Management Software

JONATHAN USUKA, PH.D., M.B.A

San Diego, CA

abnpzn@r.postjobfree.com

San Diego, CA

**** – present

ACCELRYS, INC

Senior Director

Life Science Marketing

• Developed and executed corporate strategy for the life science market, updating the Board of Directors on a regular basis

• Chaired consortium composed of Merck, Eli Lilly, and Abbott Laboratories, which developed an industry standard knowledge

sharing platform to enable biological collaboration throughout global organizations; winner of the 2009 Bio-IT World Best Practice

Award for “Pharmaceutical Knowledge Management”

• Led the successful launch of two new products, including market sizing, life cycle planning, competitive intelligence, go-to-market

implementation, and brand revenue targets

• Present scientific and corporate strategy at pharmaceutical conferences worldwide, attending an average of 1 conference per week to

lead product marketing efforts, gather competitive information, and identify new business areas

• Proposed and implemented 3 major initiatives in a complex, global environment; built support and articulated clear business goals

derived from thorough analysis of how the laboratory-based innovations filled strategic gaps in our product portfolio

• Established and developed extensive relationships with academic and institutional researchers, resulting in the prediction of industry

trends, especially in the areas of molecular diagnostics, personalized medicine, and translational research

• Maintained extensive senior level contacts throughout the pharmaceutical and diagnostic industries, and built a network composed

of CEOs of small, innovative biotechnology companies and university professors

• Managed the partner ecosystem of joint ventures and R&D collaborations, and developed the strategic target assessments for

business development or acquisition opportunities; negotiated partnership, co-marketing, and product development agreements

• Invited lecturer for “Management of Biotechnology ” at UC Berkeley (The Haas School)

Palo Alto, CA

F HOFFMANN-LA ROCHE, LTD

2007 - 2008

Director of Business Strategy

•

• Led a diverse global area of 30+ M.B.A.s, M.D.s, & Ph.D.s, including recruitment, compensation, performance management & goal

setting, succession planning, and talent management

• High visibility champion of changing corporate culture, with an emphasis on the sharing of best practices and research information

among the Roche Group (principally Roche Diagnostics, Roche Pharmaceuticals, Genentech, and Chugai)

• Contributed translational research expertise while serving on the 8 member “Emerging Technologies Team” composed of functional

heads and senior scientists dedicated to identifying and evaluating the fit of new technologies in relation to corporate strategy

• Performed scientific, informatics and financial due diligence for acquisition targets in sizes ranging from Piramed Ltd. ($175M –

kinase portfolio), Ventana ($3B - diagnostics) and ultimately Genentech ($47B – biologics/oncology)

• Responsible for planning, tracking, and deploying a $35 Million annual area budget

• Negotiated quotes and contracts with vendors and suppliers; selected preferred service providers and interfaced with internal finance

groups to achieve global pricing and discounting agreements

• Developed global strategic business requirements, including SWOT, wargame/options & ROI analysis, in consultation with senior

management; frequent presenter of written and oral recommendations to committees and key decision makers

• Conducted financial and market research to justify business models, strategies and initiatives being undertaken

• Built the Global Viral Surveillance program, a unique collaboration between Pharma and Diagnostics enabling better investment

decisions concerning emerging diseases such as Dengue and H1N1; data selectively shared with WHO, US & European governments to

support sales for emergency stockpiling programs of Tamiflu and vaccines

• Provide competitive intelligence assessments, including benchmarking against industry standards, for internal & external projects

• Negotiated terms and agreements among the various corporate entities within the Roche Group, utilizing persuasion, interpersonal

relationship skills, and a keen understanding of factions and interests to build shared goals

ROCHE PALO ALTO (now GENENTECH)

Associate Research Director

Department Head, Genome Informatics

Palo Alto, CA

2001 – 2006

• Managed a diverse department of 25 Ph.D.s and M.D.s, accountable for the discovery & qualification of biomarkers using DNA

Sequencing (Applied Biosystems), Gene Expression (Affymetrix, Illumina), Proteomics (Bruker), and Biostatistics (SAS);

submitted reports internally and to the FDA and EMEA

• Awarded an NIH grant to lead a consortium of Jackson Labs and various universities to define diversity in the mouse genome

• Published personalized medicine and translational research results in peer reviewed journals such as Science (2001: twice first

author, and 2004: senior author of cover article) and Nature

• Participant on project teams for novel targets and therapeutic compounds in Virology (Influenza, Hepatitis, HIV-AIDS),

Inflammation (Arthritis & other pain indications) and Oncology; negotiated with molecular diagnostics provider (Monogram) for

co-development of targeted therapies and diagnostics tests

• Keynote speaker in Spanish for Pharma Development Conference, Madrid, 2004

• Named “High Potential Leader,” limited to top 1% of managers globally; awarded sponsored management training from IMD

(2003) and London School of Business (2004, 2005)

• Led an operational change globally by reorganizing DNA sequencing within the global organization, reduced cost 60% and

raised productivity 10X

• Invented 3 global patents for laboratory and informatics innovations in drug discovery and personalized medicine

•

USUKA BIOINFORMATICS

Chief Executive Officer

Palo Alto, CA

1994 – 2001

• Negotiated, sourced, and delivered multiple simultaneous contracts for clients ranging from global pharmas to small biotechs

• Utilized direct marketing to pharma and biotech companies via networking, referrals, and cold calls

• Built a team of 10 programmers & engineers, with annual revenues of $2M

• Exploited an expanding market niche for custom bioinformatics software and automated laboratory solutions

•

STANFORD UNIVERSTIY

Ph.D. Candidate, Department of Chemistry

N.I.H. Fellow, Department of Genetics, School of Medicine

Stanford, CA

1996 – 2001

Digital Disease©

• Developed a database and algorithm for disease gene identification using SNPs and phenotypic data

• Collaborated with industry, government, and university scientists to acquire high quality data for proof of concept

• Roche Bioscience purchased the patent rights from Stanford University in 2001

GeneSeqer©

• Conceived and developed a software program for rapid and accurate exon identification in raw genomic sequence

• Worked with the University's Office of Technology Licensing to develop a marketing plan

• The product is still licensed annually by Monsanto and other life science companies

Philadelphia, PA

UNIVERSITY OF PENNSYLVANIA 1993 – 1995

Staff Scientist

Computational Chemistry

• Developed first computer simulation of the active site of an important human enzyme, alcohol dehydrogenase

•

EDUCATION

THE WHARTON SCHOOL, UNIVERSITY OF PENNSYLVANIA Philadelphia, PA

Master of Business Administration, Finance 2008

Concentration in Healthcare Strategy, self-financed

STANFORD UNIVERSITY Stanford, CA

Doctor of Philosophy, Department of Chemistry 2001

• Fellow, Department of Genetics, School of Medicine, National Institute of Health Genome Training Program

• Certification in Bioinformatics, School of Medicine, 1999

Princeton, NJ

PRINCETON UNIVERSITY

1992

Bachelor of Arts, Department of English

AWARDS, HONORS, & AFFILIATIONS

Best Practices Award, Pharmaceutical Knowledge Management, Bio-IT World Expo (2009)

Best of Show Award, Molecular Medicine Tri-Conference (2009)

Lecturer, The Haas School of Management, University of California Berkeley: "MBA 296 - Mgmt of Biotechnology" (2009)

Advisory Board, F.D.A. Collaborative R&D Association for Pharmacogenomics – Glaxo Smith Kline (2009)

Chairman, Industry Group, Biological Registration & Intellectual Property – Merck, Abbott, Eli Lilly (2008 – 2009)

Advisory Board, F.D.A Critical Path Institute (2006 - 2008)

Advisor, Princeton Alumni Career Network (2002 - present)

Lecturer, The School of Medicine, Stanford University (2004)

Inventor, Office of Technology Licensing, Stanford University (2000 - present)

N.I.H. Fellow, Genetics, Stanford University School of Medicine (1999)

Interviewer, Admissions Department, Princeton University

Mentor, Alumni Network, Chestnut Hill Academy

Member, American Chemical Society

Member, International Society for Computational Biology

SCIENTIFIC PUBLICATIONS

Jonathan Usuka, Ph.D., M.B.A.

1. Liu H, Lu P, Guo Y, Farrell E, Zhang X, Zheng M, Bosano B, Zhang Z, Allard J, Liao G, Fu S, Chen J, Dolim K, Kuroda A, Usuka

J, Cheng J, Tao W, Welch K, Liu Y, Pease J, Keczer S, Masjedizadeh M, Hu J, Weller P, Garrow T, Peltz G.

“An Integrative Genomic Analysis Identifies Bhmt2 as a Diet-Dependent Genetic Susceptibility Factor for Acetaminophen-Induced

Liver Toxicity.”

Submitted. 2009.

2. Ribado R, Pihil T, Brown F, Cesarone J, Flook P, Gazdzicki R, Harmon L, Kearney R, Lear J, McMenamin C, Packer J, Wuertz E,

Usuka J.

“Enterprise-Wide Biological Associations: Collaborating in a Complex Information Landscape.”

Submitted. 2009.

3. Farrell E, Usuka J.

“Pharmacogenomics and drug development: the impact of US FDA postapproval tracking on clinical pharmacology.”

Personalized Medicine. 2008 Mar;5(2):133-9.

4. Guo Y, Lu P, Farrell E, Zhang X, Weller P, Ponshouwer M, Wang J, Liao G, Zhang Z, Hu S, Allard J, Shafer S, Usuka J, Peltz G.

“In Silico and In Vitro Pharmacogenetic Analysis in Mice.”

Proceedings of the National Academy of Sciences of the United States of America. 2007 Nov;104(45):17735-40.

5. Zheng M, Lu P, Liu Y, Pease J, Usuka J, Liao G, Peltz G.

“2D NMR Metabonomic Analysis: A Novel Method for Automated Peak Alignment.”

Bioinformatics. 2007 Sep.

6. Guo Y, Weller P, Allard J, Usuka J, Masjedizadeh M, Wu SY, Fitch B, Clark JD, Shafer S, Wang J, Liao G, Peltz G.

“Understanding our drugs and our diseases.”

Proceedings of the American Thoracic Society. 2006 Jul;3(5):409-12.

7. Guo Y, Weller P, Farrell E, Cheung P, Fitch B, Clark D, Wu SY, Wang J, Liao G, Zhang Z, Allard J, Cheng J, Nguyen A, Jiang S,

Shafer S, Usuka J, Masjedizadeh M, Peltz G.

“In silico pharmacogenetics of warfarin metabolism.”

Nature Biotechnology. 2006 May;24(5):531-6.

8. Liang DY, Liao G, Wang J, Usuka J, Guo Y, Peltz G, Clark JD.

“A genetic analysis of opioid-induced hyperalgesia in mice.”

Anesthesiology. 2006 May;104(5):1054-62.

9. Guo Y, Shafer S, Weller P, Usuka J, Peltz G.

“Pharmacogenomics and drug development.”

Pharmacogenomics. 2005 Dec;6(8):857-64. Review.

10. Wang J, Liao G, Usuka J, Peltz G.

“Computational genetics: from mouse to human?”

Trends in Genetics. 2005 Sep;21(9):526-32. Review.

11. Wang J, Liao G, Cheng J, Nguyen A, Guo J, Chou C, Hu S, Jiang S, Allard J, Shafer S, Puech A, McPherson J, Foernzler D, Peltz

G, Usuka J.

“Haplotype Structure of the Mouse Genome.”

Computational Genetics & Genomics: Tools for Understanding Disease. (Book) 2005 Apr; Humana Press.

12. Peltz G, Usuka J.

“From mouse genetics to human therapeutics.”

Current Opinions in Drug Discovery & Development. 2005 Mar;8(2):253-61. Review.

13. Liao G, Wang J, Guo J, Allard J, Cheng J, Ng A, Shafer S, Puech A, McPherson JD, Foernzler D, Peltz G, Usuka J.

“In silico genetics: identification of a functional element regulating H2-E alpha gene expression.”

Science. Cover Article. 2004 Oct 22;306(5696):690-5.

14. Savov JD, Whitehead GS, Wang J, Liao G, Usuka J, Peltz G, Foster WM, Schwartz DA.

“Ozone-induced acute pulmonary injury in inbred mouse strains.”

American Journal of Respiratory & Cell Molecular Biology. 2004 Jul;31(1):69-77.

15. Usuka J, Grupe A, Germer S, Aud D, Belknap J, Klein R, Ahluwalia M, Higuchi R, Peltz G.

“In Silico Mapping of Mouse Quantitative Trait Loci.”

Science. 2001 Dec 21;294(5551):2423.

16. Grupe A, Germer S, Usuka J, Aud D, Belknap JK, Klein RF, Ahluwalia MK, Higuchi R, Peltz G.

“In silico mapping of complex disease-related traits in mice.”

Science. 2001 Jun 8;292(5523):1915-8.

17. Usuka J, Zhu W, Brendel V.

“Optimal spliced alignment of homologous cDNA to a genomic DNA template.”

Bioinformatics. 2000 Mar;16(3):203-11.

18. Usuka J, Brendel V.

“Gene structure prediction by spliced alignment of genomic DNA with protein

sequences: increased accuracy by differential splice site scoring.”

Journal of Molecular Biology. 2000 Apr 14;297(5):1075-85.

PATENTS

1. Systems and methods for processing nucleic acid chromatograms.

16 Mar 2006

United States Patent: 200********

International Patent: Pending

2. Systems and methods for predicting specific genetic loci that affect phenotypic traits.

8 Dec 2004

United States Patent: 200-***-****

International Patent: 200-***-****

3. System and method for predicting chromosomal regions that control phenotypic traits.

20 June 2002

United States Patent: 200-***-****

International Patent: 200104852

ARTICLES ABOUT JONATHAN USUKA

“Two Pharmas Are Better Than One”

2009: Bio-It World (page 28)

http://online.qmags.com/BIW0709B/Default.aspx

“Breaking News”

2009: Genetic Engineering News

http://www.genengnews.com/news/bnitem.aspx?name=53885408

“One thousand genomes is just the beginning”

2009: Bio-IT World

http://www.bio-itworld.com/uploadedFiles/Bio-IT_World/Bio-IT_Issues/2009/Mar-Apr/BIW_20090301_Mar_2009.pdf

“Life Sciences Increased Demands for More Data, More of the 'Right' Data”

2009: High Tech Views

http://www.hightechviews.com/index.php?sectionID=4&articleID=281

“Zerhouni resigns from NIH; Usuka joins Accelrys”

2008: GenomeWeb Bioinform

http://www.genomeweb.com/informatics/elias-zerhouni-jonathan-usaka

“Top 25 Hottest Articles”

2005: ScienceDirect

http://top25.sciencedirect.com/index.php?cat_id=5&subject_area_id=3&journal_id=01689525

“New Genomic Method Can Identify Disease-Causing Genes Rapidly”

2004: Medical News Today

http://www.medicalnewstoday.com/articles/15403.phps

“Science News of the Week: Faster Maps Mean Fewer Mice”

2001: Science

http://www.scienceonline.org/cgi/content/full/292/5523/1814

“Software for Finding Disease Causing Genes”

2001: BlueCross / BlueShield Provider News

http://www.msbcbs.com/PDFFiles/June%202001%20Provider%20News.pdf

“New software streamlines the search for disease-causing genes”

2001: Science Blog

http://www.scienceblog.com/community/older/2001/D/200114321.html

“Screening Genes”

2001: Stanford Magazine

http://www.stanfordalumni.org/news/magazine/2001/sepoct/farmreport/news.html

“More Mouse SNPs”

2001: Genome Biology

http://genomebiology.com/2001/2/10/reports/2013

“Researcher designs program for genes”

2001: The Stanford Daily

http://daily.stanford.org/article/2002/2/22/researcherDesignsProgramForGenes

“New software streamlines the search for disease-causing genes”

2001: Science Daily

http://www.sciencedaily.com/releases/2001/06/010*********.htm

PRESS RELEASES

“Accelrys Leads Consortium That Receives Best Practices Award for ‘Biological Knowledge Management’ at Bio-IT World

Expo in Boston”

2009: Accelrys News Release

http://ir.accelrys.com/phoenix.zhtml?c=83739&p=irol-newsArticle&ID=1284544&highlight=

“Bio-IT World Announces the Winners of its 2009 Best Practices Awards Program”

2009: CHI Press Release

http://www.chicorporate.com/Corporate_Content.aspx?id=90598

“New Genetic Research Method Sheds Light on Drug Metabolism”

2006: Roche – Corporate Media News

http://www.roche.com/med-cor-2006-05-08

“Research Publications: Publications Authored by Roche Palo Alto Researchers”

2005: Roche – Corporate Media News

http://www2.roche.com/publications/Publications.html

“New Genomic Method Can Identify Disease-Causing Genes with Unprecedented Precision and Speed”

2004: Roche – Corporate Media News

http://www.roche.com/med-cor-2004-10-22b

“Un Nuevo metodo genomico permite identificar genes patogenos con una precision y una velocidad desconocidas hasta ahora”

2004: Roche Farma Espana

http://www.roche.es/portal/eipf/Spain/spain_portal/roche_es/2004?

paf_gear_id=17400002&paf_dm=full&doc_id=re7300002/re76100002/re77200005/re752003/article/Article_eWep_03526.headline&

paf_pageId=re7188184&tostart=1

“Roche Scientists Exceed Expectations of Genetic Discoveries”

2002: Roche – Corporate Media News

http://www.roche.com/media-news-2002-11-12-e.pdf

“New software streamlines the search for disease-causing genes”

2001: Stanford University News Service

http://news-service.stanford.edu/pr/01/mousegenes613.html

“New Genotyping Tool Developed by Roche: Expected to Speed Practical Applications of Genomic Research”

2000: Roche – Corporate Media News

http://www.roche.com/media-news-2000-11-15-2-e.pdf

RECENT PRESENTATIONS

“Ask More of Your Data”

2009: Accelrys Promotional Video (San Diego)

http://cpg.accelrys.com/video/Video_AskMoreJonathan.html?KeepThis=true&TB_iframe=true&height=339&width=425

“Discovery Challenges in Pharmaceutical Informatics”

2009: International Society for Computational Biology (Stockholm)

http://www.iscb.org/ismbeccb2009/index.php

“Accelerating Biomarker Discovery: Putting It All Together”

2009: Bio-IT World Expo (Boston)

http://www.bio-itworldexpo.com/track2.asp

“Integrating Pharmaceutical Discovery in the Era of Personalized Medicine”

2009: Drug Discovery: Easing the Chemistry Bottleneck (Philadelphia)

http://www.opalevents.org/conferencehtml/2009/drug_discovery_development_summit_2009/drug_discovery_development_summit.p

hp

“Accelerate Drug Discovery for Kinase Targets”

2009: Internet Webinar (Geneva)

http://accelrys.com/events/webinars/human-kinome/index.html

“Drug Metabolism in silico: Using SNPs and Software to Understand Metabolites”

2006: Bridging Pharma and IT (Philadelphia)

http://www.healthtech.com/Conferences/2006/bpi/Track2.asp

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