Computational biologist — I build the open-source tools a field runs on. Metabolic modeling · biochemistry databases · multi-omics · physics-informed ML.
For over a decade I've built the reference resources the plant- and microbial-systems-biology community uses to reconstruct, compare, and analyze genome-scale metabolic models — ModelSEED Biochemistry, PlantSEED, and the plant apps in DOE's KBase. I'm now bringing machine learning to metabolic simulation: physics-informed, mass-balance-constrained optimization that predicts metabolic fluxes from transcriptomics.
Computational Scientist at Argonne National Laboratory (Data Science & Learning Division) and Senior Scientist at-large, University of Chicago. Wet-lab-literate biochemistry → genome-scale modeling → ML → reproducible scientific approaches.
📄 Curriculum vitae (PDF) · 📍 Chicago, IL area · ✉️ samseaver@gmail.com
Community infrastructure (maintained in their project orgs) — ModelSEED, the reference biochemistry database; PlantSEED, automated plant-metabolism annotation & genome-scale reconstruction; and the plant apps in DOE's KBase.
New direction — BioFlux: a physics-informed, mass-balance-constrained solver that predicts metabolic fluxes from 'omics data, used to simulate the iron-deficiency response in plant plastids. 📄 Preprint (bioRxiv 2026, senior author).
- ModelSEED Biochemistry Database — Nucleic Acids Research (2021) · first author · 10.1093/nar/gkaa746
- KBase: DOE Systems Biology Knowledgebase — Nature Biotechnology (2018) · co-author · 10.1038/nbt.4163
- PlantSEED — PNAS (2014) · first author · 10.1073/pnas.1401329111
- Neural-mechanistic hybrid for plastid iron deficiency — bioRxiv (2026) · senior author · 10.1101/2025.06.10.658179
~2,914 citations · h-index 13 · i10-index 16 — full list on Google Scholar.
Python · R · genome-scale / constraint-based modeling (COBRA / FBA) · cheminformatics (InChI / SMILES) · thermodynamics · comparative genomics ·
multi-omics integration (transcriptomics, metabolomics, proteomics) · reproducible pipelines