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
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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)
X Director X 10% Owner
Officer (give title below) Other (specify below)
3. Date of Earliest Transaction (Month/Day/Year)
12/23/2008
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 12/23/2008 P 8,620,690 A (1) 11,949,709(2)(3) I See Footnote
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) $0.45 12/23/2008 P 5,172,418 06/23/2009 12/23/2013 Common Stock 5,172,418(4) (1) 5,172,418(5) I See Footnote
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
X Director X 10% Owner
Officer (give title below) Other (specify below)
1. Name and Address of Reporting Person*
AGTC Partners, 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*
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
X 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
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)
Explanation of Responses:
1. The reported securities are included within units purchased by the reporting persons for $0.435 per unit. Each unit consists of (i) one share of common stock and (ii) one warrant to purchase 0.6 shares of common stock (representing the closing bid price 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"), 2,935,357 shares held by Flagship Ventures Fund 2004, L.P. ("Flagship"), 39,848 shares held by NewcoGen Elan LLC ("NewcoGen Elan"), 754,012 shares held by NewcoGen Equity Investors LLC ("NewcoGen Equity"), 833,691 shares held by NewcoGen Group, LLC ("NewcoGen Group"), 152,495 shares held by NewcoGen PE LLC ("NewcoGen PE"), 30,302 shares held by NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") and 30,256 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. Under NASDAQ Marketplace Rule 4350(i)(1)(B), stockholder approval is required for issuances of securities that will result in a change of control of the issuer. In order to comply with Rule 4350(i)(1)(B), until the offering in which the warrants were purchased has been approved by the stockholders, the warrants prohibit holders from exercising such warrant for any number of shares which would cause that holder to hold more than 19.9% of the issuer's common stock following the exercise.
5. Consists of warrants to purchase 176,513 shares held by AGTC, warrants to purchase 2,941,727 shares held by AGTC Fund, warrants to purchase 1,272,908 shares held by Flagship, warrants to purchase 330,331 shares held by NewcoGen Equity, warrants to purchase 358,445 shares held by NewcoGen Group, warrants to purchase 66,066 shares held by NewcoGen PE, warrants to purchase 13,214 shares held by NewcoGen Long Reign and 13,214 shares of ST NewcoGen.
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
/s/ Mark C. Solakian, attorney-in-fact 12/29/2008
** 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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