Amended Statement of Changes of Beneficial Ownership

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 OF SECURITIES	OMB APPROVAL OMB Number: 3235-0287 Expires: January 31, 2008 Estimated average burden hours per response... 0.5
	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(f) of the Investment Company Act of 1940

1. Name and Address of Reporting Person ^* AFEYAN NOUBAR	2. Issuer Name and Ticker or Trading Symbol HELICOS BIOSCIENCES CORP [ HLCS ]	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/YYYY) 7/27/2007
(Street) CAMBRIDGE, MA 02142 (City) (State) (Zip)	4. If Amendment, Date Original Filed (MM/DD/YYYY) 7/31/2007	6. Individual or Joint/Group Filing (Check Applicable Line) _ X _ Form filed by One Reporting Person ___ Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security (Instr. 3)	2. Trans. Date	2A. Deemed Execution Date, if any	3. Trans. 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)
1.Title of Security (Instr. 3)	2. Trans. Date	2A. Deemed Execution Date, if any	Code	V	Amount	(A) or (D)	Price		6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)

*Table II - Derivative Securities Beneficially Owned ( e.g.* , puts, calls, warrants, options, convertible securities)**
1. Title of Derivate Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Trans. Date	3A. Deemed Execution Date, if any	4. Trans. 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		7. Title and Amount of Securities Underlying Derivative Security (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)
1. Title of Derivate Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Trans. Date	3A. Deemed Execution Date, if any	Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares	8. Price of Derivative Security (Instr. 5)			11. Nature of Indirect Beneficial Ownership (Instr. 4)
Stock Option (Right to Buy)	$7.85	7/27/2007		A		11111		7/27/2008	7/27/2017	Common Stock	11111	$0.00	11111	I ⁽¹⁾	(See Footnote)

Explanation of Responses:

( 1)

Any profit from the exercise of the stock option and subsequent sale of the underlying shares is payable by Dr. Afeyan in equal parts to Flagship Ventures Fund 2004, L.P. ("Flagship 2004") and Applied Genomic Technology Capital Fund, L.P. ("AGTC Fund") pursuant to a contractual obligation to assign any fees received for service as a director of the Issuer. NewcoGen Group, Inc. ("NewcoGen Inc.") is the general partner of AGTC Partners, L.P. which is the general partner of AGTC Fund. NewcoGen Inc. is a wholly owned subsidiary Flagship Ventures Management, Inc. ("Flagship Inc."). Flagship Ventures General Partner LLC ("Flagship LLC") is the general partner of Flagship 2004. Dr. Afeyan is a director of Flagship Inc. and a manager of Flagship LLC. Dr. Afeyan disclaims beneficial ownership of such shares, except to the extent of his pecuniary interest therein, if any, as a result of his interests in Flagship.

Reporting Owners
Reporting Owner Name / Address	Relationships
Reporting Owner Name / Address	Director	10% Owner	Officer	Other
AFEYAN NOUBAR C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE, MA 02142	X	X

Signatures
/s/ Mark C. Solakian, attorney-in-fact		11/29/2007
^** Signature of Reporting Person		Date

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).
**	Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
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