Samuel M. D. Seaver

Chicago, IL area

open to remote

I’m a computational biologist who connects across systems — integrating data and tools at every scale to turn complex biology into solvable problems. For over a decade I’ve built the open-source metabolic-modeling resources the plant- and microbial-systems-biology community relies on: the ModelSEED Biochemistry Database and PlantSEED, plus the plant apps and data integration in DOE’s KBase as a core member of its plants team.

Today I work at the interface of data and modeling, utilizing the appropriate tools — statistics and linear modeling, comparative genomics, network and graph analysis, constraint-based metabolic modeling, and increasingly machine learning — to find signals in multi-omics data and turn them into predictions. I’ve handled different sources of data that span phylogeny (from microbes and fungi through crops and their wild relatives), time (diurnal cycles and stress time-courses), tissues, and experimental conditions — examining the biology at their intersection. I currently work as a Computational Scientist at Argonne National Laboratory and Senior Scientist at-large at the University of Chicago.

My path has run through four phases, each compounding the last: quantitative & structural foundations (UK training, Northwestern PhD in complex systems) → plant & microbial metabolic modeling → community-scale open-source resources (PlantSEED, ModelSEED) and a core role on the KBase plants team → and now multi-omics- and ML-driven prediction. I’m looking for my next role — national lab or biotech — where that work can have the most mission-driven impact.

See my publications.

selected publications

bioRxiv

Simulating Iron Deficiency in Plant Plastidial Metabolism With a Flexible Neural-Mechanistic Hybrid Approach

Salim El Alaoui, Christopher S. Henry, Crysten E. Blaby-Haas, and 3 more authors

bioRxiv, 2025

DOI Bib HTML

@article{elalaoui2025pinn,
  title = {Simulating Iron Deficiency in Plant Plastidial Metabolism With a Flexible Neural-Mechanistic Hybrid Approach},
  author = {El Alaoui, Salim and Henry, Christopher S. and Blaby-Haas, Crysten E. and Paape, Tim and Xie, Meng and Seaver, Samuel M.},
  journal = {bioRxiv},
  year = {2025},
  doi = {10.1101/2025.06.10.658179},
}

NAR

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, and 5 more authors

Nucleic Acids Research, 2021

Bib HTML

@article{seaver2021modelseed,
  title = {The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes},
  author = {Seaver, Samuel M. D. and Liu, Filipe and Zhang, Qizhi and Jeffryes, James and Faria, Jos{\'e} P. and Edirisinghe, Janaka N. and others and Henry, Christopher S.},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {D1},
  pages = {D575--D588},
  year = {2021},
}

Nat. Biotechnol.

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P. Arkin, Robert W. Cottingham, Christopher S. Henry, and 3 more authors

Nature Biotechnology, 2018

Bib HTML

@article{arkin2018kbase,
  title = {KBase: The United States Department of Energy Systems Biology Knowledgebase},
  author = {Arkin, Adam P. and Cottingham, Robert W. and Henry, Christopher S. and others and Seaver, Samuel M. D. and others},
  journal = {Nature Biotechnology},
  volume = {36},
  number = {7},
  pages = {566--569},
  year = {2018},
}

Plant J

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

Samuel M. D. Seaver, Claudia Lerma-Ortiz, Neal Conrad, and 1 more author

The Plant Journal, 2018

Bib

@article{seaver2018plantseed,
  title = {PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency},
  author = {Seaver, Samuel M. D. and Lerma-Ortiz, Claudia and Conrad, Neal and others},
  journal = {The Plant Journal},
  volume = {95},
  number = {6},
  year = {2018},
}

PNAS

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Samuel M. D. Seaver, Svetlana Gerdes, Océane Frelin, and 4 more authors

Proceedings of the National Academy of Sciences, 2014

Bib HTML

@article{seaver2014plantseed,
  title = {High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource},
  author = {Seaver, Samuel M. D. and Gerdes, Svetlana and Frelin, Oc{\'e}ane and Lerma-Ortiz, Claudia and others and Hanson, Andrew D. and Henry, Christopher S.},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  number = {26},
  pages = {9645--9650},
  year = {2014},
}