SEC Form 3

FORM 3

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

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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. Date of Event Requiring Statement (Month/Day/Year) 05/24/2007	3. Issuer Name and Ticker or Trading Symbol HELICOS BIOSCIENCES CORP [ HLCS ]
		4. Relationship of Reporting Person(s) to Issuer (Check all applicable) Director X 10% Owner Officer (give title below) Other (specify below)	5. 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 Beneficially Owned
1. Title of Security (Instr. 4)	2. Amount of Securities Beneficially Owned (Instr. 4)	3. Ownership Form: Direct (D) or Indirect (I) (Instr. 5)	4. Nature of Indirect Beneficial Ownership (Instr. 5)
Common Stock	120,123(1)	D

Table II - Derivative Securities Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 4)	2. Date Exercisable and Expiration Date (Month/Day/Year)		3. Title and Amount of Securities Underlying Derivative Security (Instr. 4)		4. Conversion or Exercise Price of Derivative Security	5. Ownership Form: Direct (D) or Indirect (I) (Instr. 5)	6. Nature of Indirect Beneficial Ownership (Instr. 5)
	Date Exercisable	Expiration Date	Title	Amount or Number of Shares
Series A Redeemable Convertible Preferred Stock	(2)	(2)	Common Stock	1,495,076	(2)	I	See footnote.(3)(4)
Series B Redeemable Convertible Preferred Stock	(2)	(2)	Common Stock	1,491,598	(2)	I	See footnote.(4)(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. These shares are held directly by NewcoGen Group, LLC.

2. The preferred stock is convertible at any time, at the holder's election, on a 4.5-for-one basis and has no expiration date. The preferred stock will automtaically convert upon the closing of the issuer's initial public offering, on a 4.5-for-one basis.

3. Consists of 66,281 shares held by AGTC Advisors Fund, L.P. ("AGTC"), 1,096,557 shares held by Applied Genomic Technology Capital Fund, L.P. ("AGTC Fund" and together with AGTC, the "AGTC Funds"), 28,492 shares held by NewcoGen Elan LLC ("NewcoGen Elan"), 145,473 shares held by NewcoGen Equity Investors LLC ("NewcoGen Equity"), 116,160 shares held by NewcoGen Group, LLC ("NewcoGen Group"), 30,305 shares held by NewcoGen PE LLC ("NewcoGen PE"), 5,920 shares held by NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") and 5,888 shares of ST NewcoGen LLC ("ST NewcoGen" together with NewcoGen Elan, NewcoGen Equity, NewcoGen Group, NewcoGen PE and NewcoGen Long Reign, the "NewcoGen Funds").

4. 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.

5. Consists of 40,056 shares held by AGTC, 662,678 shares held by AGTC Fund, 702,734 shares held by Flagship, 11,356 shares held by NewcoGen Elan, 57,988 shares held by NewcoGen Equity, 12,080 shares held by NewcoGen PE, 2,360 shares held by NewcoGen Long Reign and 2,346 shares of ST NewcoGen.

	/s/ Noubar B. Afeyan, Managing Partner	05/24/2007
	/s/ Noubar B. Afeyan, Managing Partner	05/24/2007
	/s/ Noubar B. Afeyan, Managing Partner	05/24/2007
	/s/ Noubar B. Afeyan, Managing Partner	05/24/2007
	** Signature of Reporting Person	Date
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