Summary of HELICOS BIOSCIENCES CORP

Item 1.01 Entry into a Material Definitive Agreement

On December 19, 2008, Helicos BioSciences Corporation ("Helicos" or the "Company") announced that it has entered into a securities purchase agreement with certain investors pursuant to which it has agreed to sell a total of 42,753,869 units (the "Units"), each Unit consisting of (i) one share of common stock (collectively, the "Shares") and (ii) one warrant (collectively, the "Warrants") to purchase 0.6 shares of common stock at an exercise price of $0.45 per share, for a purchase price of $0.435 per unit (representing the closing bid price plus an additional amount for the warrants) (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 year term and will be exercisable immediately following the closing of the transaction. The closing of the transaction is expected to occur on or about December 23, 2008, subject to the satisfaction of customary closing conditions.

Under NASDAQ Marketplace Rule 4350(i)(1)(B), stockholder approval is required for issuances of securities that will result in a change of control of the issuer. In order to comply with Rule 4350(i)(1)(B), until the offering has been approved by the stockholders, the Warrants prohibit holders from exercising such Warrant for any number of shares which would cause that holder to hold more than 19.9% of Helicos' common stock following the exercise. Helicos expects to seek approval of the offering at its next annual meeting of stockholders.

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 30 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 December 19, 2008

10.2 Registration Rights Agreement, between Helicos and each of the Holders identified therein, dated December 19, 2008

99.1 Press Release, dated December 19, 2008