Document:

Exhibit
10.17

 

HELICOS
BIOSCIENCES CORPORATION

 

Change in
Control Agreement

 

AGREEMENT made as of this 2nd day of May, 2007 by and
between Helicos BioSciences Corporation (the “Company”), and Stanley N. Lapidus
(the “Executive”).

 

1.                                       Purpose. The Company considers it essential to the best interests of its
stockholders to promote and preserve the continuous employment of key
management personnel. The Board of Directors of the Company (the “Board”)
recognizes that, as is the case with many corporations, the possibility of a
Change in Control (as defined in Section 2 hereof) exists and that such
possibility, and the uncertainty and questions that it may raise among
management, may result in the departure or distraction of key management
personnel to the detriment of the Company and its stockholders. Therefore, the
Board has determined that appropriate steps should be taken to reinforce and
encourage the continued attention and dedication of members of the Company’s key
management, including the Executive, to their assigned duties without
distraction in the face of potentially disturbing circumstances arising from
the possibility of a Change in Control. Nothing in this Agreement shall be
construed as creating an express or implied contract of employment and, except
as otherwise agreed in writing between the Executive and the Company, the
Executive shall not have any right to be retained in the employ of the Company.

 

2.                                       Change in Control. A “Change in Control” shall be deemed to have
occurred upon the occurrence of any one of the following events:

 

(a)                                  any
“Person,” as such term is used in Sections 13(d) and 14(d) of the Securities
Exchange Act of 1934, as amended (the “Act”) (other than the Company, any of
its subsidiaries, or any trustee, fiduciary or other person or entity holding
securities under any employee benefit plan or trust of the Company or any of
its subsidiaries), together with all “affiliates” and “associates” (as such
terms are defined in Rule 12b-2 under the Act) of such person, shall become the
“beneficial owner” (as such term is defined in Rule 13d-3 under the Act),
directly or indirectly, of securities of the Company representing 50 percent or more of the combined
voting power of the Company’s then outstanding securities having the right to
vote in an election of the Company’s Board of Directors (“Voting Securities”)
(in such case other than as a result of an acquisition of securities directly
from the Company); or

 

(b)                                 persons
who, as of the date hereof, constitute the Company’s Board of Directors (the “Incumbent
Directors”) cease for any reason, including, without limitation, as a result of
a tender offer, proxy contest, merger or similar transaction, to constitute at
least a majority of the Board, provided that any person becoming a director of
the Company subsequent to the date hereof shall be considered an Incumbent
Director if such person’s election was approved by or such person was nominated
for election by either (A) a vote of at least a majority of the Incumbent
Directors or (B) a vote of at least a majority of the Incumbent Directors who
are members of a nominating committee comprised, in the majority, of Incumbent
Directors; but provided further, that any such person whose initial assumption
of office is in connection with an actual or threatened election contest
relating to the election of members of the Board of Directors

 

 

or other actual or
threatened solicitation of proxies or consents by or on behalf of a Person
other than the Board, including by reason of agreement intended to avoid or
settle any such actual or threatened contest or solicitation, shall not be
considered an Incumbent Director; or

 

(c)                                  the
consummation of (A) any consolidation or merger of the Company where the
stockholders of the Company, immediately prior to the consolidation or merger,
would not, immediately after the consolidation or merger, beneficially own (as
such term is defined in Rule 13d-3 under the Act), directly or indirectly,
shares representing in the aggregate more than 50 percent of the voting shares
of the Company issuing cash or securities in the consolidation or merger (or of
its ultimate parent corporation, if any), or (B) any sale, lease, exchange or
other transfer (in one transaction or a series of transactions contemplated or
arranged by any party as a single plan) of all or substantially all of the
assets of the Company; or

 

(d)                                 the
approval by the Company’s stockholders of any plan or proposal for the
liquidation or dissolution of the Company.

 

3.                                       Terminating Event. A “Terminating Event” shall mean any of the events
provided in this Section 3:

 

(a)                                  Termination
by the Company. Termination by the Company of the employment of the
Executive with the Company for any reason other than for Cause, death or
Disability. For purposes of this Agreement, “Cause” shall mean:

 

(i)                                     the substantial and continuing failure or
refusal of the Employee, after written notice thereof, to reasonably attempt to
perform his or her job duties and responsibilities (other than failure or
refusal resulting from incapacity due to physical disability or mental illness)
which failure or refusal is committed in bad faith and is not in the best
interest of the Company;

 

(ii)                                  gross negligence, willful misconduct or
material breach of fiduciary duty to the Company;

 

(iii)                               the willful commission of an act of
embezzlement, misappropriation or fraud;

 

(iv)                              deliberate and willful disregard of the
written rules or policies of the Company which results in a material and
substantial loss, damage or injury to the Company;

 

(v)                                 the unauthorized, deliberate and willful
disclosure of any material confidential, proprietary and/or trade secret
information of the Company or its customers which disclosure is committed in
bad faith and is not in the best interest of the Company;

 

(vi)                              the willful and deliberate commission of an
act which induces any customer, supplier, employee or consultant to adversely
and substantially amend

 

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or terminate their
relationship with the Company which act is committed in bad faith and is not in
the best interest of the Company; or

 

(vii)                           the conviction of, or plea of nolo contendere
by the Employee, to a crime involving a felony of moral turpitude.

 

A Terminating Event shall not be deemed to have
occurred pursuant to this Section 3(a) solely as a result of the Executive
being an employee of any direct or indirect successor to the business or assets
of the Company, rather than continuing as an employee of the Company following
a Change in Control. For purposes hereof, the Executive will be considered “Disabled”
if, as a result of the Executive’s incapacity due to physical or mental
illness, the Executive shall have been absent from his duties to the Company on
a full-time basis for 180 calendar days in the aggregate in any 12-month
period.

 

(b)                                 Termination
by the Executive for Good Reason. Termination by the Executive of the
Executive’s employment with the Company for Good Reason. For purposes of this
Agreement, “Good Reason” shall mean the occurrence of any of the following events:

 

(i)                                     a reduction in the Employee’s then-current
annual base salary or bonus opportunity or benefits; or

 

(ii)                                  any failure to offer the Employee the same
level of benefits offered to similarly situated employees; or

 

(iii)                               a significant diminution in the Employee’s
duties or responsibilities; or

 

(iv)                              the relocation of the Employee’s primary
business location to a location that increases the Employee’s commute by more
than fifty (50)  miles compared to the
commute of the Employee to the Employee’s then-current primary business
location; or

 

(v)                                 the failure to pay the Employee any portion
of his or her current base salary, bonus or benefits within twenty (20) days of
the date such compensation is due, based upon the payment terms currently in
effect; or

 

(vi)                              the failure of the Company to obtain a
reasonably satisfactory agreement from any successor to assume and agree to
perform this Agreement.

 

4.                                       Change in Control Payment. In the event a Terminating Event occurs within 12 months after a Change in Control,
the following shall occur:

 

(a)                                  the
Company shall pay to the Executive an amount equal to the sum of (i) one and
one half of the Executive’s annual base salary in effect immediately prior to
the Terminating Event (or the Executive’s annual base salary in effect
immediately prior to the Change in Control, if higher) and (ii) an amount equal
to the Executive’s average annual bonus over the two fiscal years (or such
shorter period to the extent necessary to reflect the Executive’s

 

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actual length of
service or the time in which the Company had a bonus plan) immediately prior to
the Change in Control, payable in one lump-sum payment no later than three days
following the Date of Termination;

 

(b)                                 subject
to the Executive’s copayment of premium amounts at the active employees’ rate,
the Executive shall continue to participate in the Company’s group health and
dental program for eighteen months; provided, however, that the continuation of
health benefits under this Section shall reduce and count against the Executive’s
rights under the Consolidated Omnibus Budget Reconciliation Act of 1985, as
amended (“COBRA”); and

 

(c)                                  Notwithstanding
anything to the contrary in any applicable option agreement or stock-based
award agreement, upon a Terminating Event, all stock options and other
stock-based awards granted to the Executive by the Company shall immediately
accelerate and become exercisable or non-forfeitable as of the effective date
of such Terminating Event.

 

(d)                                 Anything
in this Agreement to the contrary notwithstanding, if at the time of the
Executive’s termination of employment, the Executive is considered a “specified
employee” within the meaning of Section 409A(a)(2)(B)(i) of the Internal
Revenue Code of 1986, as amended (the “Code”), and if any payment that the
Executive becomes entitled to under this Agreement is considered deferred
compensation subject to interest and additional tax imposed pursuant to Section
409A(a) of the Code as a result of the application of Section 409A(a)(2)(B)(i)
of the Code, then no such payment shall be payable prior to the date that is
the earliest of (i) six months after the Executive’s Date of Termination, (ii)
the Executive’s death, or (iii) such other date as will cause such payment not
to be subject to such interest and additional tax, and the initial payment
shall include a catch-up amount covering amounts that would otherwise have been
paid during the first six-month period but for the application of this Section 4(d).

 

5.                                       Additional Limitation.

 

(i)                                     Anything in this Agreement to the contrary
notwithstanding, in the event that any compensation, payment or distribution by
the Company to or for the benefit of the Executive, whether paid or payable or
distributed or distributable pursuant to the terms of this Agreement or
otherwise (the “Severance Payments”), would be subject to the excise tax
imposed by Section 4999 of the Code, the following provisions shall apply:

 

(A)                              If
the Severance Payments, reduced by the sum of (1) the Excise Tax and (2) the
total of the Federal, state, and local income and employment taxes payable by
the Executive on the amount of the Severance Payments which are in excess of
the Threshold Amount, are greater than or equal to the Threshold Amount, the
Executive shall be entitled to the full benefits payable under this Agreement.

 

(B)                                If
the Threshold Amount is less than (x) the Severance Payments, but greater than
(y) the Severance Payments reduced by the sum of (1) the Excise Tax and (2) the
total of the Federal, state, and local income and

 

4

 

employment taxes on the amount of the Severance
Payments which are in excess of the Threshold Amount, then the benefits payable
under this Agreement shall be reduced (but not below zero) to the extent
necessary so that the maximum Severance Payments shall not exceed the Threshold
Amount. To the extent that there is more than one method of reducing the
payments to bring them within the Threshold Amount, the Executive shall
determine which method shall be followed; provided that if the Executive fails
to make such determination within 45 days after the Company has sent the
Executive written notice of the need for such reduction, the Company may
determine the amount of such reduction in its sole discretion.

 

(ii)                                  For the purposes of this Section 5(a), “Threshold
Amount” shall mean three times the Executive’s “base amount” within the meaning
of Section 280G(b)(3) of the Code and the regulations promulgated thereunder
less one dollar ($1.00); and “Excise Tax” shall mean the excise tax imposed by
Section 4999 of the Code, and any interest or penalties incurred by the
Executive with respect to such excise tax.

 

(iii)                               The determination as to which of the
alternative provisions of Section 5(a)(i) shall apply to the Executive
shall be made by a nationally recognized accounting firm selected by the
Company (the “Accounting Firm”), which shall provide detailed supporting
calculations both to the Company and the Executive within 15 business days of
the Date of Termination, if applicable, or at such earlier time as is
reasonably requested by the Company or the Executive. For purposes of
determining which of the alternative provisions of Section 5(a)(i) shall
apply, the Executive shall be deemed to pay federal income taxes at the highest
marginal rate of federal income taxation applicable to individuals for the
calendar year in which the determination is to be made, and state and local
income taxes at the highest marginal rates of individual taxation in the state
and locality of the Executive’s residence on the Date of Termination, net of
the maximum reduction in federal income taxes which could be obtained from
deduction of such state and local taxes. Any determination by the Accounting
Firm shall be binding upon the Company and the Executive.

 

6.                                       Term.
This Agreement shall take effect on the date first set forth above and shall
terminate upon the earlier of (a) the termination by the Company of the
employment of the Executive for Cause or the failure by the Executive to
perform his full-time duties with the Company by reason of his death or Disability,
(b) the resignation or termination of the Executive’s employment for any reason
prior to a Change in Control, or (c)
the date which is 12 months after
a Change in Control if the Executive is still employed by the Company, provided
that the provisions of Section 10 shall survive termination of this Agreement
for a period of three years.

 

7.                                       Withholding. All payments made by the Company under this Agreement shall be net of
any tax or other amounts required to be withheld by the Company under
applicable law.

 

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8.                                       Notice and Date of Termination.

 

(a)                                  Notice
of Termination. After a Change in Control and during the term of this
Agreement, any purported termination of the Executive’s employment (other than
by reason of death) shall be communicated by written Notice of Termination from
one party hereto to the other party hereto in accordance with this Section 8. For
purposes of this Agreement, a “Notice of Termination” shall mean a notice which
shall indicate the specific termination provision in this Agreement relied upon
and the Date of Termination.

 

(b)                                 Date
of Termination. “Date of Termination,” with respect to any purported
termination of the Executive’s employment after a Change in Control and during
the term of this Agreement, shall mean the date specified in the Notice of
Termination. In the case of a termination by the Company other than a termination
for Cause (which may be effective immediately), the Date of Termination shall
not be less than 30 days after the Notice of Termination is given. In the case
of a termination by the Executive, the Date of Termination shall not be less
than 30 days from the date such Notice of Termination is given. Notwithstanding
the foregoing, in the event that the Executive gives a Notice of Termination to
the Company, the Company may unilaterally accelerate the Date of Termination
and such acceleration shall not result in a termination by the Company for
purposes of this Agreement.

 

9.                                       No Mitigation. The Company agrees that, if the Executive’s employment by the Company is
terminated during the term of this Agreement, the Executive is not required to
seek other employment or to attempt in any way to reduce any amounts payable to
the Executive by the Company pursuant to Section 4 hereof. Further, the
amount of any payment provided for in this Agreement shall not be reduced by
any compensation earned by the Executive as the result of employment by another
employer, by retirement benefits, by offset against any amount claimed to be
owed by the Executive to the Company or otherwise.

 

10.                                 Arbitration of Disputes. Any controversy or claim arising out of or
relating to this Agreement or the breach thereof or otherwise arising out of
the Executive’s employment or the termination of that employment (including,
without limitation, any claims of unlawful employment discrimination whether
based on age or otherwise) shall, to the fullest extent permitted by law, be
settled by arbitration in any forum and form agreed upon by the parties or, in
the absence of such an agreement, under the auspices of the American
Arbitration Association (“AAA”) in Boston,
Massachusetts in accordance with the Employment Dispute Resolution Rules
of the AAA, including, but not limited to, the rules and procedures applicable
to the selection of arbitrators. In the event that any person or entity other
than the Executive or the Company may be a party with regard to any such
controversy or claim, such controversy or claim shall be submitted to
arbitration subject to such other person or entity’s agreement. Judgment upon
the award rendered by the arbitrator may be entered in any court having
jurisdiction thereof. This Section 10 shall be specifically enforceable.
Notwithstanding the foregoing, this Section 10 shall not preclude either party
from pursuing a court action for the sole purpose of obtaining a temporary
restraining order or a preliminary injunction in circumstances in which such
relief is appropriate; provided that
any other relief shall be pursued through an arbitration proceeding pursuant to
this Section 10.

 

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11.                                 Consent to Jurisdiction. To the extent that any court action is permitted
consistent with or to enforce Section 10 of this Agreement, the parties hereby
consent to the jurisdiction of the Superior Court of the Commonwealth of
Massachusetts and the United States District Court for the District of
Massachusetts. Accordingly, with respect to any such court action, the
Executive (a) submits to the personal jurisdiction of such courts; (b) consents
to service of process; and (c) waives any other requirement (whether imposed by
statute, rule of court, or otherwise) with respect to personal jurisdiction or
service of process.

 

12.                                 Integration. This Agreement shall constitute the sole and entire agreement among the
parties with respect to the subject matter hereof, and supersedes and cancels
all prior, concurrent and/or contemporaneous arrangements, understandings,
promises, programs, policies, plans, practices, offers, agreements and/or
discussions, whether written or oral, by or among the parties regarding the
subject matter hereof, including, but not limited to, those constituting or
concerning employment agreements, change in control benefits and/or severance
benefits; provided, however, that this Agreement is not intended to, and shall
not, supersede, affect, limit, modify or terminate any of the following, all of
which shall remain in full force and effect in accordance with their respective
terms: (i) any written agreements, programs, policies, plans, arrangements or
practices of the Company that do not relate to the subject matter hereof; (ii) any
written stock or stock option agreements between Executive and the Company
(except as expressly modified hereby); and (iii) any written agreements between
Executive and the Company concerning noncompetition, nonsolicitation,
inventions and/or nondisclosure obligations.  

 

13.                                 Successor to the Executive. This Agreement shall inure to the benefit of and
be enforceable by the Executive’s personal representatives, executors,
administrators, heirs, distributees, devisees and legatees. In the event of the
Executive’s death after a Terminating Event but prior to the completion by the
Company of all payments due him or her under Section 4 of this Agreement,
the Company shall continue such payments to the Executive’s beneficiary
designated in writing to the Company prior to his or her death (or to his or
her estate, if the Executive fails to make such designation).

 

14.                                 Enforceability. If any portion or provision of this Agreement shall to any extent be
declared illegal or unenforceable by a court of competent jurisdiction, then
the remainder of this Agreement, or the application of such portion or
provision in circumstances other than those as to which it is so declared
illegal or unenforceable, shall not be affected thereby, and each portion and
provision of this Agreement shall be valid and enforceable to the fullest
extent permitted by law.

 

15.                                 Waiver. No waiver of any provision hereof shall be effective unless made in
writing and signed by the waiving party. The failure of any party to require
the performance of any term or obligation of this Agreement, or the waiver by
any party of any breach of this Agreement, shall not prevent any subsequent
enforcement of such term or obligation or be deemed a waiver of any subsequent
breach.

 

16.                                 Notices. Any notices, requests, demands and other communications provided for by
this Agreement shall be sufficient if in writing and delivered in person or
sent by registered or certified mail, postage prepaid, to the Executive at the
last address the Executive has filed in

 

7

 

writing with the Company, or to the Company at its main office, attention
of the Board of Directors.

 

17.                                 Amendment. This Agreement may be amended or modified only by a written instrument
signed by the Executive and by a duly authorized representative of the Company.

 

18.                                 Effect on Other Plans. An election by the Executive to resign after a
Change in Control under the provisions of this Agreement shall not be deemed a
voluntary termination of employment by the Executive for the purpose of
interpreting the provisions of any of the Company’s benefit plans, programs or
policies. Nothing in this Agreement shall be construed to limit the rights of
the Executive under the Company’s benefit plans, programs or policies except
that the Executive shall have no rights to any severance benefits under any Company
severance pay plan. In the event that the Executive is party to an employment
agreement with the Company providing for change in control payments or benefits,
the Executive must elect to receive either the benefits payable under such
other agreement or the benefits payable under this Agreement, but not both. The
Executive shall make such an election in the event of a Change in Control.

 

19.                                 Governing Law. This is a Massachusetts contract and shall be construed under and be
governed in all respects by the laws of the Commonwealth of Massachusetts,
without giving effect to the conflict of laws principles of such Commonwealth. With
respect to any disputes concerning federal law, such disputes shall be
determined in accordance with the law as it would be interpreted and applied by
the United States Court of Appeals for the First Circuit.

 

20.                                 Successors to Company. The Company shall require any successor (whether
direct or indirect, by purchase, merger, consolidation or otherwise) to all or
substantially all of the business or assets of the Company to expressly assume
and agree to perform this Agreement in the same manner and to the same extent
that the Company would be required to perform if no such succession had taken
place. Failure of the Company to obtain an assumption of this Agreement at or
prior to the effectiveness of any succession shall be a breach of this
Agreement and shall constitute Good Reason if the Executive elects to terminate
employment.

 

21.                                 Gender
Neutral. Wherever used herein, a
pronoun in the masculine gender shall be considered as including the feminine
gender unless the context clearly indicates otherwise.

 

[Remainder of Page Intentionally Left Blank]

 

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IN WITNESS WHEREOF, this
Agreement has been executed as a sealed instrument by the Company by its duly
authorized officer, and by the Executive, as of the date first above written.

 

	
   

  	
  HELICOS BIOSCIENCES CORPORATION

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Louise
  A. Mawhinney

  
	
   

  	
   

  	
  Name:  Louise A. Mawhinney

  
	
   

  	
   

  	
  Title:  Vice President and Chief Financial Officer

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  EXECUTIVE

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  /s/ Stanley
  N. Lapidus

  
	
   

  	
  Name:  Stanley N. LapidusQuickLinks
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Exhibit 10.18    
    

HELICOS BIOSCIENCES CORPORATION

Change in Control Agreement  

        AGREEMENT made as of this 7th day of May, 2007 by and between Helicos BioSciences Corporation (the "Company"), and Stephen J. Lombardi (the "Executive"). 

        1.                    Purpose.    The Company considers it essential to the best interests
of its stockholders to promote and preserve the continuous employment of key management personnel. The Board of Directors of the Company (the "Board") recognizes that, as is the case with many
corporations, the possibility of a Change in Control (as defined in Section 2 hereof) exists and that such possibility, and the uncertainty and questions that it may raise among management, may
result in the departure or distraction of key management personnel to the detriment of the Company and its stockholders. Therefore, the Board has determined that appropriate steps should be taken to
reinforce and encourage the continued attention and dedication of members of the Company's key management, including the Executive, to their assigned duties without distraction in the face of
potentially disturbing circumstances arising from the possibility of a Change in Control. Nothing in this Agreement shall be construed as creating an express or implied contract of employment and,
except as otherwise agreed in writing between the Executive and the Company, the Executive shall not have any right to be retained in the employ of the Company. 

        2.                    Change in Control.    A "Change in Control" shall be deemed to have
occurred upon the occurrence of any one of the following events: 

                                (a)    any
"Person," as such term is used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended (the "Act") (other than the Company, any
of its subsidiaries, or any trustee, fiduciary or other person or entity holding securities under any employee benefit plan or trust of the Company or any of its subsidiaries), together with all
"affiliates" and "associates" (as such terms are defined in Rule 12b-2 under the Act) of such person, shall become the "beneficial owner" (as such term is defined in
Rule 13d-3 under the Act), directly or indirectly, of securities of the Company representing 50 percent or more of the combined voting power of the Company's then outstanding
securities having the right to vote in an election of the Company's Board of Directors
("Voting Securities") (in such case other than as a result of an acquisition of securities directly from the Company); or 

                                (b)    persons
who, as of the date hereof, constitute the Company's Board of Directors (the "Incumbent Directors") cease for any reason, including, without
limitation, as a result of a tender offer, proxy contest, merger or similar transaction, to constitute at least a majority of the Board, provided that any person becoming a director of the Company
subsequent to the date hereof shall be considered an Incumbent Director if such person's election was approved by or such person was nominated for election by either (A) a vote of at least a
majority of the Incumbent Directors or (B) a vote of at least a majority of the Incumbent Directors who are members of a nominating committee comprised, in the majority, of Incumbent Directors;
but provided further, that any such person whose initial assumption of office is in connection with an actual or threatened election contest relating to the election of members of the Board of
Directors or other actual or threatened solicitation of proxies or consents by or on behalf of a Person other than the Board, including by reason of agreement intended to avoid or settle any such
actual or threatened contest or solicitation, shall not be considered an Incumbent Director; or 

                                (c)    the
consummation of (A) any consolidation or merger of the Company where the stockholders of the Company, immediately prior to the consolidation or
merger, would not, immediately after the consolidation or merger, beneficially own (as such term is defined in Rule 13d-3 under the Act), directly or indirectly, shares representing
in the aggregate more than 50 percent of the voting shares of the Company issuing cash or securities in the consolidation or merger (or of its 

 

ultimate
parent corporation, if any), or (B) any sale, lease, exchange or other transfer (in one transaction or a series of transactions contemplated or arranged by any party as a single plan)
of all or substantially all of the assets of the Company; or 

                                (d)    the
approval by the Company's stockholders of any plan or proposal for the liquidation or dissolution of the Company. 

        3.                    Terminating Event.    A "Terminating Event" shall mean any of the
events provided in this Section 3: 

                                (a)    Termination
by the Company. Termination by the Company of the employment of the Executive with the Company for any reason
other than for Cause, death or Disability. For purposes of this Agreement, "Cause" shall mean: 

          (i)  the
substantial and continuing failure or refusal of the Employee, after written notice thereof, to reasonably attempt to perform his or her job duties and
responsibilities (other than failure or refusal resulting from incapacity due to physical disability or mental illness) which failure or refusal is committed in bad faith and is not in the best
interest of the Company; 

         (ii)  gross
negligence, willful misconduct or material breach of fiduciary duty to the Company; 

        (iii)  the
willful commission of an act of embezzlement, misappropriation or fraud; 

        (iv)  deliberate
and willful disregard of the written rules or policies of the Company which results in a material and substantial loss, damage or injury to the Company; 

         (v)  the
unauthorized, deliberate and willful disclosure of any material confidential, proprietary and/or trade secret information of the Company or its customers which
disclosure is committed in bad faith and is not in the best interest of the Company; 

        (vi)  the
willful and deliberate commission of an act which induces any customer, supplier, employee or consultant to adversely and substantially amend or terminate their
relationship with the Company which act is committed in bad faith and is not in the best interest of the Company; or 

       (vii)  the
conviction of, or plea of nolo contendere by the Employee, to a crime involving a felony of moral turpitude. 

        A
Terminating Event shall not be deemed to have occurred pursuant to this Section 3(a) solely as a result of the Executive being an employee of any direct or indirect successor to
the business or assets of the Company, rather than continuing as an employee of the Company following a Change in Control. For purposes hereof, the Executive will be considered "Disabled" if, as a
result of the Executive's incapacity due to physical or mental illness, the Executive shall have been absent from his duties to the Company on a full-time basis for 180 calendar days in
the aggregate in any 12-month period. 

                                (b)    Termination
by the Executive for Good Reason. Termination by the Executive of the Executive's employment with the Company for
Good Reason. For purposes of this Agreement, "Good Reason" shall mean the occurrence of any of the following events: 

          (i)  a
reduction in the Employee's then-current annual base salary or bonus opportunity or benefits; or 

         (ii)  any
failure to offer the Employee the same level of benefits offered to similarly situated employees; or 

2

 

        (iii)  a
significant diminution in the Employee's duties or responsibilities; or 

        (iv)  the
relocation of the Employee's primary business location to a location that increases the Employee's commute by more than fifty (50) miles compared to the
commute of the Employee to the Employee's then-current primary business location; or 

         (v)  the
failure to pay the Employee any portion of his or her current base salary, bonus or benefits within twenty (20) days of the date such compensation is due,
based upon the payment terms currently in effect; or 

        (vi)  the
failure of the Company to obtain a reasonably satisfactory agreement from any successor to assume and agree to perform this Agreement. 

        4.                    Change in Control Payment.    In the event a Terminating Event
occurs within 12 months after a Change in Control, the following shall occur: 

                                (a)    the
Company shall pay to the Executive an amount equal to the sum of (i) three-fourths of the Executive's annual base salary in effect immediately
prior to the Terminating Event (or the Executive's annual base salary in effect immediately prior to the Change in Control, if higher) and (ii) an amount equal to the Executive's average annual
bonus over the two fiscal years (or such shorter period to the extent necessary to reflect the Executive's actual length of service or the time in which the Company had a bonus plan) immediately prior
to the Change in Control, payable in one lump-sum payment no later than three days following the Date of Termination; 

                                (b)    subject
to the Executive's copayment of premium amounts at the active employees' rate, the Executive shall continue to participate in the Company's group
health and dental program for nine months; provided, however, that the continuation of health benefits under this Section shall reduce and count against the Executive's rights under the Consolidated
Omnibus Budget Reconciliation Act of 1985, as amended ("COBRA"); and 

                                (c)    Notwithstanding
anything to the contrary in any applicable option agreement or stock-based award agreement, upon a Terminating Event, all stock options
and other stock-based awards granted to the Executive by the Company shall immediately accelerate and become exercisable or non-forfeitable as of the effective date of such Terminating
Event. 

                                (d)    Anything
in this Agreement to the contrary notwithstanding, if at the time of the Executive's termination of employment, the Executive is considered a
"specified employee" within the meaning of Section 409A(a)(2)(B)(i) of the Internal Revenue Code of 1986, as amended (the "Code"), and if any payment that the Executive becomes entitled
to under this Agreement is considered deferred compensation subject to interest and additional tax imposed pursuant to Section 409A(a) of the Code as a result of the application of
Section 409A(a)(2)(B)(i) of the Code, then no such payment shall be payable prior to the date that is the earliest of (i) six months after the Executive's Date of Termination,
(ii) the Executive's death, or (iii) such other date as will cause such payment not to be subject to such interest and additional tax, and the initial payment shall include a
catch-up amount covering amounts that would otherwise have been paid during the first six-month period but for the application of this Section 4(d). 

        5.                    Additional Limitation.    

                                (a)    Additional
Limitation. 

          (i)  Anything
in this Agreement to the contrary notwithstanding, in the event that any compensation, payment or distribution by the Company to or for the benefit of the
Executive, whether paid or payable or distributed or distributable pursuant to the terms 

3

 

of
this Agreement or otherwise (the "Severance Payments"), would be subject to the excise tax imposed by Section 4999 of the Code, the following provisions shall apply: 

	(A)
	If
the Severance Payments, reduced by the sum of (1) the Excise Tax and (2) the total of the Federal, state, and local income and employment taxes payable by the
Executive on the amount of the Severance Payments which are in excess of the Threshold Amount, are greater than or equal to the Threshold Amount, the Executive shall be entitled to the full benefits
payable under this Agreement.

	(B)
	If
the Threshold Amount is less than (x) the Severance Payments, but greater than (y) the Severance Payments reduced by the sum of (1) the Excise Tax and
(2) the total of the Federal, state, and local income and employment taxes on the amount of the Severance Payments which are in excess of the Threshold Amount, then the benefits payable under
this Agreement shall be reduced (but not below zero) to the extent necessary so that the maximum Severance Payments shall not exceed the Threshold Amount. To the extent that there is more than one
method of reducing the payments to bring them within the Threshold Amount, the Executive shall determine which method shall be followed; provided that if the Executive fails to make such determination
within 45 days after the Company has sent the Executive written notice of the need for such reduction, the Company may determine the amount of such reduction in its sole discretion. 

         (ii)  For
the purposes of this Section 5(a), "Threshold Amount" shall mean three times the Executive's "base amount" within the meaning of Section 280G(b)(3) of
the Code and the regulations promulgated thereunder less one dollar ($1.00); and "Excise Tax" shall mean the excise tax imposed by Section 4999 of the Code, and any interest or penalties
incurred by the Executive with respect to such excise tax. 

        (iii)  The
determination as to which of the alternative provisions of Section 5(a)(i) shall apply to the Executive shall be made by a nationally recognized
accounting firm selected by the Company (the "Accounting Firm"), which shall provide detailed supporting calculations both to the Company and the Executive within 15 business days of the Date of
Termination, if applicable, or at such earlier time as is reasonably requested by the Company or the Executive. For purposes of determining which of the alternative provisions of
Section 5(a)(i) shall apply, the Executive shall be deemed to pay federal income taxes at the highest marginal rate of federal income taxation applicable to individuals for the calendar
year in which the determination is to be made, and state and local income taxes at the highest marginal rates of individual taxation in the state and locality of the Executive's residence on the Date
of Termination, net of the maximum reduction in federal income taxes which could be obtained from deduction of such state and local taxes. Any determination by the Accounting Firm shall be binding
upon the Company and the Executive. 

                                (b)    Executive
acknowledges that, prior to the date of this Agreement, he or she has received a one-time cash payment by the Company to assist the
Executive in the repayment of certain tax obligations incurred, or that may be incurred, in connection with the Company's reevaluation in January 2007 of the price at which it issued options
and stock awards during 2006 (the "Reevaluation") (as well as tax obligations associated with such cash payment) (the "2006 Gross-Up Payment"). Executive expressly agrees that the
Gross-Up Payment represents the Company's sole obligation to Executive with respect to the Reevaluation, notwithstanding the actual amount of tax obligation incurred by the Executive in
connection therewith. In the event that the Executive terminates his or her employment with the Company other than for Good Reason, or is terminated by the Company for 

4

 

Cause,
in either case on or before the earlier of (i) July 31, 2008 or (ii) a Change in Control, the Executive shall promptly (but in no event later than 30 days following
such termination) repay to the Company the full amount of the 2006 Gross-Up Payment. 

        6.                    Term.    This Agreement shall take effect on the date first set
forth above and shall terminate upon the earlier of (a) the termination by the Company of the employment of the Executive for Cause or the failure by the Executive to perform his
full-time duties with the Company by reason of his death or Disability, (b) the resignation or termination of the Executive's employment for any reason prior to a Change in Control,
or (c) the date which is 12 months after a Change in Control if the Executive is still employed by the Company, provided that the provisions of Section 10 shall survive
termination of this Agreement for a period of three years. 

        7.                    Withholding.    All payments made by the Company under this
Agreement shall be net of any tax or other amounts required to be withheld by the Company under applicable law. 

        8.                    Notice and Date of Termination.    

                                (a)    Notice
of Termination. After a Change in Control and during the term of this Agreement, any purported termination of the
Executive's employment (other than by reason of death) shall be communicated by written Notice of Termination from one party hereto to the other party hereto in accordance with this Section 8.
For purposes of this Agreement, a "Notice of Termination" shall mean a notice which shall indicate the specific termination provision in this Agreement relied upon and the Date of Termination. 

                                (b)    Date
of Termination. "Date of Termination," with respect to any purported termination of the Executive's employment after a
Change in Control and during the term of this Agreement, shall mean the date specified in the Notice of Termination. In the case of a termination by the Company other than a termination for Cause
(which may be effective immediately), the Date of Termination shall not be less than 30 days after the Notice of Termination is given. In the case of a termination by the
Executive, the Date of Termination shall not be less than 30 days from the date such Notice of Termination is given. Notwithstanding the foregoing, in the event that the Executive gives a
Notice of Termination to the Company, the Company may unilaterally accelerate the Date of Termination and such acceleration shall not result in a termination by the Company for purposes of this
Agreement. 

        9.                    No Mitigation.    The Company agrees that, if the Executive's
employment by the Company is terminated during the term of this Agreement, the Executive is not required to seek other employment or to attempt in any way to reduce any amounts payable to the
Executive by the Company pursuant to Section 4 hereof. Further, the amount of any payment provided for in this Agreement shall not be reduced by any compensation earned by the Executive as the
result of employment by another employer, by retirement benefits, by offset against any amount claimed to be owed by the Executive to the Company or otherwise. 

        10.                    Arbitration of Disputes.    Any controversy or claim arising out of
or relating to this Agreement or the breach thereof or otherwise arising out of the Executive's employment or the termination of that employment (including, without limitation, any claims of unlawful
employment discrimination whether based on age or otherwise) shall, to the fullest extent permitted by law, be settled by arbitration in any forum and form agreed upon by the parties or, in the
absence of such an agreement, under the auspices of the American Arbitration Association ("AAA") in Boston, Massachusetts in accordance with the Employment Dispute Resolution Rules of the AAA,
including, but not limited to, the rules and procedures applicable to the selection of arbitrators. In the event that any person or entity other than the Executive or the Company may be a party with
regard to any such controversy or claim, such controversy or claim shall be submitted to arbitration subject to such other person or entity's agreement. Judgment upon the award rendered by the
arbitrator may be entered in 

5

 

any
court having jurisdiction thereof. This Section 10 shall be specifically enforceable. Notwithstanding the foregoing, this Section 10 shall not preclude either party from pursuing a
court action for the sole purpose of obtaining a temporary restraining order or a preliminary injunction in circumstances in which such relief is appropriate; provided that any other relief shall be
pursued through an arbitration proceeding pursuant to this Section 10. 

        11.                    Consent to Jurisdiction.    To the extent that any court action is
permitted consistent with or to enforce Section 10 of this Agreement, the parties hereby consent to the jurisdiction of the Superior Court of the Commonwealth of Massachusetts and the United
States District Court for the District of Massachusetts. Accordingly, with respect to any such court action, the Executive (a) submits to the personal jurisdiction of such courts;
(b) consents to service of process; and (c) waives any other requirement (whether imposed by statute, rule of court, or otherwise) with respect to personal jurisdiction or service of
process. 

        12.                    Integration.    This Agreement shall constitute the sole and entire
agreement among the parties with respect to the subject matter hereof, and supersedes and cancels all prior, concurrent and/or contemporaneous arrangements, understandings, promises, programs,
policies, plans, practices, offers,
agreements and/or discussions, whether written or oral, by or among the parties regarding the subject matter hereof, including, but not limited to, those constituting or concerning employment
agreements, change in control benefits and/or severance benefits; provided, however, that this Agreement is not intended to, and shall not, supersede, affect, limit, modify or terminate any of the
following, all of which shall remain in full force and effect in accordance with their respective terms: (i) any written agreements, programs, policies, plans, arrangements or practices of the
Company that do not relate to the subject matter hereof; (ii) any written stock or stock option agreements between Executive and the Company (except as expressly modified hereby); and
(iii) any written agreements between Executive and the Company concerning noncompetition, nonsolicitation, inventions and/or nondisclosure obligations. 

        13.                    Successor to the Executive.    This Agreement shall inure to the
benefit of and be enforceable by the Executive's personal representatives, executors, administrators, heirs, distributees, devisees and legatees. In the event of the Executive's death after a
Terminating Event but prior to the completion by the Company of all payments due him or her under Section 4 of this Agreement, the Company shall continue such payments to the Executive's
beneficiary designated in writing to the Company prior to his or her death (or to his or her estate, if the Executive fails to make such designation). 

        14.                    Enforceability.    If any portion or provision of this Agreement
shall to any extent be declared illegal or unenforceable by a court of competent jurisdiction, then the remainder of this Agreement, or the application of such portion or provision in circumstances
other than those as to which it is so declared illegal or unenforceable, shall not be affected thereby, and each portion and provision of this Agreement shall be valid and enforceable to the fullest
extent permitted by law. 

        15.                    Waiver.    No waiver of any provision hereof shall be effective
unless made in writing and signed by the waiving party. The failure of any party to require the performance of any term or obligation of this Agreement, or the waiver by any party of any breach of
this Agreement, shall not prevent any subsequent enforcement of such term or obligation or be deemed a waiver of any subsequent breach. 

        16.                    Notices.    Any notices, requests, demands and other communications
provided for by this Agreement shall be sufficient if in writing and delivered in person or sent by registered or certified mail, postage prepaid, to the Executive at the last address the Executive
has filed in writing with the Company, or to the Company at its main office, attention of the Board of Directors. 

6

 

        17.                    Amendment.    This Agreement may be amended or modified only by a
written instrument signed by the Executive and by a duly authorized representative of the Company. 

        18.                    Effect on Other Plans.    An election by the Executive to resign
after a Change in Control under the provisions of this Agreement shall not be deemed a voluntary termination of employment by the Executive for the purpose of interpreting the provisions of any of the
Company's benefit plans, programs or policies. Nothing in this Agreement shall be construed to limit the rights of the Executive under the Company's benefit plans, programs or policies except that the
Executive shall have no rights to any severance benefits under any Company severance pay plan. In the event that the Executive is party to an employment agreement with the Company providing for change
in control payments or benefits, the Executive must elect to receive either the benefits payable under such other agreement or the benefits payable under this Agreement, but not both. The Executive
shall make such an election in the event of a Change in Control. 

        19.                    Governing Law.    This is a Massachusetts contract and shall be
construed under and be governed in all respects by the laws of the Commonwealth of Massachusetts, without giving effect to the conflict of laws principles of such Commonwealth. With respect to any
disputes concerning federal law, such disputes shall be determined in accordance with the law as it would be interpreted and applied by the United States Court of Appeals for the First Circuit. 

        20.                    Successors to Company.    The Company shall require any successor
(whether direct or indirect, by purchase, merger, consolidation or otherwise) to all or substantially all of the business or assets of the Company to expressly assume and agree to perform this
Agreement in the same manner and to the same extent that the Company would be required to perform if no such succession had taken place. Failure of the Company to obtain an assumption of this
Agreement at or prior to the effectiveness of any succession shall be a breach of this Agreement and shall constitute Good Reason if the Executive elects to terminate employment. 

        21.                    Gender Neutral.    Wherever used herein, a pronoun in the masculine
gender shall be considered as including the feminine gender unless the context clearly indicates otherwise. 

        [Remainder
of Page Intentionally Left Blank] 

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        IN
WITNESS WHEREOF, this Agreement has been executed as a sealed instrument by the Company by its duly authorized officer, and by the Executive, as of the date first above written. 

	 	 	HELICOS BIOSCIENCES CORPORATION
	

 	
 	

By:	

/s/ Stanley N. Lapidus
 Name: Stanley N. Lapidus

Title: President and Chief Executive Officer
	

 	
 	
EXECUTIVE
	

 	
 	

/s/ Stephen J. Lombardi
 Name: Stephen J. Lombardi

8

QuickLinks

Exhibit 10.18

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