Exhibit 10.56

March 23, 2005

Ms. Linda M. Rubinstein
c/o Solexa, Inc.
25861 Industrial Blvd.
Hayward, CA 94545

Dear Linda:

     We are pleased to offer you a position as Vice President, with the
understanding and agreement that you will also assume the title and role of
Chief Financial Officer once the Form 10-K for the year ended December 31, 2004
has been filed, and in any event no later than April 30, 2005. You will report
to the Chief Executive Officer (“CEO”) at Solexa, Inc. (“Solexa” or the
“Company”). As agreed, the terms of your employment are as follows:

     Your start date with the Company will be March 22, 2005. As previously
noted, you will report to the CEO and you will have the duties and
responsibilities commensurate with your title and office as reasonably assigned
to you by the CEO. You shall perform your duties at the Company’s Hayward,
California offices, subject to reasonable travel to the Company’s U.K. offices
from time to time. Beginning March 22, 2005 and continuing through June 30,
2005, excluding any periods of disability, vacation and sick leave to which you
are entitled, you will devote approximately ninety percent (90%) of your
business time and attention to the business and affairs of Solexa. During this
period, you will receive a base salary of $18,750.00 per month (equivalent to an
annual salary of $225,000), less payroll deductions and all required
withholdings. As an exempt, salaried employee, you will not be eligible for
overtime compensation. During this period, you are expected to wind down and
complete any and all consulting engagements.

     Effective as of July 1, 2005, provided that you have no continuing
consulting engagements and excluding any periods of disability, vacation and
sick leave to which you are entitled, you will devote substantially all of your
business time and attention to the business and affairs of Solexa. You will
receive a base salary of $20,833.33 per month (equivalent to an annual salary of
$250,000), less payroll deductions and all required withholdings. As an exempt,
salaried employee, you will not be eligible for overtime compensation.

     During your employment with Solexa, you will also be eligible to earn an
annual performance bonus with a target of 30% of your base salary (pro-rated for
2005 commencing with your start date). For 2005, the amount of your bonus will
be determined based on your achievement (as reasonably determined by the CEO) of
written performance milestones to be negotiated in good faith and agreed upon
between you and the CEO within two months of your joining the Company. For
subsequent years, you and the CEO will negotiate written performance milestones
in good faith for bonus determination purposes.

 

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     If the Company successfully completes a financing within six (6) months
after your start date which results in the Company obtaining at least
$10,000,000 in available funds, the CEO will recommend to the Board of Directors
(the “Board”) that you be granted a nonstatutory stock option to purchase one
hundred forty-one thousand (141,000) shares of the common stock of the Company
(the “Option”) pursuant to the Company’s 1992 Stock Option Plan (the “Plan”).
The exercise price for the Option shares will be the closing sales price as
quoted on Nasdaq National Market System (“Nasdaq”) on the last market trading
day prior to the day of grant. Except as otherwise provided in this letter, the
Option will vest and become exercisable in forty-eight (48) equal monthly
installments over four (4) years, with vesting to commence as of your start
date, as long as you remain in continuous service with the Company (as defined
in the Plan). Upon the consummation of an Asset Sale, Merger, Consolidation or
Reverse Merger, each as defined in the Plan, the vesting and exercisability of
the Option and any other outstanding option grants then held by you (including
but not limited to the Anniversary Options described in the next paragraph)
shall be accelerated two (2) years. The Option is subject to Board approval, and
will be governed in full by the Plan and your individual Option agreement.

     In addition, subject to your satisfactory performance of your duties as
determined by the CEO in his reasonable discretion, the CEO will recommend to
the Board that additional option grants of no less than 45,000 shares each be
granted to you within 30 days following the first and second anniversaries of
your start date, each of which will vest and become exercisable in forty-eight
(48) equal monthly installments over four (4) years from the respective grant
dates (each such option grant shall be referred to herein as an “Anniversary
Option” and collectively as the “Anniversary Option). Of course, such grants are
subject to and contingent upon Board approval.

     The Company’s stock option plan currently provides the right to exercise
the shares in full or in part subject to any stock option grant for
consideration consisting of any combination of cash, check or cashless exercise
in conjunction with the Company’s Regulation T program. The rights set forth in
this paragraph currently are included in each of the Company’s award agreements
and option grants and will be included in your award agreements and option
grants.

     You will also be eligible to participate in all Company benefits applicable
to similarly situated executive employees of the Company, pursuant to the terms,
conditions and limitations of the benefit plans and Company policies: said
benefits include, but are not limited to, medical insurance, vacation, sick
leave and holidays. Your vacation accrual rate will be equal to a rate of four
(4) weeks per year, subject to the terms of our vacation policy. A summary of
the benefit plans is enclosed. In addition, The Company will enter into an
Indemnity Agreement with you in substantially the form enclosed herein within
five (5) business days of your start date.

     Notwithstanding anything to the contrary in this letter or in any other
agreement between you and the Company, it shall not be a violation of your
obligations to the Company for you to engage in the following activities:
(1) serve on civic or charitable boards or committees, or (2) manage personal
investments; so long as these activities are not on behalf of a competitor to
the Company and do not significantly interfere with the performance of your
duties and responsibilities to the Company. In the event you wish to serve on
corporate boards and deliver

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lectures, fulfill speaking engagements or teach at educational institutions, you
will need advance written permission from the CEO, which permission shall not be
unreasonably withheld.

     As a Solexa employee, you will be required to abide by Company rules and
regulations, and you will be required to sign an acknowledgment that you have
read, understand, and will comply with the Company’s Employee Handbook. In your
work for the Company, you will be expected not to use or disclose any
confidential information, including trade secrets, of any former employer or
other person to whom you have an obligation of confidentiality. Rather, you will
be expected to use only that information which is generally known and used by
persons with training and experience comparable to your own, which is common
knowledge in the industry or otherwise legally in the public domain, or which is
otherwise provided or developed by the Company. You agree that you will not
bring onto Company premises any unpublished documents or property belonging to
any former employer or other person to whom you have an obligation of
confidentiality. You hereby represent that you have disclosed to Solexa any
contract you have signed that may restrict your activities on behalf of the
Company.

     Your employment with Solexa is at-will, meaning that you may terminate your
employment at any time and for any reason whatsoever simply by notifying Solexa.
Likewise, Solexa may terminate your employment at any time, with or without
Cause (as defined below), and with or without advance notice. The Company also
retains sole discretion to make all other decisions concerning your employment
(e.g. position, title, reporting relationship, transfers, job duties and
responsibilities, compensation, benefits or any other managerial decisions) with
or without Cause, and with or without advance notice. This at-will employment
relationship cannot be changed except in writing, signed by you and a duly
authorized Company officer.

     Notwithstanding the at-will nature of your employment, in the event
(i) your employment is terminated without Cause (as defined below) by the
Company, (ii) you resign your employment with Good Reason (as defined below);
(iii) your employment is terminated without Cause (as defined below) by the
Company or any successor to or acquiring entity of the Company within thirty
(30) days prior to, upon or within twelve (12) months after an Asset Sale,
Merger, Consolidation, or Reverse Merger (as defined in the Plan), or (iv) you
resign your employment with Good Reason (as defined below) within thirty
(30) days prior to, upon or within twelve (12) months after an Asset Sale,
Merger, Consolidation or Reverse Merger (as defined in the Plan) of the Company,
you will be eligible to receive severance compensation as stated herein,
provided that you first execute a general release of any and all known and
unknown claims you may have against the Company, which general release will be
in a form reasonably acceptable to the Company. The amount of severance
compensation you will receive in the event of a termination or resignation of
your employment under provisions (i) or (ii) of the first sentence of this
paragraph shall be an amount equal to four and one-half (4.5) months of your
final base salary, plus an amount equal to 100% of your target annual bonus,
prorated to the percent of the year that has been completed, as of your
termination date, subject to standard payroll deductions and withholdings and
payable in a lump sum. The amount of severance compensation you will receive in
the event of a termination or resignation of your employment under provisions
(iii) or (iv) of the first sentence of this paragraph shall be an amount equal
to six (6) months of your final

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base salary, plus an amount equal to 100% of your target annual bonus, prorated
to the percent of the year that has been completed, as of your termination date,
subject to standard payroll deductions and withholdings and payable in a lump
sum, which sums shall be in addition to two years acceleration of the vesting
and exercisability of the Option and any other outstanding options grants then
held by you (including but not limited to the Anniversary Options), in the event
such accelerated vesting and exercisability has not already occurred.

     “Cause” shall mean: (a) your conviction of, guilty plea to, or plea of “no
contest” to, any felony or any crime involving dishonesty; (b) your knowing
participation in any fraud or material act of dishonesty against the Company;
(c) your persistent and willful refusal to perform your duties to the Company;
(d) intentional damage by you to any property of the Company; or (e) your use of
drugs or alcohol in such a manner as to materially interfere with the
performance of your duties.

     “Good Reason” shall mean the occurrence of any of the following without
your written consent, and your resignation due to and no later than sixty
(60) days after such occurrence: (i) a material breach by the Company of any of
its obligations to you under this letter, provided that, such resignation will
only qualify as a resignation for Good Reason if you first provide the Company
with at least thirty (30) days advance written notice of your intention to
resign and the Company does not cure its breach to your reasonable satisfaction
within that thirty (30) day timeframe; (ii) the required relocation of your
principal place of employment to a location that increases your commute by more
than twenty-five (25) miles from Hayward, California; (iii) any material
reduction in your base salary or bonus potential, with the exception of
reduction programs generally applicable to the Company’s senior executive
employees; or (iv) any material diminution in your title, reporting
relationship, duties or responsibilities.

     On your first day at Solexa, Inc., you will be required to sign the
documents listed below. Please see Cristina Alves for completion of these
documents:

1.       Proprietary Information and Inventions Agreement. Signing this
agreement is a condition of our offer of employment, and compliance with this
agreement is a condition of continued employment. A copy has been enclosed for
your review.

2.       Employment Eligibility Verification (I-9) Form. In compliance with the
Immigration Reform and Control Act of 1986, our offer of employment is subject
to satisfactory proof of your identity and right to work in the United States.
You will be required to complete the enclosed I-9 form and provide us with
original documentation as outlined in Section 2 (copy enclosed) to verify your
identity and eligibility for employment in the United States. It is very
important that you remember to bring the necessary identification documents on
your first day.

     The employment terms in this letter, and the stock plan and other
documents, policies and agreements referenced herein, including but not limited
to the stock option agreements. the Proprietary Information and Inventions
Agreement and the Indemnity Agreement, constitute the complete and exclusive
statement of your employment agreement with Solexa. It supersedes any

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agreements or promises made to you by anyone, whether oral or written. Changes
in your employment terms, other than those changes, if any, expressly reserved
to the Company’s discretion in this letter, require a written modification
signed by you and a duly authorized officer of Solexa. If you have any
questions, please contact me.

Welcome to Solexa, Inc. We look forward to working with you.

Sincerely,

/s/ John West

John West
Chief Executive Officer

/enclosures

     Please sign below indicating your acceptance of this offer of employment,
and return the original to our office by March 23, 2005 in the enclosed
self-addressed, stamped envelope.

     
Linda Rubinstein
  /s/ Linda Rubinstein
 
   
Name (print)
  Signature
 
   
March 23, 2005
  March 22, 2005
 
   
Date
  Start Date

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