82
INDEXTOEXHIBITS
Exhibit
Number
DescriptionofDocument
3.1 Amended andRestatedCertificate of Incorporation filed June 19, 1991. (1)
3.2 Certificate ofAmendment toRestatedCertificate of Incorporation filedMay3, 2006. (2)
3.3 Amended andRestatedBylaws. (13)
4.1 Certificate ofDesignationof the SeriesC Junior ParticipatingPreferredStock. (12)
4.2 SpecimenCommonStockCertificate. (1)
4.3 StockPurchaseAgreement between theRegistrant andGenzymeCorporationdated January7, 2008. (5)
4.4
Indenture, dated as ofAugust 13, 2012, between theRegistrant andWells FargoBank, NationalAssociation, as
trustee, includingFormof 2¾ percent ConvertibleSeniorNote due 2019. (30)
10.1
Formof IndemnificationAgreement entered intobetween theRegistrant and itsDirectors andOfficerswith related
schedule. (37)
10.2* Registrant’s 1989StockOptionPlan, as amended. (27)
10.3* Registrant’sAmended andRestatedEmployee StockPurchasePlan. (15)
10.4 Formof EmployeeAssignment of Patent Rights. (1)
10.5* Registrant’s 2000Broad-BasedEquity Incentive StockOptionPlan and related formof option agreement. (7)
10.6
DrugDevelopment andLicenseOptionAgreement datedDecember 2, 2009between theRegistrant andEli Lilly
andCompany. Portions of this exhibit have beenomitted and separately filedwith theSECwith a request for
confidential treatment. (24)
10.7
Patent Rights PurchaseAgreement between theRegistrant andGileadSciences, Inc., datedDecember 18, 1998.
Portions of this exhibit have beenomitted and separately filedwith theSECwith a request for confidential
treatment. (6)
10.8
Collaboration andLicenseAgreement between theRegistrant andHybridon, Inc., datedMay24, 2001. Portions of
this exhibit have beenomitted and separately filedwith the SECwith a request for confidential treatment. (14)
10.9
License andCo-DevelopmentAgreement between theRegistrant andGenzymeCorporationdated June 24, 2008.
Portions of this exhibit have beenomitted and separately filedwith theSECwith a request for confidential
treatment. (9)
10.10
Amendment #1 to theResearch, Development andLicenseAgreement datedMay11, 2011by andbetween the
Registrant andGlaxoGroupLimited. Portions of this exhibit have beenomitted and separately filedwith theSEC
with a request for confidential treatment. (10)
10.11
Amended andRestatedCollaboration andLicenseAgreement between theRegistrant andAntisenseTherapeutics
LtddatedFebruary8, 2008. Portions of this exhibit have beenomitted and separately filedwith theSECwith a
request for confidential treatment. (5)
10.12
Amended andRestatedLicenseAgreement between theRegistrant andAtlantic Pharmaceuticals Limiteddated
November 30, 2009. Portions of this exhibit have beenomitted and separately filedwith the SECwith a request for
confidential treatment. (24)
