Exhibit 10.1


 


February 11,
2010


 


Mr. Stephen
J. Lombardi


 


Re:                             Severance Agreement and Release


 


Dear
Steve:


 


This letter agreement (the “Agreement”) summarizes
the terms of your planned separation of employment from Helicos BioSciences
Corporation (the “Company”).  The purpose of this Agreement is to
establish an amicable arrangement for ending your employment relationship with
the Company, to release legal claims between you and the Company, to provide
you certain severance benefits that you are not otherwise entitled to.


 


With these understandings and in exchange for the
promises by you and the Company as set forth below, you and the Company agree
as follows.


 


1.                                      Employment Status, Severance Pay and Benefits:


 


(a)                                  You agree that
your separation of employment from the Company shall be effective as of the
date written above (the “Resignation Date”).  During the remainder of your
employment, you shall perform any reasonably requested responsibilities to
assist in the transition of your duties. 
You have agreed, separate and apart from this Agreement, to resign from
the Board of Directors of the Company. 
You acknowledge and agree that your resignation from the Board of
Directors of the Company is final and may not be revoked by you in any manner.


 


(b)                                 In exchange
for, and in consideration of, your full execution of and adherence to this
Agreement, the Company agrees to pay you the amount of your regular base salary
at the gross annual rate of $375,000.00 that you would have earned after the
Resignation Date if your employment had continued to and including August 31,
2010 (the “Severance Amount”).  The
Severance Amount shall be paid to you in two equal installments, subject to
regular deductions and withholdings (each, an “Installment”).  The first Installment shall be paid to you on
the Company’s first regular payroll date after the seven-day revocation period
set forth in Section 12 has expired. 
The second Installment shall be paid to you on the Company’s last
regular payroll date in April, 2010 (which is expected to be April 21,
2010).  Your participation in all Company
benefit programs in which you currently participate shall continue up to and
including the Resignation Date.  Effective on the Resignation Date, your
participation in all such Company benefit programs shall end pursuant to
program terms, except with respect to the Company’s group medical and dental
plans, which shall be subject to continuation pursuant to Section 1(c) below. 
To the extent permitted by and under the Company’s life insurance and long term
disability policies, you may be eligible to elect to extend your coverage under
such policies after the Resignation date at your own cost and expense.  On the Resignation Date, your 


 


1

















 


employment
and your affiliations with the Company and any of its subsidiaries in any and
all other capacities you may hold with the Company or any subsidiary shall
terminate.  Without limiting the generality of the foregoing, effective as
of the Resignation Date, you hereby resign from all officer positions with the
Company and any of its subsidiaries or affiliates.  Notwithstanding the foregoing, nothing in
this Agreement shall be construed to affect your right to receive pay for all
vacation pay that is accrued, unused and otherwise available to you as of the
Resignation Date.  Any such vacation pay
to the extent not theretofore paid, shall be paid in a lump sum in cash within
ten (10) business days after the Resignation Date.  You acknowledge and agree that you previously
received a reimbursement payment from the Company in the amount of $1,305.70 in
connection with a hotel reservation for a business conference that was
scheduled for February 2010 that you will not be attending on behalf of
the Company.  You agree that such
reimbursement amount shall be deducted from the first Installment payment
described in this Section 1(b).


 


(c)                                  The Resignation
Date shall be the date of the “qualifying event” under the Company’s group
medical and dental plans for the purpose of continuation of coverage pursuant
to the Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”). 
The Company will present you with information on COBRA under separate
cover.  If you timely elect continuation of coverage under COBRA, the
Company shall pay the premiums for coverage of you under the Company’s group
medical and dental plans in which you are currently participating (“Group
Health Plans”) at the coverage levels that currently apply to you (i.e.
yourself and your wife), subject to premium contributions by you to the same
extent as premium contributions are required for active employees with the same
coverage levels, effective until the earlier of (i) December 31, 2010
or (ii) the date when you become eligible for coverage under another group
medical plan as a result of other employment.  You shall notify the
Company in writing if you become eligible for coverage under another group
medical plan before December 31, 2010 and you shall respond promptly to
any reasonable requests for information relevant to your rights under this Section 1(c). 
You acknowledge that the Company may deduct your premium contributions for
coverage under Group Health Plans from your severance Installment payments
pursuant to Section 1(b).  Nothing
in this Agreement shall affect your right to continue participating in Group
Health Plans pursuant to COBRA after December 31, 2010 at your own premium
cost subject to the terms of COBRA.


 


(d)                                 As part of the
consideration for the payments and benefits following the Resignation Date
pursuant to Sections 1(b) and 1(c), you agree that during the period from
the day following the Resignation Date to and including August 31, 2010,
you shall provide up to five (5) hours per calendar month of transitional
assistance by telephone or email.  You shall provide such assistance at
any reasonable times requested by the Company; provided that the Company shall
not require you to provide transitional assistance at any time that would
unreasonably interfere with personal or professional commitments. 
Transitional assistance pursuant to this Section 1(d) may include but
shall not be limited to services within the scope of Section 10.


 


2.                                      Stock/Change in Control Agreements:


 


(a)                                  Stock and Stock
Options:  Your rights to stock and stock options of the Company shall be
governed by the Helicos BioSciences Corporation 2003 Stock Option and Incentive
Plan 


 


2

















 


and
the 2007 Stock Option and Incentive Plan (the “Stock Option Plans”) and your
equity award agreements for the following awards (the “Equity Award Agreements”)
based on your employment to the Resignation Date:


 


RESTRICTED STOCK AWARDS


 


	
   

  	
   

  	
  Grant

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
  As of 1/1/2010

  	
   

  
	
  Number

  	
   

  	
  Date

  	
   

  	
  Plan

  	
   

  	
  Type

  	
   

  	
  Granted

  	
   

  	
  Price

  	
   

  	
  Vested

  	
   

  	
  Unvested

  	
   

  
	
  127

  	
   

  	
  8/8/2006

  	
   

  	
  2003

  	
   

  	
  RSA

  	
   

  	
  166,666

  	
   

  	
  $

  	
  0.5850

  	
   

  	
  149,305

  	
   

  	
  17,361

  	
   

  
	
  130

  	
   

  	
  7/27/2007

  	
   

  	
  2007

  	
   

  	
  RSA

  	
   

  	
  12,778

  	
   

  	
  $

  	
  0.0000

  	
   

  	
  7,986

  	
   

  	
  4,792

  	
   

  
	
  533

  	
   

  	
  1/28/2009

  	
   

  	
  2007

  	
   

  	
  RSA

  	
   

  	
  87,500

  	
   

  	
  $

  	
  0.0000

  	
   

  	
  43,750

  	
   

  	
  43,750

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
  266,944

  	
   

  	
   

  	
   

  	
  201,041

  	
   

  	
  65,903

  	
   

  



 


STOCK OPTIONS


 


	
   

  	
   

  	
  Grant

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
  As of 1/1/2010

  	
   

  
	
  Number

  	
   

  	
  Date

  	
   

  	
  Plan

  	
   

  	
  Type

  	
   

  	
  Granted

  	
   

  	
  Price

  	
   

  	
  Vested

  	
   

  	
  Unvested

  	
   

  
	
  213/214

  	
   

  	
  2/22/2007

  	
   

  	
  2003

  	
   

  	
  ISO/NQ

  	
   

  	
  166,666

  	
   

  	
  $

  	
  11.0700

  	
   

  	
  121,525

  	
   

  	
  45,141

  	
   

  
	
  246/247

  	
   

  	
  11/20/2007

  	
   

  	
  2007

  	
   

  	
  ISO/NQ

  	
   

  	
  250,000

  	
   

  	
  $

  	
  10.7500

  	
   

  	
  135,416

  	
   

  	
  114,584

  	
   

  
	
  403/404

  	
   

  	
  8/18/2008

  	
   

  	
  2007

  	
   

  	
  ISO/NQ

  	
   

  	
  150,000

  	
   

  	
  $

  	
  4.4000

  	
   

  	
  53,124

  	
   

  	
  96,876

  	
   

  
	
  458/459

  	
   

  	
  1/28/2009

  	
   

  	
  2007

  	
   

  	
  ISO/NQ

  	
   

  	
  175,000

  	
   

  	
  $

  	
  1.0400

  	
   

  	
  87,500

  	
   

  	
  87,500

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
  741,666

  	
   

  	
   

  	
   

  	
  397,565

  	
   

  	
  344,101

  	
   

  



 


Notwithstanding anything to the contrary in this Section 2(a), you
shall further be entitled to vesting as of the Resignation Date of such
additional stock and options set forth in award numbers 127, 130, 533 and
458/459 noted above (the “Accelerated Awards”) that would have vested if your
employment had continued to and including August 31, 2010.  Subject
only to that modification of vesting rights with respect to the Accelerated
Awards, all of your rights and obligations to stock and/or stock options,
including exercise, expiration and the Company’s purchase of unvested stock,
are governed by the terms and conditions of the Stock Plans and the Equity
Award Agreements.


 


(b)                                 Change in
Control Agreement:  You agree that you shall have no further
rights under the Amended and Restated Change in Control Agreement dated as of August 18,
2008 between you and the Company (the “Change in Control Agreement”), and that
as of the Resignation Date, the Change in Control Agreement shall be null and
void.


 


3.                                      Mutual Releases:


 


(a)                                  In exchange for
the Company’s promises set forth herein, and other good and valuable
consideration, the sufficiency of which is hereby acknowledged, you, on your
own behalf and on behalf of your heirs, executors, administrators, attorneys
and assigns, hereby unconditionally and irrevocably release, waive and forever
discharge the Company and each of its affiliates, parents, successors,
predecessors, and the subsidiaries, directors, owners, members, shareholders,
officers, agents, and employees of the Company and its affiliates, parents,
successors, predecessors, and subsidiaries (collectively, all of the foregoing
are referred to as the “Company Releasees”), from any and all causes of action,
claims and damages, whether known or unknown, foreseen or unforeseen, presently
asserted or otherwise arising through the date of your signing of the
Agreement, concerning your employment, Board membership or separation from 


 


3

















 


employment
and your resignation from your Board membership.  This release includes,
but is not limited to, any claim or entitlement to salary, bonuses, any other
payments, benefits or damages arising under any federal law (including, but not
limited to, Title VII of the Civil Rights Act of 1964, the Age Discrimination
in Employment Act, the Employee Retirement Income Security Act of 1974, the
Americans with Disabilities Act, Executive Order 11246, the Family and Medical
Leave Act, and the Worker Adjustment and Retraining Notification Act, each as
amended); any claim arising under any state or local laws, ordinances or
regulations (including, but not limited to, any state or local laws, ordinances
or regulations requiring that advance notice be given of certain workforce
reductions); and any claim arising under any common law principle or public
policy, including, but not limited to, all suits in tort or contract, such as
wrongful termination, defamation, emotional distress, invasion of privacy or
loss of consortium, and any claim for attorneys’ fees.


 


You understand that by signing this Agreement you are not waiving any
claims or administrative charges which cannot be waived by law.  You are
waiving, however, any right to monetary recovery or individual relief should
any federal, state or local agency (including the Equal Employment Opportunity
Commission) pursue any claim on your behalf arising out of or related to your employment,
Board membership with and/or separation from employment and Board membership
with the Company.


 


Notwithstanding anything to the contrary provided herein, nothing
herein shall affect your rights under the Company’s certificate of
incorporation and bylaws with respect to indemnification or the Indemnification
Agreement, dated August 18, 2008, between the Company and you.


 


(b)                                 In exchange for
the release set forth in Section 3(a) above, and other good and
valuable consideration, the sufficiency of which is hereby acknowledged, the
Company unconditionally and irrevocably hereby release, waive and forever
discharge you from any and all causes of action, claims and damages, whether
known or unknown, foreseen or unforeseen, presently asserted or otherwise
arising out of your employment with, change in employment status with, and/or
separation of employment from, the Company.  This release is intended by
the Company to be all encompassing and to act as a full and total release of
any claims, whether specifically enumerated herein or not, that the Company may
have or have had against you arising from conduct occurring up to and through
the date of this Agreement, including, but not limited to, any claims arising
from any federal, state or local law, regulation or constitution dealing with
either employment or employment benefits; any contract, whether oral or
written, express or implied, including without limitation, any letter offering
employment and any stock option agreement(s), any tort; any claim for equity or
other benefits; or any other statutory and/or common law claim.  Notwithstanding the foregoing, nothing herein
shall be deemed to release or waive (i) any civil claims the Company may
have arising from any acts or omissions by you that would satisfy the elements
of a criminal offense or (ii) any claims arising from this Agreement.


 


4.                                      Waiver of Rights and Claims Under the Age Discrimination in Employment
Act of 1967:


 


Since you are 40 years of age or older, you are
being informed that you have or may have specific rights and/or claims under
the Age Discrimination in Employment Act of 1967 (ADEA) and you agree that:


 


4

















 


(a)                                 in
consideration for the Company’s promises set forth herein, you specifically and
voluntarily waive such rights and/or claims under the ADEA you might have
against the Company Releasees to the extent such rights and/or claims arose
prior to the date this Agreement was executed;


 


(b)                                you understand
that rights or claims under the ADEA which may arise after the date this
Agreement is executed are not waived by you;


 


(c)                                 you are advised
that you may take at least twenty-one (21) days within which to consider the
terms of this Agreement, subject to Section 5(a) below, and you are
advised to consult with an attorney of your choice prior to executing this
Agreement, and you acknowledge that you have not been subject to any undue or
improper influence interfering with the exercise of your free will in deciding
whether to consult with counsel;


 


(d)                                you have
carefully read and fully understand all of the provisions of this Agreement,
and you knowingly and voluntarily agree to all of the terms set forth in this
Agreement; and


 


(e)                                 in entering
into this Agreement you are not relying on any representation, promise or
inducement made by the Company or its attorneys with the exception of those
promises described in this document.


 


5.                                      Period for Review and Consideration of Agreement:


 


(a)                                  You acknowledge
that you were informed and understood that you had twenty-one (21) days from January 25,
2010 (i.e., to and including February 19,
2010) to review and consider a preceding version of this Agreement before
signing it.  You further acknowledge and agree that the revisions to such
preceding version that are reflected in this Agreement do not extend that
twenty-one (21) day period.  If you sign
this Agreement before February 19, 2010, you acknowledge that such
decision was entirely voluntary.


 


(b)                                 The 21-day
review period will not be affected or extended by any revisions, whether
material or immaterial, that might be made to this Agreement.


 


6.                                      Accord and Satisfaction:  The payments set forth
herein shall be complete and unconditional payment, settlement, accord and/or
satisfaction with respect to all obligations and liabilities of the Company
Releasees to you, including, without limitation, all claims for back wages,
salary, vacation pay, draws, incentive pay, bonuses, stock and stock options,
commissions, severance pay, reimbursement of expenses, motor vehicle expenses,
moving expenses, any and all other forms of compensation or benefits, attorney’s
fees, or other costs or sums.


 


7.                                      Company Files, Documents and Other Property:  You agree that on or before
the Resignation Date you will return to the Company all Company property and
materials, including but not limited to, (if applicable) personal computers,
laptops, palm pilots and their equivalent, fax 


 


5

















 


machines,
scanners, copiers, cellular phones, Company credit cards and telephone charge
cards, manuals, building keys and passes, courtesy parking passes, diskettes,
intangible information stored on diskettes, software programs and data compiled
with the use of those programs, software passwords or codes, tangible copies of
trade secrets and confidential information, sales forecasts, names and
addresses of Company customers and potential customers, customer lists,
customer contacts, sales information, sales forecasts, memoranda, sales
brochures, business or marketing plans, reports, projections, and any and all
other information or property previously or currently held or used by you that
is or was related to your employment with the Company (“Company Property”). 
You represent that you have not and will not take by download or otherwise any
Company Property.  You agree that in the event that you discover any
Company Property in your possession, whether in electronic form or otherwise,
after the Resignation Date, you will immediately return such materials to the
Company.


 


Following your return of your Company issued laptop (the “Laptop”), the
Company will remove all Company information from the Laptop and will then
transfer the Laptop to you for you to keep for your own personal use together
with the docking station and two (2) monitors previously used by you in
your office at the Company.


 


8.                                      No Liability or Wrongdoing:  Nothing
in this Agreement, nor any of its terms and provisions, nor any of the
negotiations or proceedings connected with it, constitutes, will be construed
to constitute, will be offered in evidence as, received in evidence as, and/or
deemed to be evidence of, an admission of liability or wrongdoing by any and/or
all of the Company Releasees, and any such liability or wrongdoing is hereby
expressly denied by each of the Company Releasees.


 


9.                                      Future Conduct:


 


(a)                                  Nondisparagement:  You
agree not to make disparaging statements to any person or entity concerning the
Company, its officers, directors or employees; the products, services or
programs provided or to be provided by the Company; the business affairs,
operation, management or the financial condition of the Company; or the
circumstances surrounding your employment and/or separation of employment from
the Company.  The Company
shall direct all current Directors, the current CEO and current Vice
Presidents of the Company not to make any disparaging statements concerning
you.


 


(b)                                Confidentiality
of this Agreement:  You agree that you shall not disclose,
divulge or publish, directly or indirectly, any information regarding the
substance, terms or existence of this Agreement and/or any discussion or
negotiations relating to this Agreement, including any assertions made in the
course of such negotiations, to any person or organization other than your immediate
family and accountants or attorneys when such disclosure is necessary for the
accountants or attorneys to render professional services.  Prior to any
such disclosure that you may make, you shall secure from your attorney or
accountant their agreement to maintain the confidentiality of such
matters.  Notwithstanding the foregoing, you may make disclosure
concerning this Agreement to the same extent as the Company makes public
disclosure for securities law reporting purposes, after the Company has made
any such disclosure.


 


6

















 


(c)                                  Disclosures:  Nothing
herein shall prohibit or bar you from providing truthful testimony in any legal
proceeding or in communicating with any governmental agency or representative
or from making any truthful disclosure required, authorized or permitted under
law; provided, however, that in providing such testimony or making such
disclosures or communications, you will use your best efforts to ensure that
this section is complied with to the maximum extent possible. 
Notwithstanding the foregoing, nothing in this Agreement shall bar or prohibit
you from contacting, seeking assistance from or participating in any proceeding
before any federal or state administrative agency to the extent permitted by
applicable federal, state and/or local law.  However, you nevertheless
will be prohibited to the fullest extent authorized by law from obtaining
monetary damages in any agency proceeding in which you do so participate.


 


(d)                                 Nondisclosure and
Developments Agreement:  You agree that the Employee
Nondisclosure and Developments Agreement between you and the Company (“Nondisclosure
and Developments Agreement”), provide restrictions regarding your conduct
following the termination of your employment.  You agree that the
agreements referenced in the preceding sentence are valid and enforceable, and
that you shall comply in all respects with the terms of such agreements.


 


10.                               Future Cooperation:


 


You agree to cooperate reasonably with the Company (including its
outside counsel) in connection with the contemplation, prosecution and defense
of all phases of existing, past and future litigation about which the Company
believes you may have knowledge or information.  You further agree to make
yourself available at mutually convenient times during and outside of regular
business hours as reasonably deemed necessary by the Company’s counsel. 
The Company shall not utilize this Section 10 to require you to make
yourself available to an extent that would unreasonably interfere with
full-time employment responsibilities that you may have.  You agree to
appear without the necessity of a subpoena to testify truthfully in any legal
proceedings in which the Company calls you as a witness.  The Company shall
compensate you at the rate of $200.00 per hour for services provided by you
pursuant to this Section 10; provided that (i) the Company shall not
be required to provide compensation for services that also come within the
scope of your obligations to provide transitional assistance pursuant to Section 1(d) (which
obligations are subject to the time period and hours limitation applicable to
services pursuant to Section 1(d)), and (ii) the Company shall not be
obligated to compensate you for any time that you could be compelled to expend
if you were subpoenaed by the Company.  The Company shall also reimburse
you for any pre-approved reasonable business travel expenses that you incur on
the Company’s behalf as a result of your litigation cooperation services, after
receipt of appropriate documentation consistent with the Company’s business
expense reimbursement policy.


 


11.                               Representations,
Governing Law and Other Terms:


 


(a)                                 This Agreement
sets forth the complete and sole agreement between the parties and supersedes any
and all other agreements or understandings, whether oral or written, except the
Stock Option Plans, Equity Agreements, Change in Control Agreement (subject to
its termination pursuant to this Agreement), and Nondisclosure and Developments
Agreement.  This Agreement may not be changed, amended, modified, altered
or rescinded except upon the express written consent of the Company and you.


 


7

















 


(b)                                If any
provision of this Agreement, or part thereof, is held invalid, void or voidable
as against public policy or otherwise, the invalidity shall not affect other
provisions, or parts thereof, which may be given effect without the invalid
provision or part.  To this extent, the provisions and parts thereof of this
Agreement are declared to be severable.  Any waiver of any provision of
this Agreement shall not constitute a waiver of any other provision of this
Agreement unless expressly so indicated otherwise.  The language of all
parts of this Agreement shall in all cases be construed according to its fair
meaning and not strictly for or against either of the parties.


 


(c)                                 This Agreement
and any claims arising out of this Agreement (or any other claims arising out
of the relationship between the parties) shall be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts and shall in all
respects be interpreted, enforced and governed under the internal and domestic
laws of Massachusetts, without giving effect to the principles of conflicts of
laws of such state.


 


(d)                                You represent
that you have not been subject to any retaliation or any other form of adverse
action by the Company Releasees for any action taken by you as an employee of
the Company or resulting from your exercise of or attempt to exercise any
statutory rights recognized under federal, state or local law.


 


(e)                                 You may not
assign any of your rights or delegate any of your duties under this
Agreement.  The rights and benefits of this Agreement shall inure to the
benefit of the Company’s successors and assigns.


 


(f)                                   This Agreement
may be executed in counterparts.  When both parties have executed their
respective counterparts, this Agreement shall be considered to be fully
executed and the counterparts shall together be considered one and the same
Agreement.


 


12.                               Effective Date:  After
signing this Agreement, you may revoke this Agreement for a period of seven (7) days
following said execution, by submitting a written revocation to counsel for the
Company, Mark C. Solakian, VP and General Counsel.  The Agreement shall
not become effective or enforceable and no payments will be made pursuant to
this Agreement until this revocation period has expired (“Effective Date”).


 


If this letter correctly states the agreement and
understanding we have reached, please indicate your acceptance by
countersigning the enclosed copy and returning it to me.


 


Finally, Steve, I want to thank you personally for
your efforts and professionalism to help Helicos achieve its goals.  I
wish you the very best in the future.


 


	
   

  	
  Very
  truly yours,

  
	
   

  	
  HELICOS
  BIOSCIENCES CORPORATION

  
	
   

  	
   

  	
   

  
	
   

  	
  By:

  	
  /s/
  Ronald A. Lowy

  
	
   

  	
   

  	
  Ronald
  A. Lowy

  
	
   

  	
   

  	
  Chief
  Executive Officer

  



 


8

















 


I
REPRESENT THAT I HAVE READ THE FOREGOING AGREEMENT, THAT I FULLY UNDERSTAND THE
TERMS AND CONDITIONS OF SUCH AGREEMENT AND THAT I AM KNOWINGLY AND VOLUNTARILY
EXECUTING THE SAME.  IN ENTERING INTO THIS AGREEMENT, I DO NOT RELY ON ANY
REPRESENTATION, PROMISE OR INDUCEMENT MADE BY THE COMPANY OR ITS REPRESENTATIVES
WITH THE EXCEPTION OF THE CONSIDERATION DESCRIBED IN THIS DOCUMENT.


 


	
  Accepted
  and Agreed to:

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/
  Stephen J. Lombardi

  	
   

  
	
  Stephen
  J. Lombardi

  	
   

  



 


9