Sec Form 4 Filing - AFEYAN NOUBAR @ BG Medicine, Inc. - 2012-05-21

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person AFEYAN NOUBAR 2. Issuer Name and Ticker or Trading Symbol BG Medicine, Inc. [ BGMD] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) X __ Director X __ 10% Owner _____ Officer (give title below) _____ Other (specify below) (Last) (First) (Middle) C/O FLAGSHIP VENTURES, ONE MEMORIAL DRIVE, 7TH FLOOR 3. Date of Earliest Transaction (MM/DD/YY) 05/21/2012 (Street) CAMBRIDGE, MA02142 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) _____ Form filed by One Reporting Person __ X __ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 05/21/2012 X 2,497 A $ 0.03 107,425 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 S( 2 ) 19 D $ 3.95 ( 3 ) 107,406 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 X 2,580 A $ 0.02 109,986 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 S( 4 ) 14 D $ 3.95 ( 3 ) 109,972 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 X 7,001 A $ 0.02 116,973 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 S( 5 ) 36 D $ 3.95 ( 3 ) 116,937 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 X 7,001 A $ 0.02 123,938 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 S( 6 ) 36 D $ 3.95 ( 3 ) 123,902 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 X 7,001 A $ 0.02 130,903 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/21/2012 S( 7 ) 36 D $ 3.95 ( 3 ) 130,867 I By NewcoGen-PE LLC ( 1 ) Common Stock 05/23/2012 J( 8 ) 130,867 D $ 0 0 I By NewcoGen-PE LLC ( 1 ) Common Stock 526,560 I By NewcoGen Equity Investors LLC ( 1 ) Common Stock 276,600 I By NewcoGen-Elan LLC ( 1 ) Common Stock 92,294 I By NewcoGen-Long Reign Holding LLC ( 1 ) Common Stock 92,126 I By ST NewcoGen LLC ( 1 ) Common Stock 140,013 I By AGTC Advisors Fund, L.P. ( 1 ) Common Stock 2,351,447 I By Applied Genomic Technology Capital Fund, L.P. ( 1 ) Common Stock 2,184,800 I By NewcoGen Group LLC ( 1 ) Common Stock 4,232 I By OneLiberty Advisors Fund 2000 L.P. ( 9 ) Common Stock 80,424 I By OneLiberty Ventures 2000 L.P. ( 9 ) Common Stock 714,286 I By Flagship Ventures Fund 2007, L.P. ( 10 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares Warrant to Purchase Common Stock (right to buy) $ 0.03 05/21/2012 X 2,497 ( 11 ) 07/10/2016 Common Stock 2,497 $ 0 0 I By NewcoGen-PE LLC ( 1 ) Warrant to Purchase Common Stock (right to buy) $ 0.02 05/21/2012 X 2,580 ( 11 ) 03/28/2018 Common Stock 2,580 $ 0 0 I By NewcoGen-PE LLC ( 1 ) Warrant to Purchase Common Stock (right to buy) $ 0.02 05/21/2012 X 7,001 ( 11 ) 03/30/2020 Common Stock 7,001 $ 0 0 I By NewcoGen-PE LLC ( 1 ) Warrant to Purchase Common Stock (right to buy) $ 0.02 05/21/2012 X 7,001 ( 11 ) 09/27/2020 Common Stock 7,001 $ 0 0 I By NewcoGen-PE LLC ( 1 ) Warrant to Purchase Common Stock (right to buy) $ 0.02 05/21/2012 X 7,001 ( 11 ) 12/04/2020 Common Stock 7,001 $ 0 0 I By NewcoGen-PE LLC ( 1 )

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other AFEYAN NOUBAR C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA02142 X X NewcoGen PE LLC C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA02142 X KANIA EDWIN M JR C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA02142 X Flagship Ventures Management, Inc. C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA02142 X NewcoGen Group, Inc. C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA02142 X Signatures /s/ Linda Rockett, Attorney-in-fact for Noubar Afeyan 05/23/2012 Signature of Reporting Person Date /s/ Linda Rockett, Attorney-in-fact for NewcoGen-PE LLC 05/23/2012 Signature of Reporting Person Date /s/ Linda Rockett, Attorney-in-fact for Edwin M. Kania, Jr. 05/23/2012 Signature of Reporting Person Date /s/ Linda Rockett, Attorney-in-fact for Flagship Ventures Management, Inc. 05/23/2012 Signature of Reporting Person Date /s/ Linda Rockett, Attorney-in-fact for NewcoGen Group, Inc. 05/23/2012 Signature of Reporting Person Date

Explanation of Responses:

( 1 )NewcoGen Group, Inc. ("NG") is the manager of each of NewcoGen Group LLC ("NGG"), NewcoGen Equity Investors LLC ("NEI"), NewcoGen-Elan LLC ("NGE"), NewcoGen-Long Reign Holding LLC ("NGLRH"), NewcoGen-PE LLC ("NGP") and ST NewcoGen LLC ("STN", and together with NGG, NEI, NGE, NGLRH and NGP, the "NewcoGen Funds"). NG is also the general partner of AGTC Partners, L.P., which is the general partner of AGTC Advisors Fund, L.P. ("AGTCA") and Applied Genomic Technology Capital Fund L.P. ("AGTCF", and together with AGTCA, the "AGTC Funds"). NG is a wholly-owned subsidiary of Flagship Ventures Management, Inc. ("Flagship"). Noubar Afeyan and Edwin M. Kania, Jr. are directors of Flagship and may be deemed to beneficially own the securities held by the NewcoGen Funds and the AGTC Funds. Each of Messrs. Afeyan and Kania disclaim beneficial ownership of the securities except to the extent of his pecuniary interest therein. ( 2 )On May 21, 2012, NGP exercised a warrant to purchase 2,497 shares of Common Stock for $0.03 per share. NGP exercised the warrant on a cashless basis, resulting in the Issuer's withholding of 19 of the warrant shares to pay the exercise price and issuing to NGP the remaining 2,478 shares. ( 3 )The price reflects the average of the closing prices of the Common Stock over the five day period prior to the exercise date. ( 4 )On May 21, 2012, NGP exercised a warrant to purchase 2,580 shares of Common Stock for $0.02 per share. NGP exercised the warrant on a cashless basis, resulting in the Issuer's withholding of 14 of the warrant shares to pay the exercise price and issuing to NGP the remaining 2,566 shares. ( 5 )On May 21, 2012, NGP exercised a warrant to purchase 7,001 shares of Common Stock for $0.02 per share. NGP exercised the warrant on a cashless basis, resulting in the Issuer's withholding of 36 of the warrant shares to pay the exercise price and issuing to NGP the remaining 6,965 shares. ( 6 )On May 21, 2012, NGP exercised a warrant to purchase 7,001 shares of Common Stock for $0.02 per share. NGP exercised the warrant on a cashless basis, resulting in the Issuer's withholding of 36 of the warrant shares to pay the exercise price and issuing to NGP the remaining 6,965 shares. ( 7 )On May 21, 2012, NGP exercised a warrant to purchase 7,001 shares of Common Stock for $0.02 per share. NGP exercised the warrant on a cashless basis, resulting in the Issuer's withholding of 36 of the warrant shares to pay the exercise price and issuing to NGP the remaining 6,965 shares. ( 8 )In addition to the cashless exercises of the warrants reported above, this Form 4 is being filed to report an in-kind distribution for no consideration by NGP to its sole member. The beneficial ownership of the entities named in this Form 4, other than the Reporting Persons filing this Form 4, did not change as a result of this transaction. ( 9 )Noubar Afeyan and Edwin M. Kania, Jr. are managing members of OneLiberty Partners 2000, LLC, which is the general partner of OneLiberty Advisors Fund 2000 L.P. ("OLA") and OneLiberty Ventures 2000 L.P. ("OLV"), and may be deemed to beneficially own the securities held by OLA and OLV. Each of Messrs. Afeyan and Kania disclaim beneficial ownership of the securities except to the extent of his pecuniary interest therein. ( 10 )Noubar Afeyan and Edwin M. Kania, Jr. are managers of Flagship Ventures 2007 General Partner, LLC, which is the general partner of Flagship Ventures Fund 2007, L.P., and may be deemed to beneficially own the securities held by Flagship Ventures Fund 2007, L.P. Each of Messrs. Afeyan and Kania disclaim beneficial ownership of the securities except to the extent of his pecuniary interest therein. ( 11 )This warrant is immediately exercisable.

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).

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