Exhibit
10.1


 


August 6, 2009


 


Mr. Stephen P. Hall




Re:                             Severance Agreement and
Release


 


Dear Steve:


 


This letter summarizes the terms of your continuing
employment and planned separation from employment with Helicos BioSciences
Corporation (the “Company”), pursuant to the Corporate Officer Severance Plan
effected December 11, 2008 (“Severance Plan”) between you and the Company
(the “Agreement”).  The purpose of this
Agreement is to establish an amicable arrangement for ending your employment
relationship, to release legal claims between you and the Company, to provide you
with an overview of your severance pay and related benefits under the Severance
Plan and to permit you to receive additional severance benefits not provided under
the Severance Plan.  Defined terms not
defined herein shall have the same meanings as ascribed to them in the
Severance Plan.


 


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 shall be an employee of the
Company up to August 31, 2009 (the “Departure Date”).  Until August 14, 2009, you shall
continue to hold the position of and serve as Senior Vice President, Chief
Financial Officer and Treasurer of the Company (“CFO”).  To the extent that you retain
responsibilities as CFO until August 14, 2009, you shall use your best
efforts to perform such responsibilities, including without limitation using
your best efforts to complete the Company’s financial statements and filing of
its Quarterly Report on Form 10-Q for the quarter ended June 30,
2009.  During the remainder of your
employment, you shall also perform any reasonably requested responsibilities to
assist in the transition of your duties.


 


(b)                                Pursuant to the Severance Plan, the
Company shall pay you the sum of (i) $92,666.67 which represents your
regular base salary as if you had been employed through December 31, 2009
at your current gross annual salary rate of $278,000 and (ii) any accrued
vacation pay to the extent not theretofore paid, in a lump sum in cash within
ten (10) business days of the Departure Date, provided, however,
that you execute the Waiver and Release Agreement attached hereto as Schedule
A.  Pursuant to the Severance Plan, the
Company will also provide you with outplacement services consistent with past
Company practice which shall include a comprehensive career transition with
private career consulting and administrative services for three months.  On the Departure Date, your 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.  If so requested by the
Company, you shall sign any reasonably requested written notices confirming
your resignation from the Company as CFO, Treasurer and/or from your
affiliation with the Company or any subsidiary in any other capacity.


 

















 


(c)                                  The Departure 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, 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, 2009
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, 2009 and you
shall respond promptly to any reasonable requests for information relevant to
your rights under this Section 1(c). 
Nothing in this Agreement shall affect your right to continue
participating in Group Health Plans pursuant to COBRA after December 31,
2009 at your own premium cost subject to the terms of COBRA.


 


(d)                                 As part of the
consideration for the payments and benefits pursuant to Sections 1(b) and
1(c), you agree that during the period from the close of business on August 14,
2009 to and including August 31, 2009, you shall provide transitional
assistance at any reasonable times requested by the Company.  Transitional assistance pursuant to this Section 1(d) may
include but shall not be limited to services within the scope of Section 9.  In connection with your transitional
assistance, your current monthly housing allowance and reimbursement of
commuting expenses shall continue up until the Departure Date.


 


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 2007 Stock Option and Incentive Plan (“Stock
Option Plan”), your Incentive Stock Option Agreement dated May 8, 2008 (“May 8,
2008 ISO Agreement”), your Restricted Stock Agreement dated January 28,
2009 (“January 28, 2009 Restricted Stock Agreement”), and your Incentive
Stock Option Agreement dated January 28, 2009 (“January 28, 2009 ISO
Agreement”, together with the January 28, 2009 Restricted Stock Agreement,
the “January 28, 2009 Equity Award Agreements” and together with the May 8,
2008 ISO Agreement, collectively, the “Equity Award Agreements”) based on your
employment to the Departure Date, except that you shall further be entitled to
vesting as of the Departure Date of such additional stock and options set forth
in the January 28, 2009 Equity Award Agreements that would have vested if your
employment had continued to and including January 1, 2010.  Subject only to that modification of vesting
rights with respect to January 28,
2009 Equity Award Agreements, 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 Equity Award
Agreements.  Pursuant to the provisions
of the Helicos BioSciences Corporation Insider Trading Policy (the “Insider
Trading Policy”) applicable to former employees, you further understand and
agree that you shall be subject to restrictions on trading of stock that are in
effect as of the Departure Date until the first regularly scheduled open “trading
window” following the Departure Date.


 


(b)                                 Change in Control Agreement: 
You agree that you shall have no further rights under the Change in
Control Agreement, and that as of the Departure Date, the Change in Control
Agreement shall be null and void.


 

















 


3.                                      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:


 


(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 4(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.


 


4.                                      Period for Review and
Consideration of Agreement:


 


(a)                                              You acknowledge that you are informed and
understand that you have twenty-one (21) days from August 6, 2009 (i.e., to and including August 27, 2009) 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 August 27, 2009, 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.


 


5.                                      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 (defined to include the Company and/or any of its parents,
subsidiaries or affiliates, predecessors, successors or assigns, and its and
their respective current and/or former partners, directors,
shareholders/stockholders, officers, employees, attorneys and/or agents, all
both individually and in their official capacities) 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.


 


6.                                      Company Files, Documents
and Other Property:  You agree that on or before the
Departure 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 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 Departure Date, you will immediately
return such materials to the Company.


 


7.                                      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.


 


8.                                      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.


 


(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.


 


(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)                                 Noncompetition, and
Nondisclosure and Developments Agreement:  You agree that the Employee Noncompetition
Agreement between you and the Company, dated April 27, 2008 (“Noncompetition
Agreement”), and the Employee Nondisclosure and Developments Agreement between
you and the Company, dated April 27, 2008 (“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.


 


9.                                      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 9 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 9;
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.


 


10.                               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
Plan, Restricted Stock Agreement, ISO Agreement, Insider Trading Policy, Change
in Control Agreement (subject to its termination pursuant to this Agreement),
Noncompetition 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.


 


(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.


 


11.                               Effective Date:  After signing
this letter, you may revoke this Agreement for a period of seven (7) days
following said execution.  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

  



 


 


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 P. Hall

  	
   

  
	
  Stephen P. Hall

  	
   

  



 

















 


Schedule
A


 


WAIVER AND RELEASE AGREEMENT


 


THIS WAIVER AND RELEASE
AGREEMENT is entered into as of August 6, 2009 (the “Effective Date”), by
Stephen P. Hall (the “Employee”) in consideration of the severance payments
provided to the Employee by Helicos BioSciences Corporation (the “Company”)
pursuant to the Helicos BioSciences Corporation Corporate Officer Severance
Plan (the “Severance Payment”).


 


1.                                       Waiver and Release. 
The Employee, on his or her own behalf and on behalf of his or her
heirs, executors, administrators, attorneys and assigns, hereby unconditionally
and irrevocably releases, waives and forever discharges 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 “Employer”),
from any and all causes of action, claims and damages, including attorneys’
fees, whether known or unknown, foreseen or unforeseen, presently asserted or
otherwise arising through the date of his or her signing of the Waiver and
Release Agreement, concerning his or her employment or separation from
employment.  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.


 


The Employee understands
that by signing this Waiver and Release Agreement he or she is not waiving any
claims or administrative charges which cannot be waived by law.  He or she is 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 his or her behalf arising out of or related to his or her employment with
and/or separation from employment with the Company.


 


The Employee further
agrees without any reservation whatsoever, never to sue the Employer or become
a party to a lawsuit on the basis of any and all claims of any type lawfully
and validly released in this Waiver and Release Agreement.


 


2.                                       Acknowledgments. 
The Employee is signing this Waiver and Release Agreement knowingly and
voluntarily.  He or she acknowledges
that:


 


(a)                                  He or she is hereby advised in writing to
consult an attorney before signing this Waiver and Release Agreement;


 

















 


(b)                                 He or she has relied solely on his or her
own judgment and/or that of his or her attorney regarding the consideration for
and the terms of this Waiver and Release Agreement and is signing this Waiver
and Release Agreement knowingly and voluntarily of his or her own free will;


 


(c)                                  He or she is not entitled to the
Severance Payment unless he or she agrees to and honors the terms of this
Waiver and Release Agreement;


 


(d)                                 He or she has been given at least
twenty-one (21) calendar days to consider this Waiver and Release Agreement, or
he or she expressly waives his or her right to have at least twenty-one (21)
days to consider this Waiver and Release Agreement;


 


(e)                                  He or she may revoke this Waiver and
Release Agreement within seven (7) calendar days after signing it by
submitting a written notice of revocation to the Employer.  He or she further understands that this
Waiver and Release Agreement is not effective or enforceable until after the
seven (7) day period of revocation has expired without revocation, and
that if he or she revokes this Waiver and Release Agreement within the seven (7) day
revocation period, he or she will not receive the Severance Payment;


 


(f)                                    He or she has read and understands the
Waiver and Release Agreement and further understands that it includes a general
release of any and all known and unknown, foreseen or unforeseen claims
presently asserted or otherwise arising through the date of his or her signing
of this Waiver and Release Agreement that he or she may have against the
Employer; and


 


(g)                                 No statements made or conduct by the
Employer has in any way coerced or unduly influenced him or her to execute this
Waiver and Release Agreement.


 


3.                                       No Admission of Liability. 
This Waiver and Release Agreement does not constitute an admission of
liability or wrongdoing on the part of the Employer, the Employer does not
admit there has been any wrongdoing whatsoever against the Employee, and the
Employer expressly denies that any wrongdoing has occurred.


 


4.                                       Entire Agreement. 
There are no other agreements of any nature between the Employer and the
Employee with respect to the matters discussed in this Waiver and Release
Agreement, except as expressly stated herein, and in signing this Waiver and
Release Agreement, the Employee is not relying on any agreements or representations,
except those expressly contained in this Waiver and Release Agreement.


 


5.                                       Execution.  It is not
necessary that the Employer sign this Waiver and Release Agreement following
the Employee’s full and complete execution of it for it to become fully
effective and enforceable.


 


6.                                       Severability. 
If any provision of this Waiver and Release Agreement is found, held or
deemed by a court of competent jurisdiction to be void, unlawful or
unenforceable under 


 

















 


any applicable statute or
controlling law, the remainder of this Waiver and Release Agreement shall
continue in full force and effect.


 


7.                                       Governing Law. 
This Waiver and Release Agreement shall be governed by the laws of the
Commonwealth of Massachusetts, excluding the choice of law rules thereof.


 


8.                                       Headings.  Section and
subsection headings contained in this Waiver and Release Agreement are inserted
for the convenience of reference only.  Section and
subsection headings shall not be deemed to be a part of this Waiver and Release
Agreement for any purpose, and they shall not in any way define or affect the
meaning, construction or scope of any of the provisions hereof.


 


IN WITNESS WHEREOF, the
undersigned has duly executed this Agreement as of the day and year first
herein above written.


 


	
   

  	
  EMPLOYEE:

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  /s/ Stephen P. Hall

  
	
   

  	
  Stephen P. Hall