-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 SkiexYRQdB54l2cg3XkYLpOH6yeq5Ko6p9kK8jXeDo6lDhc/CPHBF2N40R8Dorvt
 tH8U/hoOJSB9Yp1dvjTY1w==

<SEC-DOCUMENT>0001179110-09-011862.txt : 20090810
<SEC-HEADER>0001179110-09-011862.hdr.sgml : 20090810
<ACCEPTANCE-DATETIME>20090810174344
ACCESSION NUMBER:		0001179110-09-011862
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20090806
FILED AS OF DATE:		20090810
DATE AS OF CHANGE:		20090810

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			KANIA EDWIN M JR
		CENTRAL INDEX KEY:			0001255927

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001236

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			HELICOS BIOSCIENCES CORP
		CENTRAL INDEX KEY:			0001274563
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				050587367

	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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Flagship Ventures General Partner LLC
		CENTRAL INDEX KEY:			0001400249

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001241

	BUSINESS ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		617 868-1888

	MAIL ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			AGTC Partners, L.P.
		CENTRAL INDEX KEY:			0001419730
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001238

	BUSINESS ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		(617) 868-1888

	MAIL ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Flagship Ventures Fund 2004 L P
		CENTRAL INDEX KEY:			0001299790

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001242

	BUSINESS ADDRESS:	
		STREET 1:		150 CAMBRIDGEPARK DR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02140
		BUSINESS PHONE:		617-868-1888

	MAIL ADDRESS:	
		STREET 1:		150 CAMBRIDGEPARK DR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02140

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Applied Genomic Technology Capital Fund LP
		CENTRAL INDEX KEY:			0001399779

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001237

	BUSINESS ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		617 868-1888

	MAIL ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Flagship Ventures Management, Inc.
		CENTRAL INDEX KEY:			0001400240

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001240

	BUSINESS ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		617 868-1888

	MAIL ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			NewcoGen Group, Inc.
		CENTRAL INDEX KEY:			0001400241

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33484
		FILM NUMBER:		091001239

	BUSINESS ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		617 868-1888

	MAIL ADDRESS:	
		STREET 1:		C/O FLAGSHIP VENTURES
		STREET 2:		ONE MEMORIAL DRIVE, 7TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>FORM 4 -
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-08-06</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001274563</issuerCik>
        <issuerName>HELICOS BIOSCIENCES CORP</issuerName>
        <issuerTradingSymbol>HLCS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001299790</rptOwnerCik>
            <rptOwnerName>Flagship Ventures Fund 2004 L P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001400249</rptOwnerCik>
            <rptOwnerName>Flagship Ventures General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001400240</rptOwnerCik>
            <rptOwnerName>Flagship Ventures Management, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001400241</rptOwnerCik>
            <rptOwnerName>NewcoGen Group, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001419730</rptOwnerCik>
            <rptOwnerName>AGTC Partners, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001399779</rptOwnerCik>
            <rptOwnerName>Applied Genomic Technology Capital Fund LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001255927</rptOwnerCik>
            <rptOwnerName>KANIA EDWIN M JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O FLAGSHIP VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>ONE MEMORIAL DRIVE, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.79</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2009-08-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5555</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2010-08-06</value>
            </exerciseDate>
            <expirationDate>
                <value>2019-08-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5555</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5555</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The stock option was granted to Noubar Afeyan, who is a director of the Issuer. Dr. Afeyan also is a director of Flagship Ventures Management, Inc. (&quot;Flagship Inc.&quot;) and a manager of Flagship Ventures General Partner LLC (&quot;Flagship LLC&quot;). Edwin M. Kania is also a director of Flagship Inc. and manager of Flagship LLC. NewcoGen Group, Inc. (&quot;NewcoGen Inc.&quot;) is the general partner of AGTC Partners, L.P. (&quot;AGTC Partners&quot;), which is the general partner of Applied Genomic Technology Capital Fund, L.P. (&quot;AGTC Fund&quot;). NewcoGen Inc. is a wholly owned subsidiary of Flagship Inc. Flagship LLC is the general partner of Flagship Ventures Fund 2004, L.P. (&quot;Flagship Fund 2004&quot;). Any profit from the exercise of the stock option and subsequent sale of the underlying shares is payable 50% each to Flagship Fund 2004 and AGTC Fund pursuant to a contractual obligation of Dr. Afeyan to assign any fees received for service as a director of the Is
suer.</footnote>
        <footnote id="F2">Each of Mr. Kania, Flagship Inc., Flagship LLC, NewcoGen Inc., AGTC Partners, AGTC Fund and Flagship Fund 2004 disclaims beneficial ownership of such shares, except to the extent of their respective pecuniary interests, if any, therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark C. Solakian, attorney-in-fact</signatureName>
        <signatureDate>2009-08-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----