, Illinois 60606.

         (c) Exhibit B attached hereto contains information as to all
transactions in the Stock by the Reporting Persons in the last sixty (60)
days. All transactions made with a broker were made for cash in open market,
over-the-counter transactions. The remainder were private transactions made
without a broker involving transfers to BVF2 from BVF and certain managed
accounts as well as between a managed account and either its beneficial
owners directly or a liquidating fund established for the benefit of the
owners. No other transactions in the Stock have been effected by the
Reporting Persons in the last sixty (60) days.

         (d) The Accounts are entitled to receive dividends and any sale
proceeds with respect to the Stock in proportion to their respective
ownership interests therein.

Item 7 is hereby amended to read in its entirety as follows:

ITEM 7.      MATERIAL TO BE FILED AS EXHIBITS.

         Exhibit A - Agreement Regarding Joint Filing

         Exhibit B - Transactions in the Stock by the Reporting Persons
during the past sixty (60) days.

<PAGE>

- -------------------------                                   ------------------
 CUSIP NO. 00753P 10 3                  13D                 Page 9 of 9 Pages
- -------------------------                                   ------------------

         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: January 10, 2000

         BIOTECHNOLOGY VALUE FUND, L.P.

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

                  By:      BVF Inc., its general partner


                           By:
                                -------------------------------------
                                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:
                                -------------------------------------
                                Mark N. Lampert
                                President


         BVF PARTNERS L.P.

         By:               BVF Inc., its general partner


                           By:
                              ---------------------------------------
                              Mark N. Lampert
                              President

         BVF INC.


                           By:
                              ---------------------------------------
                              Mark N. Lampert
                              President

<PAGE>

                                    EXHIBIT A

                        AGREEMENT REGARDING JOINT FILING

         The undersigned, Biotechnology Value Fund, L.P., a Delaware limited
partnership, Biotechnology Value Fund II, L.P., a Delaware limited
partnership, BVF Partners L.P., a Delaware limited partnership, and BVF Inc.,
a Delaware corporation, hereby agree and acknowledge that the statement
containing the information required by this amendment to Schedule 13D, to
which this Agreement is attached as an exhibit, is filed on behalf of each of
them. The undersigned further agree that any further amendments or
supplements thereto shall also be filed on behalf of each of them.

Dated: January 10, 2000

         BIOTECHNOLOGY VALUE FUND, L.P.

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

                  By:      BVF Inc., its general partner


                           By:
                                -------------------------------------
                                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:
                                -------------------------------------
                                Mark N. Lampert
                                President


         BVF PARTNERS L.P.

         By:               BVF Inc., its general partner


                           By:
                               --------------------------------------
                               Mark N. Lampert
                               President

         BVF INC.


                           By:
                              ---------------------------------------
                              Mark N. Lampert
                              President


<PAGE>

                                    EXHIBIT B

               TRANSACTIONS IN THE STOCK BY THE REPORTING PERSONS
                           DURING THE PAST SIXTY DAYS

<TABLE>
<CAPTION>
- -------------------------------------------------------------------------------------------------------------
    SETTLEMENT         BY          FOR THE          QUANTITY        PRICE PER        TYPE OF TRADE     BROKER
    ----------         --          -------          --------        ---------        -------------     ------
       DATE                       ACCOUNT OF                          SHARE
       ----                       ----------                          -----
<S>                 <C>             <C>             <C>            <C>               <C>               <C>
- -------------------------------------------------------------------------------------------------------------
12/17/99            Partners        BVF             111,287        $3.6368              Transfer        NB
- -------------------------------------------------------------------------------------------------------------
12/17/99            Partners        BVF2            111,287        $3.6368              Transfer        NB
- -------------------------------------------------------------------------------------------------------------
12/17/99            Partners        BVF Ltd.        232,970        $3.6368              Transfer        NB
- -------------------------------------------------------------------------------------------------------------
12/17/99            Partners        BVF2            232,970        $3.6368              Transfer        NB
- -------------------------------------------------------------------------------------------------------------
12/21/99            Partners        BVF               7,000        $3.8717              Purchase        HRZG
- -------------------------------------------------------------------------------------------------------------
12/21/99            Partners        BVF2             10,000        $3.8717              Purchase        HRZG
- -------------------------------------------------------------------------------------------------------------
12/22/99            Partners        BVF2              5,000        $4.5625              Purchase        HRZG
- -------------------------------------------------------------------------------------------------------------
12/28/99            Partners        BVF2             25,000        $3.9328              Purchase        HRZG
- -------------------------------------------------------------------------------------------------------------
12/30/99            Partners        BVF2             10,000        $3.9375              Purchase        HRZG
- -------------------------------------------------------------------------------------------------------------
01/03/00            Partners        BVF Ltd.        180,185        $4.1250              Transfer        NB
- -------------------------------------------------------------------------------------------------------------
</TABLE>

HRZG        =        Herzog, Heine & Geduld
NB          =        No Broker


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