Atlas Venture Fund V SC 13D/A HELICOS BIOSCIENCES / ATLAS VENTURE FUND V ownership change

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13D/A

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT

TO RULE 13d-2(a)

(Amendment No. 2)*

Helicos BioSciences Corporation

(Name of Issuer)

Common Stock, Par Value $0.001 Per Share

(Title of Class of Securities)

42326R109

(CUSIP Number)

Atlas Venture

Attention: Frank Castellucci

25 First Street, Suite 303

Cambridge, MA 02141

617-588-2600

(Name, Address and Telephone Number of Person
Authorized to Receive Notices and Communications)

November 16, 2010

(Date of Event Which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box o.

(Continued on the following pages)

* The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Fund V, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

2

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Entrepeneurs’ Fund V, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

3

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Fund VI, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

4

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Entrepreneurs’ Fund VI, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

5

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Fund VI GmbH & Co. KG
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Germany
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

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CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Associates V, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

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CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Associates VI, L.P.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person PN

8

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Associates V, Inc.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person CO

9

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Atlas Venture Associates VI, Inc.
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Delaware
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person CO

10

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Axel Bichara
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization Germany
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person IN

11

CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Jean-Francois Formela
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization France
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person IN

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CUSIP No. 42326R109
	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Christopher Spray
	2.	Check the Appropriate Box if a Member of a Group
		(a)			o
		(b)			x
	3.	SEC Use Only
	4.	Source of Funds* OO
	5.	Check Box if Disclosure of Legal Proceedings Is Required Pursuant to Item 2(d) or 2(e)  o
	6.	Citizenship or Place of Organization United Kingdom
Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 0 shares
			8.	Shared Voting Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
			9.	Sole Dispositive Power 0 shares
			10.	Shared Dispositive Power 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 11,851,387 shares and 5,333,238 shares issuable upon the exercise of warrants
	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shareso
	13.	Percent of Class Represented by Amount in Row 9 19.5%
	14.	Type of Reporting Person IN

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AMENDMENT NO. 2 TO STATEMENT ON SCHEDULE 13D

This Amendment No. 2 (“Amendment No. 2”) amends and supplements Amendment No. 1 to statement on Schedule 13D filed by the Reporting Persons with the Securities and Exchange Commission on September 23, 2009 (the “Schedule 13D”), with respect to shares of Common Stock, par value $0.001 per share, of Helicos BioSciences Corporation (the “Company”). Capitalized terms used herein but not defined shall have the meaning ascribed thereto in the Schedule 13D. The Schedule 13D is hereby amended and supplemented as follows and, except as expressly amended below, the Schedule 13D remains in full force and effect.

Item 2	Identity and Background
Item 2 of the Schedule 13D is hereby supplemented by adding the following: (b) As of November 1, 2010, the principal business office of each of the Reporting Persons is: c/o Atlas Venture 25 First Street, Suite 303 Cambridge, MA 02141
Item 4.	Purpose of Transaction.
Item 4 of the Schedule 13D is hereby supplemented, with effect from the date of this Amendment No. 2, by adding the following: (a) On November 16, 2010, certain of the Reporting Persons (the “Purchasers”) and certain other purchasers (the “Other Purchasers”) entered into a Subordinated Secured Note Purchase Agreement (the “Note Purchase Agreement”) with the Company, pursuant to which the Company has agreed to sell up to an aggregate of $4,000,000 of convertible promissory notes (the “Notes”), a portion of which is committed and a portion of which is optional.  The Purchasers agreed to purchase Notes with a value of up to $2,000,000, with $1,000,000.02 committed upon the effective date of the Note Purchase Agreement and $999,999.98 at the option of the Purchasers as more fully described below.  On November 16, 2010, the Purchasers purchased Notes having an aggregate principal amount of $166,666.67, as follows:

Purchasing Fund	Aggregate Principal Amount of Notes Purchased at Initial Closing
Atlas Venture Fund V, L.P.	$	65,789.48
Atlas Venture Entrepreneurs’ Fund V, L.P.	$	877.19
Atlas Venture Fund VI, L.P.	$	95,338.79
Atlas Venture Fund VI GmbH & Co. KG	$	1,745.70
Atlas Venture Entrepreneurs’ Fund VI, L.P.	$	2,915.51

Subject to the Company’s continued compliance with the terms of the Note Purchase Agreement, including that there not be an event of default thereunder, upon notice from the Company, the Purchasers are committed to purchase an aggregate of an additional $166,666.67 of Notes in each of five subsequent closings, for a total aggregate committed amount of $1,000,000.02.  The Purchasers also have the right, but not the obligation, upon the Company’s request to purchase up to an additional $999,999.98 of Notes on or before December 31, 2012.

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The Notes will accrue interest at a rate of 10% per annum.  The outstanding principal and any unpaid accrued interest on all of the Notes shall be due and payable in full (i) upon demand by the Purchasers and certain of the Other Purchasers, which demand shall be no earlier than December 31, 2012, (ii) upon the Company receiving at least $10,000,000 in proceeds from a subsequent equity financing, (iii) upon a change of control of the Company or (iv) upon an event of default.  A Purchaser may elect to convert principal and interest outstanding under any of the Notes and any unpaid amounts under the Risk Premium Agreement (as defined below) upon the closing of any future round of equity or debt financing of the Company into shares of the securities issued at such financing at a conversion price equal to the per share price of such financing.

As an inducement for the Purchasers to purchase the Notes, the Company entered into a Risk Premium Payment Agreement, dated as of November 16, 2010, with the Purchasers and the Other Purchasers (the “Risk Premium Agreement”) simultaneous with the execution of, and as required by, the Note Purchase Agreement.  Under the terms of the Risk Premium Agreement, the Company has agreed to pay the Purchasers and the Other Purchasers the following portions of the consideration the Company receives (the “Payment Consideration”) in Liquidity Transactions (as defined therein): (i) until the aggregate Payment Consideration equals $10 million, 60% of the Payment Consideration; (ii) for aggregate Payment Consideration in excess of $10 million to $20 million, 50% of the Payment Consideration; (iii) for aggregate Payment Consideration in excess of $20 million to $30 million, 40% of the Payment Consideration; (iv) for aggregate Payment Consideration in excess of $30 million to $40 million, 30% of the Payment Consideration; and (v) for aggregate Payment Consideration in excess of $40 million, 10% of the Payment Consideration; with the payment tranches pursuant to clauses (i) through (v) cumulative and additive to payments under the previous tranche.  For purposes of determining amounts payable under the Risk Premium Agreement the Payment Consideration will not include amounts the Company uses to first satisfy specified existing obligations as set forth in the Risk Premium Agreement.

Item 6.	Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.
Item 6 of Schedule 13D is hereby supplemented, with effect from the date of this Amendment No. 2, by adding the following: Note Purchase Agreement As disclosed in Item 4(a) above, the Purchasers entered into a Note Purchase Agreement with the Company, dated November 16, 2010, pursuant to which such Purchasers purchased Notes having an aggregate principal amount of $166,666.67 at the initial closing and the Purchasers have agreed to purchase up to an aggregate of $2,000,000 of Notes, a portion of which is committed and a portion of which is optional. Risk Premium Payment Agreement As disclosed in Item 4(a) above, in connection with the Note Purchase Agreement, the Purchasers entered into a Risk Premium Payment Agreement, dated November 16, 2010, pursuant to which the Company has agreed to pay the Purchasers and the other purchasers of Notes at the initial closing the specified portions of the consideration the Company receives in Liquidity Transactions. Amendment No. 1 to Investor Rights Agreement In connection with the Note Purchase Agreement, on November 16, 2010, the Company and the requisite parties entered into an Amendment to the Amended and Restated Investor Rights Agreement, dated as of March 1, 2006, by and among the Company and the parties specified therein, including the Purchasers, pursuant to which the Purchasers will be entitled to demand and piggyback registration rights consistent with the terms of the Purchasers’ existing registration rights for any securities issued upon conversion of the Notes.
Item 7.	Materials to be Filed as Exhibits.

The following documents are filed as exhibits to this Schedule 13D/A:

Exhibit 99.1: Subordinated Secured Note Purchase Agreement, dated as of November 16, 2010, by and among Helicos BioSciences Corporation and each of the Purchasers identified therein (incorporated herein

15

	by reference to Exhibit 10.1 to the Current Report on Form 8-K filed by Helicos BioSciences Corporation on November 19, 2010).
Exhibit 99.2:	Risk Premium Payment Agreement, dated as of November 16, 2010, by and among Helicos BioSciences Corporation and each of the Lenders identified therein (incorporated herein by reference to Exhibit 10.2 to the Current Report on Form 8-K filed by Helicos BioSciences Corporation on November 19, 2010).
Exhibit 99.3:	Amendment No. 1, dated as of November 16, 2010, to Amended and Restated Investor Rights Agreement, dated as of March 1, 2006, by and among Helicos BioSciences Corporation and the Investors identified therein.

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SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, each of the undersigned hereby certifies that the information set forth in this statement is true, complete and correct.

EXECUTED as a sealed instrument this 9th day of December, 2010.

*
Axel Bichara
*
Jean-Francois Formela
*
Christopher Spray
Atlas Venture Fund V, L.P.
Atlas Venture Entrepreneurs’ Fund V, L.P.
By: Atlas Venture Associates V, L.P.
their general partner
By: Atlas Venture Associates V, Inc.
its general partner
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President
Atlas Venture Associates V, L.P.
By: Atlas Venture Associates V, Inc.
its general partner
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President
Atlas Venture Associates V, Inc.
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President

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Atlas Venture Fund VI, L.P.
Atlas Venture Entrepreneurs’ Fund VI, L.P.
By: Atlas Venture Associates VI, L.P.
their general partner
By: Atlas Venture Associates VI, Inc.
its general partner
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President
Atlas Venture Fund VI GmbH & Co. KG
By: Atlas Venture Associates VI, L.P.
its managing limited partner
By: Atlas Venture Associates VI, Inc.
its general partner
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President
Atlas Venture Associates VI, L.P.
By: Atlas Venture Associates VI, Inc.
its general partner
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President
Atlas Venture Associates VI, Inc.
By:	/s/ Kristen Laguerre
Name:	Kristen Laguerre
Title:	Vice President

*By:	/s/ Kristen Laguerre
By Kristen Laguerre as
Attorney-in-Fact

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EXHIBIT INDEX

Exhibit 99.1:	Subordinated Secured Note Purchase Agreement, dated as of November 16, 2010, by and among Helicos BioSciences Corporation and each of the Purchasers identified therein (incorporated herein by reference to Exhibit 10.1 to the Current Report on Form 8-K filed by Helicos BioSciences Corporation on November 19, 2010).
Exhibit 99.2:	Risk Premium Payment Agreement, dated as of November 16, 2010, by and among Helicos BioSciences Corporation and each of the Lenders identified therein (incorporated herein by reference to Exhibit 10.2 to the Current Report on Form 8-K filed by Helicos BioSciences Corporation on November 19, 2010).
Exhibit 99.3:	Amendment No. 1, dated as of November 16, 2010, to Amended and Restated Investor Rights Agreement, dated as of March 1, 2006, by and among Helicos BioSciences Corporation and the Investors identified therein.

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