Thomas Jefferson Sharpton



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Department of Microbiology

Oregon State University

226 Nash Hall, Corvallis, OR 97331

tel: (541) 737-8623 fax: (541) 737-0496
thomas.sharpton@gmail.com

lab.sharpton.org

@tjsharpton

github.com/sharpton



Education

2009 University of California, Berkeley, CA

Ph.D., Microbiology, Designated Emphasis in Computational Biology

2003 Oregon State University, Corvallis, OR

B.S. (Cum Laude), Biochemistry and Biophysics.

Appointments

2013- Assistant Professor

Departments of Microbiology and Statistics, Oregon State University

2009-2013 Bioinformatics Fellow

Gladstone Institute of Cardiovascular Disease, Gladstone Institutes

Mentors: Katherine Pollard & Jonathan Eisen (UC Davis)

2003-2009 Graduate Student Researcher

Department of Microbiology, University of California, Berkeley

Mentors: John Taylor & Sandrine Dudoit

2005 Bioinformatics Research Intern

The Broad Institute

Mentor: James Galagan

2002-2003 Research Assistant

Department of Zoology, Oregon State University

2001 Research Assistant

International Arctic Research Center, University of Alaska, Fairbanks, AK
Honors & Awards

2014 Carter Award for Outstanding and Inspirational Teaching in Science (Finalist)

2013 Gladstone Scientific Leadership Award

2007 Dean’s Council Student Research Representative

2007 Effectiveness in Teaching Award, UC Berkeley

2006-2008 Chang-Lin Tien Graduate Research Fellowship

2002 Student Leadership Fellowship

2002 HHMI Undergraduate Research Fellowship

2002-2003 Dr. Donald MacDonald Excellence in Science Scholarship

2002 OSU College of Science's Excellence in Science Scholarship

1999-2003 Provost Scholarship

1999 American Legion Student Ethics Award



Publications

Refereed Journal Articles

18. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ^. (In Print) Automated and accurate estimate of gene family abundance from shotgun metagenomes. PLOS Computational Biology.

17. O’Dwyer JP, Kembel SW, Sharpton TJ (2015) Backbones of Evolutionary History Test Biodiversity Theory for Microbes. The Proceedings of the National Academy of Sciences. 112(27):8356-61. PMCID: In process

16. Quandt AC, Kohler A, Hesse C, Sharpton TJ, Martin F, Spatafora JW. (2015) Metagenomic sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome. Environmental Microbiology. doi: 10.1111/1462-2920.12840. PMCID: In process

15. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. (2014) Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLOS ONE 9(8): e105067.

14. Kent M, Soderlund K, Thomann E, Schreck CB, Sharpton TJ. (2014) Post-mortem sporulation of Ceratomyxa Shasta (Myxozoa) after dealth in adult Chinook salmon. Journal of Parasitology. 100(5):679-83

13. Sharpton TJ^. (2014) An Introduction to the Analysis of Shotgun Metagenomic Data Frontiers in Plant Genetics and Genomics. 5(209) PMCID: PMC4059276.

12. 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, Henn BM. (2014) Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data. BMC Genomics. 15(262). PMCID: PMC4051168

11. Finucane M, Sharpton TJ, Laurant T, Pollard KS (2014) A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter PLOS ONE. 9(1): e84689. PMCID: PMC3885756

10. Ladau J, Sharpton TJ, Jospin G, Kembel SW, O'Dwyer JP, Koeppel A, Green JL, Pollard KS. (2013) Global marine bacterial diversity peaks at high latitudes in winter. International Society of Microbial Ecology Journal. Published online March 21, 2013; DOI: 10.1038/ismej.2013.37. PMCID: PMC3749493

9. Sharpton TJ*^, Jospin G*, Wu D, Langille MG, Pollard KS, Eisen JA (2012). Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource, BMC Bioinformatics, 13(1): 264. PMCID: PMC3481395

8. Whiston E, Wise HZ, Jui G, Sharpton TJ, Cole GT, Taylor JW. (2012) “Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in Coccidioides spp.” PLOS ONE. 7(7): e41034. PMCID: PMC3401177

7. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS (2012). Novel bacterial taxa in the human microbiome, PLOS ONE, 7(6): e3529. PMCID: PMC3374617

6. The Human Microbiome Project Consortium (2012) A Framework for Human Microbiome Research, Nature, 486: 215–221. PMCID: PMC3377744

5. The Human Microbiome Project Consortium (2012). Structure, function and diversity of the human microbiome in an adult reference population, Nature, 486: 207-214. PMCID: PMC3564958

4. Sharpton TJ^, Riesenfeld SJ, Kembel SW, Ladau J, 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): e1001061. PMCID: PMC3024254

3. 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: 938–946. PMCID: PMC2892095

2. 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: 1722–1731. PMCID: PMC2765278

1. Sharpton TJ^, Neafsey DE, Galagan JE, and Taylor JW. (2008) Mechanisms of Intron Gain and Loss in Cryptococcus, Genome Biology, 9(1): R24. PMCID: PMC2395259

*Indicates co-first author

^Indicates corresponding author

Other Publications

Sharpton TJ, Gaulke C. (2015) Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health. mBio, 6(5): e01387-15.

Sharpton TJ, Jhaveri AA. (2006) Leveraging the Knowledge of Our Peers: Online Communities Hold the Promise to Enhace Scientific Research. PLOS Biology, 4(6): e199.

Professional Membership & Service

Academic Service

2015 Lead Author. Oregon State University’s response to the White House Office of Science and Technology’s Request for Information regarding microbiome research.

2015- Editor. mSystems.

2015- Committee Member. Graduate Bioinformatics Minor Curriculum Committee, OSU

2015- Member. American Society of Microbiology.

2014- Committee Member. BioHealth Sciences Undergraduate Curriculum Committee, OSU

2014- Committee Member. Microbiology Graduate Admissions, OSU

2014-2015 Committee Member. (Under)graduate Bioinformatics Curriculum Task Force, OSU

2014-2015 Subcommittee Co-Chair. Graduate Bioinformatics Curriculum Task Force, OSU

2014- Review Editor. Frontiers in Systems Microbiology

2013-2014 Committee Member. Center for Genome Research and Biocomputing Spring Colloquium Steering Committee, OSU

2013- Biological Consultant. Informal advisor for statisticians, OSU

2013- Statistical Consultant. Informal advisor for microbiologists, OSU

2013- Member. Scientists for Advancing Microbiome Research

2010- Member. The Human Microbiome Project Consortium

2009- Ad Hoc Referee. Science, PLoS Computational Biology, BMC Genomics, Molecular Ecology, FEMS Microbial Ecology, Microbiome, Bioinformatics, PLoS ONE, Frontiers in Systems Biology, Frontiers in Microbiology, mBio, Applied Environmental Microbiology

2010 Advisor. UCSF Biomedical Informatics Graduate Program Review

2007 President. Plant and Microbial Graduate Group, UC Berkeley

2007 President. Microbiology Student Group, UC Berkeley

2006 Chair. Microbiology Student Symposium, UC Berkeley

2006-2008 Webmaster. Microbiology Student Group, UC Berkeley

2005 Reviewer. Joint Genome Institute’s IUMS Genome Browser Review


Teaching and Training

Academic Courses

2015 Symbiosis and the Environment. BI358

Guest Lecture – “The Human Gut Microbiome” (2/5)

2014- Introduction to Quantitative Genomics. ST599

Course Developer and Instructor (Fall Quarter, Alternate Years)

2014 Molecular Host-Microbe Interactions. MCB637

Guest Lecture – “The Human Gut Microbiome” (5/30)

2014- Microbial Bioinformatics and Genome Evolution. OSU MB668

Course Developer and Lead Instructor. (Spring Quarter, Annual)

2014 Neuroendrocrine Regulation of Energy Metabolism. OSU NUTR 599/699

Guest Lecture – “The Human Gut Microbiome” (4/14)

2014 Nucleic Acid Bioinformatics. OSU BB499/599 CS419/519

Guest Lecture – “Inferring functional elements from conservation” (2/17)

2013 Microbial Systems. OSU MB511

Guest Lecture - “Mapping the Diversity of Marine Bacteria” (11/25)

2013 Microbiomes and Host-Microbiome Interactions. OSU HC407

Guest Lecture - “The Human Gut Microbiome” (11/12)

2007 Comparative Genomics Seminar UC Berkeley PMB290

Course Organizer

2006 The Diversity of Fungi. UC Berkeley PMB110

Graduate Student Assistant Instructor

2004 Introduction to Biology. UC Berkeley BIO1B

Graduate Student Assistant Instructor

2003 Cell and Molecular Biology. OSU BI314

Undergraduate Student Assistant Instructor

Advising

2014- Melissa Conley, PhD Co-Advisor, Nutrition

2014 Martin Guyer. MS Co-Advisor, Statistics

2014- Nicole Kirchoff, PhD Advisor, Microbiology

2014- Christopher Gaulke, Postdoctoral Fellow, Microbiology

2014-2015 Kyle Duyck, Undergraduate Researcher, Biochemistry/Biophysics

2014-2015 Holman Jue, Undergraduate Researcher, Microbiology

2014- Sean McNall, Undergraduate Researcher, Microbiology

2014 Courtney Armour, Rotation Student, MCB

2015- Courtney Armour, PhD Advisor, MCB

2015- Lexi Gauthier, Undergraduate Researcher, Microbiology

Mentorship: Informal

2013 Dr. Mariel Finucane – The obesity-associated gut microbiome

2013 Timothy Laurent – Ascertaining protein family quality and function

2012 Rachel Radnor – Computational analysis of marine microbial diversity

2012 Guillaume Jospin – Iterative clustering to identify novel proteins

2012 Stephen Nayfach – Assessing microbial functional diversity estimations

2011 Peter Skews-Cox – Building Viral HMMs for metagenomic data analysis

2011 Aram Avila-Herrera – Identification of CRISPRs in metagenomic data

2010 Dr. Rebecca Truty – Quantifying novel human microbiota

Thesis/Dissertation Committee Member and Service

2015- Sarah Nalven, College of Earth, Atmospheric, Oceanic Sciences, MS Committee

Member

2015- Mudra Choudhury, Bioresources Research Program Committee Member



2015- Brandon Kieft, Dept. of Microbiology, PhD Committee Member

2014- Ryan McMinds, Dept. of Microbiology, PhD Committee Member

2014- Trevor Tivey, Dept. Integrative Biology, PhD Committee Member

2014-2015 Kimberly Kenny, Honors Thesis Com mittee Member

2014 Krista Soderlund, Honors Thesis Committee Member

2014 Martin Guyer, Dept. Statistics, MS Committee Member

2014- Edward Davis, Dept. Botany & Plant Pathology, PhD Committee Member

2014- 2015 Kevin Vergin, Dept. Microbiology, PhD Committee Member

2013- Melissa Conley. Dept. Nutrition, PhD Committee Member

2013-2014 Robbie Eberhard-Garah. BRR Honors Student Committee Member



Open Source Software

vFams (http://derisilab.ucsf.edu/software/price/vFam)

Protein family database for the metagenomic identification of viruses



ShotMAP (https://github.com/sharpton/shotmap)

Distributed computing workflow to classify metagenomic data into protein families



SFams Database (http://edhar.genomecenter.ucdavis.edu/sifting_families/)

Diverse protein family database that rapidly incorporates new genomic data



PhylOTU (https://github.com/sharpton/PhylOTU)

Identifies metagenomic OTUs using a phylogenetic approach



ModAlign (https://github.com/sharpton/modalign)

An HMM-based multiple sequence aligner



Bio::SearchIO::HMMER3 (https://github.com/kblin/bioperl-hmmer3)

BioPerl module that transforms HMMER result files into a BioPerl SearchIO object



Grants

Active

NIH R21 AI108953-01A1 (Co-I)

Longitudinal and functional dynamics of autoimmune gut microbiomes

Contact PI: Pollard

Submitted: 11/2013

Collaborators: Katherine Pollard, Shomyseh Sanjabi

Requested Amount: $525,250

Subcontract Request: $49,609

Department: Microbiology

College: Ag. Science

Person Months: 2

Location of Project: J. David Gladstone Institutes (Subcontract to OSU)

Active Dates: 10/2014-09/2016
Environmental Health Sciences Center Pilot Project Grant (PI)

High-throughput Discovery of Environmental Mechanisms of Dysbiosis

Award Amount: $10,000

Active Dates: 6/2015– 3/2016

NIH R01 1R01DK103761 (Co-I)

Gut microbiota mediate the interplay between immunity and glucose metabolism

Contact PI: Shulzhenko

Collaborators: Natalia Shulzhenko, Andrey Morgun, Aleksandra Sikora

Subaward Amount: $144,905

Active Dates: 09/01/2015-08/31/2020

NIH R01 1R01AT009168 (Co-I)

Vitamin D, xanthohumol and nuclear receptors: targeting immunity, microbiota and the gut metabolome

Contact PI: Gombart

Collaborators: Adrian Gombart, Claudia Maier, Fred Stevens, Balz Frei, Paul Blackmore, Malcolm Lowry, Miranda Cristobal, Andriy Morgun, Gerd Bobe, Natalia Shulzenko

Person Months: 0.6

Subaward amount: $34,471

Active Dates: 09/01/2015-8/31/2020



Completed

Gordon & Betty Moore Foundation 3300 (Co-PI)

The Environmental Niche Atlas: Global Mapping of Microbial Functions

Contact PI: Pollard

Submitted 8/2011

Collaborators: Katherine Pollard, Jonathan Eisen

Total Award Amount: $1,510,227

Subcontract Amount: $25,484

Department: Microbiology

College: Science

Active Dates: 11/01/2013 – 10/31/2014

Person-Months Per Year Committed to Project: 2

Location of Project: J. David Gladstone Institutes (Subcontract to OSU)

Pending
National Science Foundation (DEB)

Using Phylogenetic Structure to Clarify the Evolutionary Ecological Distribution of Microorganisms

Role: PI


Source of Support:

Total Award Amount: $731,791

Total Award Period Covered: 4/1/16 – 3/31/19

Location: Oregon State University, subaward ($326,965) to University of Illinois

Person Months per Year Committed to the Project: 1.0 calendar month
National Science Foundation (DMS)/National Institutes of Health (NIGMS)

Network-based statistical methods reveal microbial and host interactions from microbiome data

Role: Co-PI

Total Award Amount: $760,767

Total Award Period Covered: 07/01/16 – 06/30/19 

Location: Oregon State University (Sharpton subaward $77,228)

Person Months per Year Committed to the Project: 0.5 calendar months


National Science Foundation (ABI)

ABI Innovation: An Ecophylogenetic Framework for the Analysis of Microbial Communities

Role: PI


Total Award Amount: $429,398

Total Award Period Covered: 7/1/16 – 6/30/18

Location: Oregon State University

Person Months per Year Committed to the Project: 1.0 calendar month



Submitted

NIH NIEHS R21 (PI)

The Longitudinal Impact of Triclosan Exposure on the Enteric Microbiome

Contact PI: Sharpton

Submitted: 2/2015

Department: Microbiology

College: Science

Requested Amounts: $275,000 (Direct)

Collaborators: R. Tanguay

W.M. Keck Foundation Research Program (Co-PI)

W.M. Keck Foundation



Developing Next-Generation High-Throughput Culturing Technology to Identify the Mechanisms Underlying Microbial Interaction Networks

Contact PI: Giovannoni

Submitted: 8/2014 – Internal Review, 10/2014 Keck Foundation Review

Collaborators: S. Giovannoni

Department: Microbiology

College: Science

Requested Amount: $1,893,098

Person Months: 1

Location of Project: Oregon State University

Status: Phase I application submitted



Sloan Foundation Early Career Award (PI)

Analyzing inter-protein relationships to infer molecular, evolutionary, and ecological functions

Contact PI: Sharpton

Submitted: 2/2014

Collaborators: None



NIH P01 (Core Co-Leader)

CAM Center for Mechanistic Evaluation of Vitamin D and Xanthohumol

Contact PI: Stevens

Submitted: 9/2013

Collaborators: Fred Stevens, Cathy Abney, Joe Beckman, Paul Blakemore, Gerd Bobe, Jaewoo Choi, Adrian Gombart, Arup Indra, Yuan Jiang, LeeCole Legette, Malcolm Lowry, Claudia Maier, Barbara McVica, Cristobal Miranda, , Andrey Morgun, Ralph Reed, Natalia Shulzhenko, Brett Tyler

Requested Amount: 9,160,816

Status: Rejected



DOD MURI (Co-PI)

Building a predictive understanding of skin bacterial community ecology, body odor, and mosquito attractiveness

Contact PI: Fierer

Submitted: 12/2013

Collaborators: Noah Fierer, Brendan Bohannan, Detlev Helmig, James O’Dwyer, Leslie Vosshall

Requested Amount: $5,296,466

Subcontract Request: $290,621

Status: Rejected

NIH R01 (Co-I)

Gut microbiota mediate the interplay between immunity and glucose metabolism

Contact PI: Shulzhenko

Submitted: 2/2014

Collaborators: Natalia Shulzhenko, Andrey Morgun, Aleksandra Sikora

Department: Microbiology

College: Science

Requested Amount: $1,825,000

Subaward Amount: $144,905

Department: Microbiology

Person Months: 1

Location of Project: Oregon State University

Pending Dates: 09/01/2014-08/31/2019

Status: Resubmitted

NSF DOB (Co-PI)

National Science Foundation



The Elaphomyces microbiome – a model for the ecological evolution of fungal-bacterial interactions

Contact PI: Spatafora

Submitted: 4/2014

Collaborators: Joey Spatafora, Mike Castellano, Jeff Chang, Francis Martin

Department: Microbiology

College: Science

Requested Amount: $2,000,000

Subcontract Amount: $500,000

Person Months: 0.5

Location of Project: Oregon State University

Pending Dates: 10/2014-9/2019

Status: Rejected


NIH NIEHS (PI)

The Longituindal Impact of Triclosan Exposure on the Enteric Microbiome

Submitted: 2/2015

Collaborators: R. Tanguay (Co-I)

Department: Microbiology

College: Science

Requested Amount: $275,000

Status: Rejected



Joint Genome Institutes Community Science Program (Co-PI)

Mechanisms of Rapid Adaptation in Globally Abundant SAR11 Carbon Oxidizing Bacteria

Submitted: 6/2015

Collaborators: S. Giovannoni (PI)

Status: Pending



Preproposals/Whitepapers

NSF DEB – Systematics and Biodiversity Science (PI)

Using Phylogenetic Structure to Clarify the Evolutionary Ecological Distribution of Microorganisms

Contact PI: Sharpton

Submitted: 1/2015

Collaborators: J. O’Dwyer, S. Kembel



NSF IOS (PI)

Quantifying Ecological Impacts on Host-Microbioe Interaction in Zebrafish

Contact PI: Sharpton

Submitted: 1/2015

Collaborators: None

Gordon and Betty Moore Foundation DDD (PI)

Analyzing inter-protein relationships to infer molecular, evolutionary, and ecological functions

Contact PI: Sharpton

Submitted: 2/2014

Collaborators: None



USDA AFRI (Co-PI)

Diet and microbiome interactions during age-related inflammation

Contact PI: Ho

Submitted: 2/2014

Collaborators: Emily Ho, Kathy Magnusson



NSF DEB – Systematics and Biodiversity (Co-PI)

A metagenomic and culture-based analysis of bacterial diversity in the gut microbiome of a model marine mollusk

Contact PI: King

Submitted: 1/2014

Collaborators: Gary King, Cameron Thrash



NSF DEB – Evolutionary Processes (Co-PI)

Mechanisms that produce pan-genome diversity in globally abundant bacteria

Contact PI: Giovannoni

Submitted: 1/2014

Collaborators: Stephen Giovannoni



US ARMY ONRBAA13-022 (Co-PI)

Modes of Evolution in Genome Streamlining: The Role of Enzyme Promiscuity in Microbial Survival

Contact PI: Giovannoni

Submitted: 10/2013

Collaborators: Stephen Giovannoni, Patrick Deleenheer, Trent Northen


NSF IOS – Physiological and Structural Systems Cluster (PI)

Quantifying Ecological Impacts on Host-Microbiome Interaction in Zebrafish

Submitted: 1/2015

Collaborators: None

Status: Rejected



NSF DEB – Phylogenetic Systematics Cluster (PI)

Using Phylogenetic Structure to Clarify the Evolutionary Ecological Distribution of Microorganisms

Submitted: 1/2015

Collaborators: James O’Dwyer (Co-PI, SISU), Steven Kembel (Collaborator, U. Quebec)

Status: Invited

All amounts listed are total costs

Presentations

Invited Talks

5/2015 The Microbiome Inside

TRIAD, Oregon State University, Corvallis, OR

4/2015 The Human Microbiome: Getting to the Guts of the Matter

Microbiology Student Association, Oregon State University, Corvallis, OR

2/2015 Human Microbiome Evolution, Ecology, and Function

IGERT Healthy Aging Seminar, Oregon State University, Corvallis, OR

2/2015 Data Mining the Microbiome



MathBio Seminar, Oregon State University, Corvallis, OR

1/2015 Human Microbiome Evolution, Ecology, and Function

Department of Microbiology Colloquium, Oregon State University, Corvallis, OR

11/2014 Metagenomic Investigations of the Human Microbiome

Biology Department Seminar Series, Willamette University, Salem, OR

10/2014 High-Throughput Prediction of Microbiome Physiology

International Symposium on Gut Microbiology, Nanjing, China

5/2014 Data Mining the Microbiome

Department of Statistics Seminar. Oregon State University, Corvallis, OR

5/2014 Metagenomic Investigations of the Human Microbiome



Department of Nutrition Seminar. Oregon State University, Corvallis, OR

5/2014 From Noise to Signal: Mining Human Exome Sequences Reveals the Hunter-Gatherer Oral Microbiome



Center for Genome Research and Biocomputing Spring Colloquium. Oregon State University, Corvallis, OR.

12/2013 Metagenomic Investigations of the Microbiome

META Center Seminar. University of Oregon, Eugene, OR.

10/2012 Understanding the Human Microbiome through Metagenomic Analysis



CGRB Seminar Series, Oregon State University, Corvallis, OR.

6/2012 Identifying novel bacteria in the human microbiome

American Society of Microbiology General Meeting. San Francisco, CA.

5/2012 Characterizing oral microbiome diversity using exome captured sequences from saliva

Stanford Symposium on the Biology of Hunter-Gatherers. Palo Alto, CA.

5/2012 Your Microbiome: What is it and why does it matter?

Gladstone Institutes Science for Administration. San Francisco, CA.

10/2011 Mining the Metagenome: Computational approaches quantify the diversity of microbial communities

San Francisco State University Dept. of Biology. San Francisco, CA.

12/2010 Characterizing microbial diversity from metagenomic data

UCSF Evolution Club. San Francisco, CA.

11/2010 Characterizing microbial diversity from metagenomic data

UC Berkeley Division of Biostatistics Seminar. Berkeley, CA.

6/2010 Characterizing microbial diversity from metagenomic data

Banfield Lab Meeting. UC Berkeley, Berkeley, CA.

3/2009 Evolutionary genomics identifies proteins important to the interaction between Coccidioides and its host

Fungal Genetics Conference. Asilomar, CA.

6/2008 The comparative genomics of Coccidioides and the rise of virulence

American Society for Microbiology General Meeting. Boston MA.

11/2007 The comparative genomics of Coccidioides.

UCB College of Life Sciences Dean’s Advisory Meeting. Berkeley, CA.

4/2007 What makes a pathogenic fungus? A comparative genomics investigation of Coccidioides evolution.

UC Berkeley Microbiology Student Symposium. Berkeley, CA.

5/2002 The effect of light intensity on Sym 32 expression in Anthopleura elegantissima.

HHMI Student Symposium. Corvallis, OR.

Solicited

6/2015 Accurate and Rapid Metagenome Annotation Clarifies the Relationship between Enteric Microbiome Function and Inflammatory Bowel Disease. (Talk)

American Society of Microbiology Annual Meeting, New Orleans, LA

9/2014 High-throughput annotation of metagenomes reveals community physiological variation in the mammalian microbiome (Poster)



Lake Arrowhead Microbial Genomics Meeting, Lake Arrowhead, CA

8/2014 High-throughput annotation of metagenomes reveals community physiological variation in the mammalian microbiome (Talk)



META Center Symposium on Host-Microbe Systems Biology, Eugene, OR

5/2012 Characterizing the diversity of the human microbiome to understand disease (Poster)

Gladstone Institutes Scientific Retreat. San Francisco, CA.

3/2012 Quantifying human microbiome functional variation using Operational Protein Families (Poster)

International Human Microbiome Consortium. Paris, France.

2/2012 Characterizing the diversity of the human microbiome to understand disease (Poster)

Gladstone Scientific Advisory Board Meeting. San Francisco, CA.

10/2011 Novel methods to quantify human microbiome diversity (Talk)

Mission Bay RIPS. UCSF, San Francisco, CA.

8/2010 PhylOTU: A high-throughput procedure that identifies Operational Taxonomic Units from metagenomic data (Poster)

International Society for Microbial Ecology Annual Meeting. Seattle, WA.

6/2010 Resolving the Hidden Biosphere: A high-throughput procedure that identifies OTUs from metagenomic data (Talk)

Evolution. Portland, OR.

5/2010 Characterizing microbial diversity from metagenomic data (Talk)

GICD Research in Progress Seminar Series. San Francisco, CA.

4/2010 Using Metagenomics to Study Uncultured Microbes: Who is out there, where do they live, and what are they doing? (Poster)

Gladstone Institutes Annual Retreat. San Francisco, CA.

11/2008 Comparative evolutionary genomics of the pathogenic fungus Coccidioides (Talk)

UC Berkeley DE Computational and Genomic Biology Retreat. Berkeley, CA.

3/2008 The comparative genomics of Neurospora (Talk)

Neurospora. Asilomar, CA.

3/2007 What makes a pathogenic fungus? (Poster)

Bay Area Meeting on Pathogenesis. University of California, San Francisco, CA.

3/2007 What makes a pathogenic fungus? (Poster)

Fungal Genetics Meeting. Asilomar, CA.

3/2006 The evolution of spliceosomal introns in Cryptococcus neoformans (Poster)

Bay Area Meeting on Pathogenesis. University of California, San Francisco, CA

Media Coverage

Arbanas, C. Census of microbes in healthy humans reported. Washington University Newsroom. June 13, 2012. http://news.wustl.edu/news/Pages/23956.aspx


Holden, A. From Trash to Treasure. Gladstone Institutes News. June 17, 2013. http://gladstoneinstitutes.org/node/11311
Bradley, L. You’re not alone. The Daily Barometer. Nov. 20, 2014. http://www.dailybarometer.com/news/you-re-not-alone/article_fc8964f0-713b-11e4-9b08-e32e374f4d59.html
Green, M. Genetic variety in gut critters tied to disease. The Columbia Chronicle. Feb. 2, 2015. http://www.columbiachronicle.com/health_and_tech/article_58d3b600-b8bf-11e4-a207-f3c635020d35.html
Shikh-Lesko, R. Microbiome Meals. The Scientist. Oct. 1, 2015.

http://www.the-scientist.com/?articles.view/articleNo/44144/title/Microbiome-Meals/


Houtman, N. Gut Check. Intestinal microbes affect our health. Terra Magazine. Oct. 15, 2015. http://oregonstate.edu/terra/2015/10/gut-check/

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