SEC Form 4

FORM 4		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 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* AGTC ADVISORS FUND LP (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE MA 02142 (City) (State) (Zip)	2. Issuer Name and Ticker or Trading Symbol HELICOS BIOSCIENCES CORP [ HLCS ]	5. Relationship of Reporting Person(s) to Issuer (Check all applicable) Director X 10% Owner Officer (give title below) Other (specify below)
	3. Date of Earliest Transaction (Month/Day/Year) 05/30/2007
	4. If Amendment, Date of Original Filed (Month/Day/Year)	6. Individual or Joint/Group Filing (Check Applicable Line) Form filed by One Reporting Person X 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. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	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	05/30/2007		C		2,986,674	A	(1)	3,106,797	I	See footnote.(2)(3)
Common Stock	05/30/2007		P		222,222	A	$9	3,329,019	I	See footnote.(3)(6)

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 (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	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 (Month/Day/Year)		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: 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
Series A Redeemable Convertible Preferred Stock	(1)	05/30/2007		C			6,727,857(4)	(1)	(1)	Common Stock	1,495,076	(1)	0	I	See footnote(3)(4)
Series B Redeemable Convertible Preferred Stock	(1)	05/30/2007		C			6,712,209(5)	(1)	(1)	Common Stock	1,491,598	(1)	0	I	See footnote.(3)(5)

1. Name and Address of Reporting Person* AGTC ADVISORS FUND LP (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE MA 02142 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* Applied Genomic Technology Capital Fund LP (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE MA 02142 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* Flagship Ventures Fund 2004 L P (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE MA 02142 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* Flagship Ventures Management, Inc. (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE MA 02142 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

Explanation of Responses:

1. The preferred stock automatically converted upon the closing of the issuer's initial public offering, on a 4.5-for-one basis.

2. Consists of 106,337 shares held by AGTC Advisors Fund, L.P. ("AGTC"), 1,759,235 shares held by Applied Genomic Technology Capital Fund, L.P. ("AGTC Fund" and together with AGTC, the "AGTC Funds"), 702,734 shares held by Flagship Ventures Fund 2004, L.P. ("Flagship"), 39,848 shares held by NewcoGen Elan LLC ("NewcoGen Elan"), 203,461 shares held by NewcoGen Equity Investors LLC ("NewcoGen Equity"), 236,283 shares held by NewcoGen Group, LLC ("NewcoGen Group"), 42,385 shares held by NewcoGen PE LLC ("NewcoGen PE"), 8,280 shares held by NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") and 8,234 shares of ST NewcoGen LLC ("ST NewcoGen" together with NewcoGen Elan, NewcoGen Equity, NewcoGen Group, NewcoGen PE and NewcoGen Long Reign, the "NewcoGen Funds").

3. NewcoGen Group, Inc. ("NewcoGen Inc.") is the manager of each of the NewcoGen Funds and the general partner of AGTC Partners, L.P. which is the general partner of each of AGTC Funds. 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 Ventures Fund 2004, L.P. Noubar B. Afeyan PhD and Edwin M. Kania, Jr. are the directors of Flagship Inc. and managers of Flagship LLC and may be deemed to share voting and investment power with respect to all shares held by the NewcoGen Funds, Flagship and the AGTC Funds. Each of Dr. Afeyan and Mr. Kania disclaim beneficial ownership of such shares except to the extent of any pecuniary interest therein.

4. Consists of 298,268 shares held by AGTC, 4,934,510 shares held byAGTC Fund, 128,215 shares held by NewcoGen Elan, 654,631 shares held by NewcoGen Equity, 522,720 shares held by NewcoGen Group, 136,373 shares held by NewcoGen PE, 26,643 shares held by NewcoGen Long Reign and 26,497 shares of ST NewcoGen.

5. Consists of 180,252 shares held by AGTC, 2,982,055 shares held by AGTC Fund, 3,162,306 shares held by Flagship, 51,108 shares held by NewcoGen Elan, 260,946 shares held by NewcoGen Equity, 54,360 shares held by NewcoGen PE, 10,620 shares held by NewcoGen Long Reign and 10,562 shares of ST NewcoGen.

6. Consists of 111,893 shares held by AGTC, 1,864,790 shares held by AGTC Fund, 813,845 shares held by Flagship, 39,848 shares held by NewcoGen Elan, 203,461 shares held by NewcoGen Equity, 236,283 shares held by NewcoGen Group, 42,385 shares held by NewcoGen PE, 8,280 shares held by NewcoGen Long Reign, and 8,234 shares of ST NewcoGen.

	/s/ Noubar B. Afeyan, managing partner	05/30/2007
	/s/ Noubar B. Afeyan, managing partner	05/30/2007
	/s/ Noubar B. Afeyan, managing partner	05/30/2007
	/s/ Noubar B. Afeyan, managing partner	05/30/2007
	** Signature of Reporting Person	Date
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