Thomas Sharpton
Burgess And Elizabeth Jamieson Chair In Healthspan Research at Linus Pauling Institute
Berkeley, California, United States
Summary
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Senior🎓
Top SchoolThomas Sharpton is a microbiome scientist and endowed Jamieson Chair in Healthspan Research who integrates microbiology, statistics, and computer science to build reproducible frameworks for metagenomic and multi-omic analysis. Based at Oregon State University with joint appointments in Microbiology and Statistics and located in Berkeley, he directs the OSU Microbiome Core and Initiative, leading multidisciplinary teams that apply AI-driven modeling across zebrafish, murine, and human cohorts. Over a 16+ year research career he has published 120+ peer-reviewed papers, developed influential computational tools (e.g., PhylOTU, SFams, ShotMap) during his Gladstone postdoc, and maintained continuous NIH and NSF funding. His work uniquely frames microbiome effects through evolutionary theory to ask how modern lifestyles disrupt long-standing host–microbe interactions and drive chronic disease. He also translates basic discoveries into microbiome-derived therapeutic leads via global academic, clinical, and industry partnerships. Beyond research, he is committed to inclusive mentorship and training the next generation of interdisciplinary scientists.
16 years of coding experience
14 years of employment as a software developer
PhD, Microbiology and Computational Biology, PhD, Microbiology and Computational Biology at University of California, BerkeleyB.S., Biochemistry and Biophysics, B.S., Biochemistry and Biophysics at Oregon State University
Github Skills (12)
shotgun10
pipeline9
sequence8
throughput7
bioperl7
bioinformatics7
mass-spectrometry6
perl6
modular4
open-source2
r-package1
r1
Programming languages (3)
Github contributions (5)
sharpton/shotcleaner
Jan 2016 - Jul 2017
A high-throughput and modular workflow to quality control shotgun metagenomic DNA sequence libraries
Contributions:1 release, 1 PR, 11 pushes in 1 year 7 months
quality-controlsequencepipelinednadna-sequence
sharpton/shotmap
Aug 2013 - Aug 2015
A Shotgun Metagenome Annotation Pipeline
Contributions:1 release, 99 commits, 1 PR in 2 years
annotationpipelinemetagenomeshotgun
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