-----BEGIN PRIVACY-ENHANCED MESSAGE----- Proc-Type: 2001,MIC-CLEAR Originator-Name: webmaster@www.sec.gov Originator-Key-Asymmetric: MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB MIC-Info: RSA-MD5,RSA, SKMDuSBKaInYkhdUP6mTk7wabqTdLcjizswmoyhb2+VkouON6wdy3HxR0uD20bom KjuoI1q5aHq3bOi/pxt2gw== 0001104659-10-061909.txt : 20101209 0001104659-10-061909.hdr.sgml : 20101209 20101209135033 ACCESSION NUMBER: 0001104659-10-061909 CONFORMED SUBMISSION TYPE: SC 13D/A PUBLIC DOCUMENT COUNT: 2 FILED AS OF DATE: 20101209 DATE AS OF CHANGE: 20101209 GROUP MEMBERS: AGTC PARTNERS, L.P. GROUP MEMBERS: APPLIED GENOMICS TECHNOLOGY CAPITAL FUND, L.P. GROUP MEMBERS: EDWIN M. KANIA, JR. GROUP MEMBERS: FLAGSHIP VENTURES FUND 2004, L.P. GROUP MEMBERS: FLAGSHIP VENTURES GENERAL PARTNER LLC GROUP MEMBERS: FLAGSHIP VENTURES MANAGEMENT, INC. GROUP MEMBERS: NEWCOGEN ELAN LLC GROUP MEMBERS: NEWCOGEN EQUITY INVESTORS LLC GROUP MEMBERS: NEWCOGEN GROUP LLC GROUP MEMBERS: NEWCOGEN GROUP, INC. GROUP MEMBERS: NEWCOGEN LONG REIGN HOLDING LLC GROUP MEMBERS: NEWCOGEN PE LLC GROUP MEMBERS: NOUBAR B. AFEYAN, PHD GROUP MEMBERS: ST NEWCOGEN LLC FILED BY: COMPANY DATA: COMPANY CONFORMED NAME: AGTC ADVISORS FUND LP CENTRAL INDEX KEY: 0001131095 FILING VALUES: FORM TYPE: SC 13D/A BUSINESS ADDRESS: STREET 1: 150 CAMBRIDGEPARK DRIVE CITY: CAMBRIDGE STATE: MA ZIP: 02140 BUSINESS PHONE: 6174972233 SUBJECT COMPANY: COMPANY DATA: COMPANY CONFORMED NAME: HELICOS BIOSCIENCES CORP CENTRAL INDEX KEY: 0001274563 STANDARD INDUSTRIAL CLASSIFICATION: PHARMACEUTICAL PREPARATIONS [2834] IRS NUMBER: 050587367 STATE OF INCORPORATION: DE FISCAL YEAR END: 1231 FILING VALUES: FORM TYPE: SC 13D/A SEC ACT: 1934 Act SEC FILE NUMBER: 005-83580 FILM NUMBER: 101241873 BUSINESS ADDRESS: STREET 1: ONE KENDALL SQUARE STREET 2: BUILDING 700 CITY: CAMBRIDGE STATE: MA ZIP: 02139 BUSINESS PHONE: 617-649-0540 MAIL ADDRESS: STREET 1: ONE KENDALL SQUARE STREET 2: BUILDING 700 CITY: CAMBRIDGE STATE: MA ZIP: 02139 SC 13D/A 1 a10-22722_2sc13da.htm SC 13D/A

	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)

Harry Wilcox

Chief Financial Officer and Partner

Flagship Ventures

One Memorial Drive, 7th Floor

Cambridge, MA 02142

617-868-1888

(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) AGTC Advisors Fund, 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 582,593

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 582,593

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 582,593

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 0.7%

	14.	Type of Reporting Person PN

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Applied Genomic Technology Capital Fund, 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 9,726,061

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 9,726,061

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 9,726,061

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 11.1%

	14.	Type of Reporting Person PN

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Flagship Ventures Fund 2004, 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 4,359,720

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 4,359,720

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 4,359,720

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 5.0%

	14.	Type of Reporting Person PN

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen Élan LLC

	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 80,845

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 80,845

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 80,845

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 0.1%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen Equity Investors LLC

	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 1,130,929

			8.	Shared Voting Power - 0 -

			9.	Sole Dispositive Power 1,130,929

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,130,929

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 1.3%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen Group, LLC

	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 1,238,722

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 1,238,722

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 1,238,722

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 1.4%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen PE LLC

	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 311,735

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 311,735

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 311,735

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 0.4%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen Long Reign Holding LLC

	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 64,326

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 64,326

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 64,326

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 0.1%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) ST NewcoGen LLC

	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 64,280

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 64,280

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 64,280

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 0.1%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) NewcoGen Group, 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 13,199,491

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 13,199,491

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 13,199,491

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 15.0%

	14.	Type of Reporting Person CO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) AGTC Partners, 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 10,308,654

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 10,308,654

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 10,308,654

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 11.7%

	14.	Type of Reporting Person PN

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Flagship Ventures Management, 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 13,199,491

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 13,199,491

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 13,199,491

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 15.0%

	14.	Type of Reporting Person CO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Flagship Ventures General Partner LLC

	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 4,359,720

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 4,359,720

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 4,359,720

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 5.0%

	14.	Type of Reporting Person OO

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Noubar B. Afeyan, PhD

	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 States

Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 17,542,545

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 17,542,545

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 17,542,545

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 19.9%

	14.	Type of Reporting Person IN

CUSIP No. 42326R109

	1.	Names of Reporting Persons I.R.S. Identification No. of Above Persons (Entities Only) Edwin M. Kania, Jr.

	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 States

Number of Shares Beneficially Owned by Each Reporting Person With			7.	Sole Voting Power 17,542,545

			8.	Shared Voting Power - 0 –

			9.	Sole Dispositive Power 17,542,545

			10.	Shared Dispositive Power - 0 -

	11.	Aggregate Amount Beneficially Owned by Each Reporting Person 17,542,545

	12.	Check Box if the Aggregate Amount in Row (9) Excludes Certain Shares o

	13.	Percent of Class Represented by Amount in Row 9 19.9%

	14.	Type of Reporting Person IN

AMENDMENT NO. 2 TO STATEMENT ON SCHEDULE 13D

This Amendment No. 2 (“Amendment No. 2”) amends and supplements the Statement on Schedule 13D filed on January 5, 2009 (the “Original Schedule 13D”), as amended by Amendment No. 1 to Statement on Schedule 13D filed on September 22, 2009 (the Original Schedule 13D, as amended by Amendment No. 1, 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 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

Applied Genomic Technology Capital Fund, L.P.	$	92,333.87

AGTC Advisors Fund, L.P.	$	5,540.31

Newcogen Group LLC	$	11,779.93

Newcogen Equity Investors LLC	$	10,754.83

Newcogen-Elan LLC	$	768.84

Newcogen-PE LLC	$	2,964.52

Newcogen-Long Reign Holding LLC	$	611.72

ST Newcogen LLC	$	611.31

Flagship Ventures Fund 2004, L.P.	$	41,301.34

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.

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 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.

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.

	NEWCOGEN GROUP LLC
	NEWCOGEN EQUITY INVESTORS LLC
	NEWCOGEN PE LLC
	NEWCOGEN ÉLAN LLC
	ST NEWCOGEN LLC
	NEWCOGEN LONG REIGN HOLDING LLC

	Each by its Manager NewcoGen Group Inc.

	By:	*
		Noubar Afeyan
		President

	APPLIED GENOMIC TECHNOLOGY CAPITAL FUND, L.P.
	AGTC ADVISORS FUND, L.P.

	Each by its General Partner, AGTC Partners, L.P.
	By its General Partner, NewcoGen Group Inc.


	By:	*
		Noubar B. Afeyan, PhD
		President


	AGTC PARTNERS, L.P.

	By its General Partner, NewcoGen Group Inc.

	By:	*
		Noubar B. Afeyan, PhD
		President


	NEWCOGEN GROUP INC.


	By:	*
		Noubar B. Afeyan, PhD
		President

	FLAGSHIP VENTURES FUND 2004, L.P.

	By: Flagship Ventures General Partner LLC, its
	General Partner

	By:	*
		Noubar B. Afeyan, PhD
		Manager


	FLAGSHIP VENTURES GENERAL PARTNER
	LLC

	By:	*
		Noubar B. Afeyan, PhD
		Manager


	FLAGSHIP VENTURES MANAGEMENT, INC.

	By:	*
		Noubar B. Afeyan, PhD
		Manager


	/s/ Edwin M. Kania, Jr.
	Edwin M. Kania, Jr.


	*
	Noubar B. Afeyan, PhD

* The undersigned, by signing his name below, does hereby sign this statement on behalf of the above indicated filers in his capacity noted for such filers.

	/s/ Noubar B. Afeyan
	Noubar B. Afeyan, PhD

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.

EX-99.3 2 a10-22722_2ex99d3.htm EX-99.3

Exhibit 99.3

AMENDMENT NO. 1 TO AMENDED AND RESTATED

INVESTOR RIGHTS AGREEMENT

This Amendment No. 1 (this “Amendment”) to the Amended and Restated Investor Rights Agreement (the “IRA”), dated as of March 1, 2006, by and between Helicos BioSciences Corporation, a Delaware corporation (the “Company”), and the Investors specified therein, is made and entered into as of November 16, 2010. Capitalized terms used and not otherwise defined herein shall have the respective meanings ascribed to them in the IRA.

WHEREAS, the undersigned stockholders of the Company (the “Holders”) are holders of at least a majority in interest of the Restricted Stock held by Investors and at least a majority in voting power of the currently outstanding Registrable Shares held by Investors, and, consequently, pursuant to Sections 15(d) and 15(i) of the IRA, may, with the consent of the Company, which is indicated by the signature of its authorized signatory below, consent to an amendment of the IRA on behalf of all parties thereto granting further rights thereunder with respect to the Company’s registration of its securities under the Securities Act of 1933, as amended (the “Securities Act”);

WHEREAS, concurrently with the execution of this Amendment, the Company and certain of the Holders are entering into a Subordinated Secured Note Purchase Agreement (the “Purchase Agreement”) providing for the issuance and sale by the Company to such Holders of certain subordinated secured promissory notes (the “Notes”) that are convertible into equity securities of the Company under certain circumstances;

WHEREAS, the Holders that are parties to the Purchase Agreement would be unwilling to enter into the Purchase Agreement without also obtaining the further rights provided under this Amendment with respect to the Company’s registration under the Securities Act of its equity securities that may be issuable from time to time upon the conversion of the Notes;

WHEREAS, the Company desires to enter into the Purchase Agreement and the Company and each of the Holders believes that the Company’s entry into the Purchase Agreement is advisable and in the Company’s best interests;

NOW THEREFORE, for good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties hereto agree as follows:

1. Amendment to the IRA

(a) The definition of “Registrable Shares” in Section 1 of the IRA is hereby deleted in its entirety and replaced with the following definition:

“Registrable Shares” shall mean (1) the Common Stock issuable upon conversion of the Preferred Stock, (2) any Common Stock issued or issuable (to the extent then determinable) upon the conversion of notes issued by the Company pursuant to that certain Subordinated Secured Note Purchase Agreement, dated as of November 16, 2010, by and among the Company and the Purchasers named therein, or upon the conversion of any other securities of the Company issued or issuable

(to the extent then determinable) pursuant to the conversion rights of such notes, (3) any Common Stock purchased by an Investor (or its permitted transferees) pursuant to Section 12 hereof (or Common Stock issuable with respect to other securities so purchased), (4) any Common Stock of the Company issued as a dividend or other distribution with respect to, or in exchange or in replacement of, the Preferred Stock or Common Stock described in clauses (1)-(3) of this sentence, (5) 540,556 shares of Common Stock issued to NewcoGen Group LLC upon the exercise of that certain warrant dated November 12, 2003, and (6) for the purposes of Section 5 only, Common Stock held by Stanley N. Lapidus and Stephen R. Quake.

2. Remaining Provisions of the IRA. Except as provided herein, each of the other provisions of the IRA shall remain in full force and effect.

3. Entire Agreement. The IRA, as supplemented and modified by this Amendment, together with the any other writings referred to in the IRA or delivered pursuant thereto which form a part thereof, contain the entire agreement among the parties with respect to the subject matter thereof and amend and supersede all prior and contemporaneous arrangements or understandings with respect thereto.

4. References. Upon the effectiveness of this Amendment, on and after the date hereof, each reference in the IRA to “this Agreement, “hereunder,” “hereof,” “herein” or words of like import, and each reference in the other documents entered into in connection with the IRA, shall mean and be a reference to the IRA, as amended hereby.

5. Governing Law. This Amendment shall be governed by and construed in accordance with the General Corporation Law of the State of Delaware as to matters within the scope thereof, and as to all other matters shall be governed by and construed in accordance with the internal laws of the Commonwealth of Massachusetts, without regard to its principles of conflicts of laws.

6. Counterparts. This Amendment may be executed in any number of counterparts, and each such counterpart shall be deemed to be an original instrument, but all such counterparts together shall constitute but one agreement.

[Signature pages follow]

EXECUTED as of the date first above written.

		COMPANY:


		HELICOS BIOSCIENCES CORPORATION


		By:	/s/ Ivan Trifunovich
			Name: Ivan Trifunovich
			Title: President & Chief Executive Officer


		HOLDERS:


		NEWCOGEN GROUP LLC;
		NEWCOGEN EQUITY INVESTORS LLC;
		NEWCOGEN PE LLC;
		NEWCOGEN ÉLAN LLC;
		ST NEWCOGEN LLC;
		NEWCOGEN LONG REIGN HOLDING LLC

		Each by its Manager NewcoGen Group Inc.


		By:	/s/ Noubar Afeyan
			Name: Noubar Afeyan
			Title: President


		APPLIED GENOMIC TECHNOLOGY CAPITAL FUND, L.P.;
		AGTC ADVISORS FUND, L.P.

		Each by its General Partner, AGTC Partners, L.P.
		By its General Partner, NewcoGen Group Inc.

		By:	/s/ Noubar Afeyan
			Name: Noubar Afeyan
			Title: President

[Signature Page to IRA Amendment]

		HOLDERS:

		FLAGSHIP VENTURES FUND 2004, L.P.

		By: Flagship Ventures General Partner LLC, its General Partner


		By:	/s/ Noubar Afeyan
			Name: Noubar Afeyan
			Title: Manager

[Signature Page to IRA Amendment]

		HOLDERS:

		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

		Notice Address:

		25 First Street, Suite 303
		Cambridge, MA 02141
		Attention: General Counsel


		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

		Notice Address:

		25 First Street, Suite 303
		Cambridge, MA 02141
		Attention: General Counsel

[Signature Page to IRA Amendment]

		HOLDERS:

		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

		Notice Address:

		25 First Street, Suite 303
		Cambridge, MA 02141
		Attention: General Counsel

[Signature Page to IRA Amendment]

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