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* 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)	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)
	3. Date of Earliest Transaction (Month/Day/Year) 09/18/2009
	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	09/18/2009		P		242,931	A	(1)	12,192,640(2)(3)	I	See Footnotes

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
Common Stock Warrants (Right to Buy)	$2.61	09/18/2009		P		160,821		03/18/2010	03/18/2015	Common Stock	160,821	(1)	160,821(4)	I(3)(4)	See Footnotes

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 X Director X 10% Owner Officer (give title below) Other (specify below)

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

1. Name and Address of Reporting Person* KANIA EDWIN M JR (Last) (First) (Middle) C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR (Street) CAMBRIDGE 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* NewcoGen Elan LLC (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 X Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* NEWCOGEN EQUITY INVESTORS LLC (Last) (First) (Middle) C/O FLAGSHIP VENTURES (Street) CAMBRIDGE MA 02142 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer X Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* NEWCOGEN GROUP LLC (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 X Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* NewcoGen Group, 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 X Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* NewcoGen PE LLC (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 X Director X 10% Owner Officer (give title below) Other (specify below)

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

Explanation of Responses:

1. The reported securities are included within units purchased by the reporting persons consisting of (i) one share of common stock and (ii) one warrant to purchase 0.662 shares of common stock. Each unit was purchased for $2.57 per unit which represented the closing bid price of the common stock on the day the transaction was signed plus an additional amount for the warrants. Units were not issued or certificated. The shares of common stock and warrants are immediately separable and were issued separately.

2. Consists of 406,080 shares held by AGTC Advisors Fund, L.P. ("AGTC"), 6,767,668 shares held by Applied Genomic Technology Capital Fund, L.P. ("AGTC Fund" and together with AGTC, the "AGTC Funds"), 3,016,458 shares held by Flagship Ventures Fund 2004, L.P. ("Flagship"), 64,515, shares held by NewcoGen Elan LLC ("NewcoGen Elan"), 782,042 shares held by NewcoGen Equity Investors LLC ("NewcoGen Equity"), 861,721 shares held by NewcoGen Group, LLC ("NewcoGen Group"), 208,556 shares held by NewcoGen PE LLC ("NewcoGen PE"), 42,823 shares held by NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") and 42,777 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 warrants to purchase 53,688 shares held by Flagship, warrants to purchase 18,556 shares held by NewcoGen Equity, warrants to purchase 18,556 shares held by NewcoGen Group, warrants to purchase 37,113 shares held by NewcoGen PE, warrants to purchase 8,289 shares held by NewcoGen Long Reign, warrants to purchase 8,289 shares held by ST NewcoGen and warrants to purchase 16,330 shares held by NewcoGen Elan.

	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	/s/ Mark C. Solakian, attorney-in-fact	09/22/2009
	** 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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