X0303 4 2009-09-18 0 0001274563 HELICOS BIOSCIENCES CORP HLCS 0001291895 Barrett Peter C/O ATLAS VENTURE 890 WINTER STREET SUITE 320 WALTHAM MA 02451 1 0 1 0 Common Stock 2009-09-18 4 P 0 242931 A 11851387 I See footnote 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 footnote The reported securities are included within units purchased by the Reporting Person. Each unit consists of (i) one share of common stock and (ii) one warrant to purchase 0.662 shares of common stock. The purchase price per unit paid by the Reporting Person was $2.57275, which represents the closing bid price of the common stock on the NASDAQ Global Market on September 15, 2009 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. Represents 62,375 shares held by Atlas Venture Entrepreneurs' Fund V, L.P., 4,678,179 shares held by Atlas Venture Fund V, L.P., 6,779,386 shares held by Atlas Venture Fund VI, L.P., 124,132 shares held by Atlas Venture Fund VI GmbH & Co. KG and 207,315 shares held by Atlas Venture Entrepreneurs' Fund VI, L.P. The Reporting Person is a partner with Atlas Venture. The Reporting Person disclaims beneficial ownership of these securities except to the extent of his pecuniary interest therein. Represents warrants to purchase 847 shares held by Atlas Venture Entrepreneurs' Fund V, L.P., warrants to purchase 63,481 shares held by Atlas Venture Fund V, L.P., warrants to purchase 91,995 shares held by Atlas Venture Fund VI, L.P., warrants to purchase 1,685 shares held by Atlas Venture Fund VI GmbH & Co. KG and warrants to purchase 2,813 shares held by Atlas Venture Entrepreneurs' Fund VI, L.P. The Reporting Person is a partner with Atlas Venture. The Reporting Person disclaims beneficial ownership of these securities except to the extent of his pecuniary interest therein. /s/ Peter Barrett 2009-09-22