X0303 4/A 2009-09-18 2009-09-22 0 0001274563 HELICOS BIOSCIENCES CORP HLCS 0001222012 AFEYAN NOUBAR C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE MA 02142 1 0 1 0 0001473273 NewcoGen Long Reign Holding LLC C/O FLAGSHIP VENTURES ONE MEMORIAL DRIVE, 7TH FLOOR CAMBRIDGE MA 02142 1 0 1 0 Common Stock 2009-09-18 4 P 0 242931 A 12192640 I See Footnotes Common Stock Warrants (Right to Buy) 2.61 2009-09-18 4 P 0 160821 A 2010-03-18 2015-03-18 Common Stock 160821 160821 I See Footnotes The reported securities are included within units purchased by the reporting persons consisting of (i) one share of common stock and (ii) one warrant to purchase 0.662 shares of common stock. Each unit was purchased for $2.57 per unit which represented the closing bid price of the common stock on the day the transaction was signed 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. 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"), 3,016,458 shares held by Flagship Ventures Fund 2004, L.P. ("Flagship"), 64,515, shares held by NewcoGen Elan LLC ("NewcoGen Elan"), 782,042 shares held by NewcoGen Equity Investors LLC ("NewcoGen Equity"), 861,721 shares held by NewcoGen Group, LLC ("NewcoGen Group"), 208,556 shares held by NewcoGen PE LLC ("NewcoGen PE"), 42,823 shares held by NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") and 42,777 shares of ST NewcoGen LLC ("ST NewcoGen" together with NewcoGen Elan, NewcoGen Equity, NewcoGen Group, NewcoGen PE and NewcoGen Long Reign, the "NewcoGen Funds"). 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. Consists of warrants to purchase 53,688 shares held by Flagship, warrants to purchase 18,556 shares held by NewcoGen Equity, warrants to purchase 18,556 shares held by NewcoGen Group, warrants to purchase 37,113 shares held by NewcoGen PE, warrants to purchase 8,289 shares held by NewcoGen Long Reign, warrants to purchase 8,289 shares held by ST NewcoGen and warrants to purchase 16,330 shares held by NewcoGen Elan. This amended Form 4 is filed to add NewcoGen Long Reign Holding LLC ("NewcoGen Long Reign") as a named reporting person, which was inadvertently omitted from the original Form 4 filed on September 22, 2009 (the "Original Form 4") due to clerical error. NewcoGen Long Reign's holdings pursuant to the transactions reported on the Original Form 4 were previously disclosed in footnotes 2 and 4 on the Original Form 4; this amended Form 4 is filed solely to correct the clerical omission of NewcoGen Long Reign as a reporting person from the Original Form 4. Except for the updating amendment in this amended Form 4, the Original Form 4 filed on September 22, 2009 remains in effect. /s/ Mark C. Solakian, attorney-in-fact 2009-10-05 /s/ Mark C. Solakian, attorney-in-fact 2009-10-05