Summary of HELICOS BIOSCIENCES CORP

Item 1.01. Entry into a Material Definitive Agreement.

On September 15, 2009, Helicos BioSciences Corporation ("Helicos" or the "Company") announced that it has entered into a securities purchase agreement (the "Securities Purchase Agreement") with certain investors pursuant to which it has agreed to (i) sell to Atlas Ventures, Flagship Ventures, Highland Capital Partners and Versant Ventures, up to an aggregate of 1,030,028 units, each unit consisting of (A) one share of Common Stock and (B) one Warrant to purchase 0.662 shares of Common Stock at a per share exercise price equal to $2.61 (105% of the closing bid price of the Common Stock on September 15, 2009), each such unit to be at a purchase price equal to $2.57 per unit, and (ii) sell to certain new investors, up to an aggregate of 3,281,252 units, each unit consisting of (A) one share of Common Stock and (B) one Warrant to purchase 0.50 shares of Common Stock at a per share exercise price equal to $2.61, each such unit to be at a purchase price equal to $2.24 per unit (together, the "Offering").

Units will not be issued or certificated. The Shares and Warrants are immediately separable and will be issued separately. The Warrants will have a five and a half year term and include a six-month "lock-up" provision, meaning that the Warrants will not be exercisable until six months following the consummation of the Offering. The closing of the transaction is expected to occur on or about September 18, 2009, subject to the satisfaction of customary closing conditions.

In connection with the Offering, the Company has entered into a registration rights agreement (the "Registration Rights Agreement") with each of the investors. The Registration Rights Agreement provides that the Company will file a "resale" registration statement (the "Initial Registration Statement") covering all of the Shares and the shares issuable upon exercise of the Warrants (the "Warrant Shares"), up to the maximum number of shares able to be registered pursuant to applicable Securities and Exchange Commission ("SEC") regulations, within 15 days of the closing of the Offering. If any Shares or Warrant Shares are unable to be included on the Initial Registration Statement, the Company has agreed to file subsequent registration statements until all the Shares and Warrant Shares have been registered. Under the terms of the Registration Rights Agreement, the Company is obligated to maintain the effectiveness of the "resale" registration statement until all securities therein are sold or are otherwise can be sold pursuant to Rule 144, without any restrictions. A cash penalty at the rate of 2% per month will be triggered for any filing or effectiveness failures or if, at any time after six months following the closing of the Offering, the Company ceases to be current in its periodic reports with the SEC. The aggregate penalty accrued with respect to each investor may not exceed 12% of the original purchase price paid by that investor.

The foregoing description of each of the Securities Purchase Agreement, the Registration Rights Agreement and the form of warrant is qualified in its entirety by reference thereto, which are filed as Exhibits 10.1, 10.2 and 4.1 to this Current Report, respectively, and are incorporated herein by reference. The press release announcing the Offering is attached hereto as Exhibit 99.1 and is incorporated herein by reference.

Item 9.01. Financial Statements and Exhibits.

(d) Exhibits

Exhibit No. Description

4.1 Form of Warrant

10.1 Securities Purchase Agreement, between Helicos and each of the Purchasers identified therein, dated September 15, 2009

10.2 Registration Rights Agreement, between Helicos and each of the Holders identified there, dated September 15, 2009

99.1 Press Release, dated September 16, 2009