Joshua Hamilton
Owner at Trophic Nexus Bioinformatics Consulting
South San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolJoshua Hamilton is a data-driven bioinformatics entrepreneur and scientist with 11 years of experience accelerating therapeutic development from bench to early clinical programs, particularly in the microbiome space. As founder of Trophic Nexus Bioinformatics Consulting and former senior data scientist roles at Federation Bio and AmplifyBio, he combines hands-on wet-lab experience with production bioinformatics, cloud pipelines, and machine learning to translate complex assays into actionable program milestones. He has led teams, built data science roadmaps, and customized LIMS to support TCR and mRNA programs, balancing scientific rigor with speed in fast-paced organizations. His academic work produced algorithms and genome-scale metabolic models that improved species-level taxonomic assignment and metabolic reconstructions, reflecting a rare blend of experimental and computational expertise. Based in South San Francisco, he actively advises startups on scalable genomic pipelines and infrastructure, and is comfortable stepping into new domains to deliver practical, measurable impact.
11 years of coding experience
14 years of employment as a software developer
PhD Chemical and Biological Engineering, PhD Chemical and Biological Engineering at University of Wisconsin-MadisonB.S. Chemical Engineering, B.S. Chemical Engineering at Case Western Reserve University
Github Skills (31)
taxonomy9
bioinformatics9
nextflow8
reproducible-research8
singularity8
reproducible-science8
slurm8
aws7
pipeline7
groovy7
ecosystem6
wdl6
database6
docker6
pipeline-framework6
Programming languages (6)
Github contributions (5)
celawson87/reverseEcology
Apr 2015 - May 2016
Contributions:368 commits in 1 year 1 month
McMahonLab/Scripts
Jun 2015 - Jun 2016
Contributions:48 commits, 15 PRs, 16 pushes in 11 months
workflowpythonanalysesworkflowscomputational
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