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* ATLAS VENTURE FUND V LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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
Ccmmon Stock	09/18/2009		P		242,931	A	(1)	11,851,387	I	See footnote(2)

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	I	See footnote(3)

1. Name and Address of Reporting Person* ATLAS VENTURE FUND V LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* Atlas Venture Fund VI GmbH & Co KG (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* ATLAS VENTURE FUND VI LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* ATLAS VENTURE ASSOCIATES V LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* Atlas Venture Associates VI, L.P. (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* ATLAS VENTURE ENTREPRENEURS FUND V LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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* ATLAS VENTURE ENTREPRENEURS FUND VI LP (Last) (First) (Middle) C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 (Street) WALTHAM MA 02451 (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. Each unit consists of (i) one share of common stock and (ii) one warrant to purchase 0.662 shares of common stock. The purchase price per unit paid by the Reporting Persons was $2.57275, which represents the closing bid price of the common stock on the NASDAQ Global Market on September 15, 2009 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. Represents 62,375 shares held by Atlas Venture Entrepreneurs' Fund V, L.P., 4,678,179 shares held by Atlas Venture Fund V, L.P., 6,779,386 shares held by Atlas Venture Fund VI, L.P., 124,132 shares held by Atlas Venture Fund VI GmbH & Co. KG and 207,315 shares held by Atlas Venture Entrepreneurs' Fund VI, L.P. Each of the Reporting Persons disclaims beneficial ownership of these securities except to the extent of its pecuniary interest therein.

3. Represents warrants to purchase 847 shares held by Atlas Venture Entrepreneurs' Fund V, L.P., warrants to purchase 63,481 shares held by Atlas Venture Fund V, L.P., warrants to purchase 91,995 shares held by Atlas Venture Fund VI, L.P., warrants to purchase 1,685 shares held by Atlas Venture Fund VI GmbH & Co. KG and warrants to purchase 2,813 shares held by Atlas Venture Entrepreneurs' Fund VI, L.P. Each of the Reporting Persons disclaims beneficial ownership of these securities except to the extent of its pecuniary interest therein.

	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	(See signatures included in Exhibit 99.1 hereto)	09/22/2009
	** Signature of Reporting Person	Date
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