NIMBLEGEN SYSTEMS INC S-1/A

AMENDMENT NO. 3 TO FORM S-1

RESTATED CERTIFICATE OF INCORPORATION OF THE REGISTRANT

AMENDED AND RESTATED BYLAWS OF THE REGISTRANT

SEVENTH AMENDED AND RESTATED STOCKHOLDERS AGREEMENT

FIRST AMENDMENT TO SEVENTH AMENDED AND RESTATED STOCKHOLDERS AGREEMENT

STOCKHOLDERS AGREEMENT WITH STANLEY D. ROSE

FORM OF STOCKHOLDERS AGREEMENT

2007 EQUITY INCENTIVE PLAN

2007 EMPLOYEE STOCK PURCHASE PLAN

SEVERANCE AGREEMENT BETWEEN THE REGISTRANT AND STEVEN W. SMITH

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND STANLEY D. ROSE

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND DAVID S. SNYDER

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND EMILE NUWAYSIR

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND ROLAND GREEN

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND DANIEL CLUTTER

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND STEVEN SMITH

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND LEROY HOOD

AWARD AGREEMENTS BETWEEN THE REGISTRANT AND GREGG C. FERGUS

FORM OF INDEMNIFICATION AGREEMENT

SUMMARY OF NON-EMPLOYEE DIRECTOR COMPENSATION ARRANGEMENTS

MIXER SUPPLY AGREEMENT BETWEEN THE REGISTRANT AND BIOMICRO SYSTEMS, INC.

LETTER FROM VIRCHOW, KRAUSE & COMPANY, LLP

CONSENT OF GRANT THORTON LLP

CONSENT OF BUSINESS APPRAISAL SERVICES, LLC

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