Computational Biologist · Oak Ridge National Laboratory
I’m a computational biologist. Most of my work is in microbial ecology, and lately on data infrastructure and AI tooling for large biological datasets.
Currently working on the Microbial Discovery Forge, an AI co-scientist.
Interests
How microbial communities are put together, and what holds them there.
Lakehouses and pipelines for genomic and trait data.
Agents and tooling for working with large biological datasets.
Predicting traits from sequence.
Work
Scientific AI
An AI co-scientist and research observatory at KBase. It connects an agent to the BER data lakehouse through a set of reusable skills. Part of the BERIL project.
I built it and am its main contributor.
agent
lakehouse
Data infrastructure
A genotype-to-phenotype data lakehouse at Oak Ridge, holding data from GPTgp, PMI and other projects behind one queryable model.
I work on G2PAI.
one store
Not a public repository.
Data infrastructure
A Nextflow pipeline for annotating bacterial genomes and predicting traits from them: quality control, then gene annotation, then several annotation tools run in parallel.
I built it.
Not a public repository.
Machine learning
Predicting what a bacterium can do from its genome sequence.
I lead this work.
Microbial ecology
Interaction scores computed from pairs of genome-scale metabolic models, and a classifier that turns them into a predicted ecological outcome.
I work on CommScores with Andrew Freiburger and Chris Henry.