INDEXTOEXHIBITS
Exhibit
Number
Description of Document
3.1
Amended and Restated Certificate of Incorporation filed June 19, 1991. (1)
3.2
Certificate of Amendment to Restated Certificate of Incorporation filed June 17, 2014. (42)
3.3
Amended and Restated Bylaws. (13)
4.1
Certificate of Designation of the Series C Junior Participating Preferred Stock. (12)
4.2
Specimen Common Stock Certificate. (1)
4.3
Stock PurchaseAgreement between the Registrant and Genzyme Corporation dated
January 7, 2008. (5)
4.4
Indenture, dated as of August 13, 2012, between the Registrant andWells Fargo Bank,
National Association, as trustee, including Form of 2 ¾ percent Convertible Senior Note due
2019. (30)
4.5
Indenture, dated as of November 17, 2014, between the Registrant andWells Fargo Bank,
National Association, as trustee, including Form of 1.00 percent Convertible Senior Note due
2021. (41)
10.1
Form of IndemnificationAgreement entered into between the Registrant and its Directors
and Officers with related schedule. (37)
10.2*
Registrant’s 1989 Stock Option Plan, as amended. (27)
10.3*
Registrant’s Amended and Restated Employee Stock Purchase Plan. (15)
10.4
Form of EmployeeAssignment of Patent Rights. (1)
10.5*
Registrant’s 2000 Broad-Based Equity Incentive Stock Option Plan and related form of
option agreement. (7)
10.6
Drug Development and License OptionAgreement dated December 2, 2009 between the
Registrant and Eli Lilly and Company. Portions of this exhibit have been omitted and
separately filed with the SECwith a request for confidential treatment. (24)
10.7
Patent Rights PurchaseAgreement between the Registrant and Gilead Sciences, Inc., dated
December 18, 1998. Portions of this exhibit have been omitted and separately filed with the
SECwith a request for confidential treatment. (6)
10.8
Collaboration and LicenseAgreement between the Registrant and Hybridon, Inc., dated
May 24, 2001. Portions of this exhibit have been omitted and separately filed with the SEC
with a request for confidential treatment. (14)
10.9
License and Co-Development Agreement between the Registrant and Genzyme Corporation
dated June 24, 2008. Portions of this exhibit have been omitted and separately filed with the
SECwith a request for confidential treatment. (9)
10.10
Amendment #1 to the Research, Development and LicenseAgreement datedMay 11, 2011
by and between the Registrant and Glaxo Group Limited. Portions of this exhibit have been
omitted and separately filed with the SECwith a request for confidential treatment. (10)
10.11
Amended and Restated Collaboration and LicenseAgreement between the Registrant and
Antisense Therapeutics Ltd dated February 8, 2008. Portions of this exhibit have been
omitted and separately filed with the SECwith a request for confidential treatment. (5)
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