AVRX Avalon Pharmaceuticals (MM)

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CUSIP No. 05346P106 13G/A Page 2 of 10 Pages
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 1. NAMES OF REPORTING PERSONS

 Great Point Partners, LLC

 I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

 37-1475292

 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

 (a) [ ]

 (b) [ ]

--------------------------------------------------------------------------------
 3. SEC USE ONLY


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

 4. CITIZENSHIP OR PLACE OF ORGANIZATION

 Delaware

NUMBER OF SHARES 5. SOLE VOTING POWER
 BENEFICIALLY
 OWNED BY EACH 0
REPORTING PERSON
 WITH 6. SHARED VOTING POWER

 960,000

 7. SOLE DISPOSITIVE POWER

 0

 8. SHARED DISPOSITIVE POWER

 960,000

 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 960,000

 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 (See Instructions)
 [ ]

 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 4.65%

 12. TYPE OF REPORTING PERSON (See Instructions)

 OO


 2

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CUSIP No. 05346P106 13G/A Page 3 of 10 Pages
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 1. NAMES OF REPORTING PERSONS

 Dr. Jeffrey R. Jay, M.D.

 I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

 (a) [ ]

 (b) [ ]

--------------------------------------------------------------------------------
 3. SEC USE ONLY


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

 4. CITIZENSHIP OR PLACE OF ORGANIZATION

 USA

NUMBER OF SHARES 5. SOLE VOTING POWER
 BENEFICIALLY
 OWNED BY EACH 0
REPORTING PERSON
 WITH 6. SHARED VOTING POWER

 960,000

 7. SOLE DISPOSITIVE POWER

 0

 8. SHARED DISPOSITIVE POWER

 960,000

 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 960,000

 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 (See Instructions)
 [ ]

 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 4.65%

 12. TYPE OF REPORTING PERSON (See Instructions)

 IN


 3

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CUSIP No. 05346P106 13G/A Page 4 of 10 Pages
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 1. NAMES OF REPORTING PERSONS

 Mr. David Kroin

 I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP

 (a) [ ]

 (b) [ ]

--------------------------------------------------------------------------------
 3. SEC USE ONLY


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

 4. CITIZENSHIP OR PLACE OF ORGANIZATION

 USA

NUMBER OF SHARES 5. SOLE VOTING POWER
 BENEFICIALLY
 OWNED BY EACH 0
REPORTING PERSON
 WITH 6. SHARED VOTING POWER

 960,000

 7. SOLE DISPOSITIVE POWER

 0

 8. SHARED DISPOSITIVE POWER

 960,000

 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

 960,000

 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
 (See Instructions)
 [ ]

 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

 4.65%

 12. TYPE OF REPORTING PERSON (See Instructions)

 IN


 4

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CUSIP No. 05346P106 13G/A Page 5 of 10 Pages
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 ITEM 1.

 (a) Name of Issuer

 Avalon Pharmaceuticals, Inc.

 (b) Address of Issuer's Principal Executive Offices
 20358 Seneca Meadows Parkway
 Germantown, MD 20876

 ITEM 2.

 (a) Name of Person Filing

 Great Point Partners, LLC
 Dr. Jeffrey R. Jay, M.D.
 Mr. David Kroin

 The Reporting Persons have entered into a Joint Filing
 Agreement, dated February 17, 2009, a copy of which is filed
 with this Schedule 13G/A as Exhibit A, pursuant to which the
 Reporting Persons have agreed to file this statement jointly
 in accordance with the provisions of Rule 13d-1(k)(1) under
 the Act.

 (b) Address of Principal Business Office, or if none,
 Residence

 The address of the principal business office of
 each of the Reporting Persons is

 165 Mason Street - 3rd Floor
 Greenwich, CT 06830

 (c) Citizenship

 Great Point Partners, LLC is a limited liability company
 organized under the laws of the State of Delaware. Dr.
 Jeffrey R. Jay, M.D. is a citizen of the United States. Mr.
 David Kroin is a citizen of the United States.

 (d) Title of Class of Securities

 Common Stock

 (e) CUSIP Number

 05346P106

 ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO ss.240.13d-1(b) OR
 240.13d.2(b) OR (c), CHECK WHETHER THE PERSON FILING IS A:

 Not Applicable.

 (a) [ ] Broker or dealer registered under Section 15 of
 the Act (15 U.S.C. 78o)

 (b) [ ] Bank as defined in Section 3(a)(6) of the Act (15
 U.S.C. 78c).

 (c) [ ] Insurance company as defined in Section 3(a)(19)
 of the Act (15. U.S.C. 78c).


 5

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CUSIP No. 05346P106 13G/A Page 6 of 10 Pages
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 (d) [ ] Investment Company registered under Section 8 of
 the Investment Company Act of 1940 (15 U.S.C.
 80a-8).

 (e) [ ] An investment adviser in accordance with
 ss.240.13d-1(b)(1)(ii)(E).

 (f) [ ] An employee benefit plan or endowment fund in
 accordance with ss.240.13d-1(b)(1)(ii)(F).

 (g) [ ] A parent holding company or control person in
 accordance with ss.240.13d-1(b)(1)(ii)(G).

 (h) [ ] A savings associations as defined in Section 3(b)
 of the Federal Deposit Insurance Act (12 U.S.C.
 1813).

 (i) [ ] A church plan that is excluded from the definition
 of an investment company under Section 3(c)(14) of
 the Investment Company Act of 1940 (15 U.S.C.
 80a-3).

 (j) [ ] Group, in accordance with
 ss.240.13d-1(b)(1)(ii)(J).

 ITEM 4. OWNERSHIP

 Great Point Partners, LLC ("Great Point") is the investment
 manager of Biomedical Value Fund, L.P. ("BVF"), and by
 virtue of such status may be deemed to be the beneficial
 owner of the 518,399 shares of Common Stock (including
 108,000 shares which BVF has the right to acquire pursuant
 to the exercise of warrants held by BVF) of the Issuer owned
 by BVF (the "BVF Shares"). Each of Dr. Jeffrey R. Jay, M.D.
 ("Dr. Jay"), as senior managing member of Great Point, and
 Mr. David Kroin ("Mr. Kroin"), as special managing member of
 Great Point, has voting and investment power with respect to
 the BVF Shares, and therefore may be deemed to be the
 beneficial owner of the BVF Shares.

 Great Point is the investment manager of Biomedical Offshore
 Value Fund, Ltd. ("BOVF"), and by virtue of such status may
 be deemed to be the beneficial owner of the 441,601 shares
 of Common Stock (including 92,000 shares which BOVF has the
 right to acquire pursuant to the exercise of warrants held
 by BOVF) of the Issuer owned by BOVF (the "BOVF Shares").
 Each of Dr. Jay, as senior managing member of Great Point,
 and Mr. Kroin, as special managing member of Great Point,
 has voting and investment power with respect to the BOVF
 Shares, and therefore may be deemed to be the beneficial
 owner of the BOVF Shares.

 Great Point, Dr. Jay and Mr. Kroin disclaim beneficial
 ownership of the BVF Shares and the BOVF Shares, except to
 the extent of their respective pecuniary interest.


 Provide the following information regarding the aggregate
 number and percentage of the class of securities of the
 issuer identified in Item 1.

 1. GREAT POINT PARTNERS, LLC

 (a) Amount beneficially owned: 960,000

 (b) Percent of class: 4.65%.

 (c) Number of shares as to which the person has:

 (i) Sole power to vote or to direct the vote:
 - 0 -


 6

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CUSIP No. 05346P106 13G/A Page 7 of 10 Pages
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 (ii) Shared power to vote or to direct the
 vote: 960,000

 (iii) Sole power to dispose or to direct the
 disposition of: - 0 -.

 (iv) Shared power to dispose or to direct the
 disposition of: 960,000

 2. DR. JEFFREY R. JAY, M.D.

 (a) Amount beneficially owned: 960,000

 (b) Percent of class: 4.65%.

 (c) Number of shares as to which the person has:

 (i) Sole power to vote or to direct the vote:
 0.

 (ii) Shared power to vote or to direct the
 vote: 960,000

 (iii) Sole power to dispose or to direct the
 disposition of: 0.

 (iv) Shared power to dispose or to direct the
 disposition of: 960,000

 3. MR. DAVID KROIN

 (a) Amount beneficially owned: 960,000

 (b) Percent of class: 4.65%.

 (c) Number of shares as to which the person has:

 (i) Sole power to vote or to direct the vote:
 0.

 (ii) Shared power to vote or to direct the
 vote: 960,000

 (iii) Sole power to dispose or to direct the
 disposition of: 0.

 (iv) Shared power to dispose or to direct the
 disposition of: 960,000

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 each of the Reporting Persons has 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:

 See item 4.

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 THE GROUP

 Not Applicable.


 7

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CUSIP No. 05346P106 13G/A Page 8 of 10 Pages
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ITEM 9. NOTICE OF DISSOLUTION OF GROUP

 Not Applicable.

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
participant in any transaction having that purpose or effect.


 8

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CUSIP No. 05346P106 13G/A Page 9 of 10 Pages
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 SIGNATURE
 ---------

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.

Date: February 17, 2009


 GREAT POINT PARTNERS, LLC

 By: /s/ Dr. Jeffrey R. Jay, M.D.
 ----------------------------------
 Dr. Jeffrey R. Jay, M.D.,
 as senior managing member

 /s/ Dr. Jeffrey R. Jay, M.D.
 ---------------------------------------
 DR. JEFFREY R. JAY, M.D.

 /s/ Mr. David Kroin
 ---------------------------------------
 MR. DAVID KROIN


 9