Thomas Jefferson Sharpton Gladstone Institutes 1650 Owens Street San Francisco, CA 94158

[email protected] (510) 545-2501 http://docpollard.ucsf.edu/sharpton/

Research Interests • • •

The interaction between microorganisms and their environment, especially hosts Understanding and diagnosing human health through microbial signatures The evolution and biodiversity of microorganisms

Education and Training J. David Gladstone Institutes, University of California, San Francisco, CA Postdoctoral Fellow, June 2009 – present Advisor: Katherine S. Pollard Co-Advisor: Jonathan A. Eisen (University of California, Davis) University of California, Berkeley, CA Ph.D., Microbiology, Designated Emphasis in Computational Biology. May 2009 Advisors: John W. Taylor and Sandrine Dudoit Dissertation: Investigations of Natural Genomic Variation in the Fungi. The Broad Institute, Boston, MA Research Intern, Jan. 2005 – May 2005 Advisor: James Galagan Oregon State University, Corvallis, OR B.S., Cum Laude, Biochemistry and Biophysics. 2003.

Publications 1. Sharpton TJ and Jhaveri, AJ. (2006) “Leveraging the Knowledge of our Peers: Online Communities Hold the Promise to Enhance Scientific Research.” PLoS Biology 4(6). 2. Sharpton TJ, Neafsey DE, Galagan JE, and Taylor JW. (2008) Mechanisms of Intron Gain and Loss in Cryptococcus.” Genome Biology 9(1). 3. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C, McMahan C, Muszewksa A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. (2009) “Comparative Genomic Analyses of the Human Fungal Pathogens Coccidioides and their Relatives.” Genome Research 19. 4. Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park D, Whiston E, Hung C, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. (2010) “Population Genomic Sequencing of Coccidioides Fungi Reveals Recent Hybridation and Transposon Control.” Genome Research 20. 5. Sharpton TJ, Riesenfeld SJ, Kembel SW, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. (2011) “PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data” PLoS Computational Biology. 7(1). 6. HMP Consortium (2012) “Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population.” Nature. 486. 7. HMP Consortium (2012) “A Framework for Human Microbiome Research.” Nature. 486.

 

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Thomas Jefferson Sharpton 8. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Sodergren E, Weinstock GM, Pollard KS. (2012) “Novel Bacterial Taxa in Stool Samples from Healthy Human Subjects.” PLoS ONE. 7(6). 9. Whiston E, Wise HZ, Jui G, Sharpton TJ, Cole GT, Taylor JW. (Accepted) “Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in Coccidioides spp.” PLoS ONE. 10. Sharpton TJ, Jospin G, Langille MGI, Wu D, Pollard KS, Eisen JA (In Review) “Sifting through Genomes with Iterative Sequence Clustering produces a Large, Phylogenetically Diverse Protein Family Resource.” 11. HMP Consortium (Submitted). “A Comprehensive Strategy for Sampling the Human Microbiome.” 12. Ladau J, Sharpton TJ, Jospin G, Kembel SW, O'Dwyer JP, Koeppel A, Green JL, Pollard KS. (Submitted) “The Global Biogeography of Marine Bacteria.”

Manuscripts In Preparation 13. Sharpton TJ, Nayfach S, Eisen JA, Pollard KS (In Preparation) “Quantifying the Functional Diversity of Metagenomes using Sifted Protein Families” 14. Henn BM, Kidd JM, Sharpton TJ, Norman PJ, Carpenter M, Sikora M, Gignoux CR, Gorgani NN, Agilent Technologies, Pollard KS, Parham P, Feldman MW, Wall J, Bustamante CD (In Preparation) “Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data” 15. Skewes-Cox P, Sharpton TJ, Ruby GR, Pollard KS, DeRisi JL (In Preparation) “Profile hidden Markov models for the detection of viruses within metagenomic sequence data” 16. Stajich JE, Ellison C, Sharpton TJ, Taylor JW (In Preparation) “Genome evolution and discovery by transcriptional and comparative genomes of a reference filamentous fungus”

Honors and Awards Dean’s Council Student Research Representative

2007

UC Berkeley Effectiveness in Teaching Award

2007

Chang-Lin Tien Graduate Research Fellowship

2006—2008

Student Leadership Fellowship

2002

HHMI Undergraduate Research Fellowship

2002

Dr. Donald MacDonald Excellence in Science Scholarship OSU College of Science's Excellence in Science Scholarship Provost Scholarship American Legion Student Ethics Award

2002—2003 2002 1999—2003 1999

Major Open—Source Software Contributions I maintain several public software packages and data resources: • • • •

 

SFams Database (http://edhar.genomecenter.ucdavis.edu/sifted_families/) Diverse protein family database that rapidly incorporates new genomic data. SF_MRC (https://github.com/sharpton/MRC) Classifies metagenomic data into SFams. PhylOTU (https://github.com/sharpton/PhylOTU) Identifies metagenomic OTUs using a phylogenetic approach Bio::SearchIO::HMMER3 (https://github.com/kblin/bioperl-hmmer3) BioPerl module that transforms HMMER result files into a BioPerl SearchIO object.

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Thomas Jefferson Sharpton Successful Proposal Contributions Exploring the niche space of human microbiome functions through convex geometry and evolutionary genomics (grant #DMS1069303) PI: Katherine S. Pollard NSF/DMS (NSF/NIGMS Joint Program in Mathematical Biology) Duration: 8/15/2011–7/31/2013 Global Mapping of Microbial Functions (grant #3300) PI: Katherine S. Pollard Gordon & Betty Moore Foundation Duration: 6/1/12–5/31/13

Invited Talks “Identifying novel bacteria in the human microbiome” American Society of Microbiology, San Francisco, CA. June 2012. “Characterizing oral microbiome diversity using exome captured sequences from saliva” Stanford Symposium on the Biology of Hunter-Gatherers, Palo Alto, CA. May 2012. “Your Microbiome: What is it and why does it matter?” Gladstone Institutes Science for Administration. San Francisco, CA. May 2012. “Mining the Metagenome: Computational approaches quantify the diversity of microbial communities” San Francisco State University Department of Biology. San Francisco, CA. October 2011. “Characterizing microbial diversity from metagenomic data.” UCSF Evolution Club. San Francisco, CA. December 2010. “Characterizing microbial diversity from metagenomic data.” UC Berkeley Division of Biostatistics Seminar, Berkeley, CA. November 2010. “Characterizing microbial diversity from metagenomic data.” Banfield Lab Meeting. UC Berkeley, Berkeley, CA. June 2010. “Evolutionary genomics identifies proteins important to the interaction between Coccidioides and its host.” Fungal Genetics Conference. Asilomar, CA. March 2009. “The comparative genomics of Coccidioides and the rise of virulence.” American Society for Microbiology. Boston MA. June 2008. “The comparative genomics of Coccidioides.” UC Berkeley College of Life Sciences Dean’s Advisory Meeting, Berkeley, CA. November 2007. “What makes a pathogenic fungus? A comparative genomics investigation of Coccidioides evolution.” UC Berkeley Microbiology Student Symposium, Berkeley, CA. April 2007.

 

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Thomas Jefferson Sharpton “The effect of light intensity on Sym 32 expression in Anthopleura elegantissima.” HHMI Student Symposium Corvallis, OR. May 2002.

Presentations “Characterizing the diversity of the human microbiome to understand disease” J. David Gladstone Institutes Scientific Retreat. San Francisco, CA. May 2012 (Poster) “Quantifying human microbiome functional variation using Operational Protein Families.” International Human Microbiome Consortium. Paris, France. March 2012. (Poster) “Characterizing the diversity of the human microbiome to understand disease” J. David Gladstone Institutes Scientific Advisory Board Meeting. San Francisco, CA. February 2012. (Poster) “Novel methods to quantify human microbiome diversity” Mission Bay RIPS, UCSF. San Francisco, CA. October 2011. (Talk) “PhylOTU: A high-throughput procedure that identifies Operational Taxonomic Units from metagenomic data.” International Society for Microbial Ecology Annual Meeting. Seattle, WA. August 2010 (Poster). “Resolving the Hidden Biosphere: A high-throughput procedure that identifies OTUs from metagenomic data.” Evolution. Portland, OR. June 2010 (Talk). “Characterizing microbial diversity from metagenomic data.” GICD Research in Progress Seminar Series. San Francisco, CA. May 2010 (Talk). “Using Metagenomics to Study Uncultured Microbes: Who is out there, where do they live, and what are they doing?” Gladstone Institutes Annual Retreat. San Francisco, CA. April 2010 (Poster). “Comparative evolutionary genomics of the pathogenic fungus Coccidioides.” UC Berkeley DE Computational and Genomic Biology Retreat. Berkeley, CA. November 2008. (Talk) “The comparative genomics of Neurospora.” Neurospora. Asilomar, CA. March 2008. (Talk) “What makes a pathogenic fungus?” Bay Area Meeting on Pathogenesis. University of California, San Francisco, CA. March 2007. (Poster) “What makes a pathogenic fungus?” Fungal Genetics Meeting. Asilomar, CA. March 2007. (Poster) “The evolution of spliceosomal introns in Cryptococcus neoformans.” Bay Area Meeting on Pathogenesis. University of California, San Francisco, CA. 2006. (Poster)

 

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Thomas Jefferson Sharpton Service Member. The Human Microbiome Project Consortium

2010—present

Journal Referee. PLoS Computational Biology, BMC Genomics, Molecular Ecology, FEMS Microbial Ecology

2009—present

Advisor. UCSF Biomedical Informatics Graduate Program Review Webmaster. UC Berkeley Microbiology Student Group

2010 2006—2008

President. UC Berkeley Plant and Microbial Graduate Group

2007

President. UC Berkeley Microbiology Student Group

2007

Chair. UC Berkeley Microbiology Student Symposium

2006

Reviewer. Joint Genome Institute’s IUMS Genome Browser Review

2005

Scientific Teaching Experience Mentor. University of California, San Francisco Mentored three graduate students and a postdoctoral researcher: •

Stephen Nayfach – Comparing database estimations of microbial diversity

2012

•

Peter Skews-Cox – Building Viral HMMs for analysis of metagenomic data

2011

•

Aram Avila-Herrera – Identification of CRISPRs in metagenomic data

2011

•

Dr. Rebecca Truty – Quantifying novel diversity in the human microbiome

2010

Seminar Organizer. Comparative Genomics Seminar. University of California

2007

Graduate Student Instructor. The Diversity of Fungi. University of California

2006

Graduate Student Instructor. Introduction to Biology. University of California

2004

Student Instructor. Cell and Molecular Biology. Oregon State University

2003

Other Experience President, co-founder, and core programmer. Smbzen.com, an online knowledge distribution service provider (SMBZEN, LLC).

2005—2008

Contributing Author. FungalGenomes.org, a current events blog of mycological news.

2006—2009

Instructor. University of California Martial Arts Program

2008—present

References Katherine S. Pollard, Ph.D. (Postdoctoral Advisor) Associate Investigator Gladstone Institutes of Cardiovascular Disease J. David Gladstone Institutes University of California, San Francisco 1650 Owens Street San Francisco, CA 94158-2261 (415) 734-2711 [email protected]

 

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Thomas Jefferson Sharpton Jonathan A. Eisen, Ph.D. (Co-Postdoctoral Advisor) Professor University of California, Davis UC Davis Genome Center 451 East Health Sciences Drive Davis, CA 95616-8816 (530) 400-6066 [email protected] John W. Taylor, Ph.D. (Graduate Advisor) Professor Plant and Microbial Biology University of California, Berkeley 111 Koshland Hall Berkeley, CA 94720-3102 (510) 642-5366 [email protected] Shomyseh Sanjabi, Ph.D. (Collaborator) Assistant Investigator Gladstone Institutes of Virology and Immunology J. David Gladstone Institutes University of California, San Francisco 1650 Owens Street San Francisco, CA 94158-2261 (415) 734-4814 [email protected]

 

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