publications | Samuel M. D. Seaver

2026

JMB

KBase: Open-source platform for collaborative biological data analysis and publication

Elisha M. Wood-Charlson, Christopher S. Henry, Paramvir S. Dehal, and 4 more authors

Journal of Molecular Biology, 2026

@article{woodcharlson2026kbase,
  title = {KBase: Open-source platform for collaborative biological data analysis and publication},
  author = {Wood-Charlson, Elisha M. and Henry, Christopher S. and Dehal, Paramvir S. and others and Seaver, Sam and others and Arkin, Adam P.},
  journal = {Journal of Molecular Biology},
  volume = {438},
  number = {18},
  pages = {169676},
  year = {2026},
  doi = {10.1016/j.jmb.2026.169676},
}

2025

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},
}

Plant Biol.

Time-series multi-omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation

Ankita Mishra, Aparajita Bhat, Sunita Kumari, and 4 more authors

Plant Biology (Stuttgart), 2025

Bib HTML

@article{mishra2025sorghum,
  title = {Time-series multi-omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation},
  author = {Mishra, Ankita and Bhat, Aparajita and Kumari, Sunita and others and Seaver, Samuel and others and Paape, Tim},
  journal = {Plant Biology (Stuttgart)},
  year = {2025},
}

2023

bioRxiv

ModelSEED v2: High-throughput genome-scale metabolic model reconstruction

José P. Faria, Filipe Liu, Janaka N. Edirisinghe, and 1 more author

bioRxiv, 2023

Bib

@article{faria2023modelseed2,
  title = {ModelSEED v2: High-throughput genome-scale metabolic model reconstruction},
  author = {Faria, Jos{\'e} P. and Liu, Filipe and Edirisinghe, Janaka N. and others},
  journal = {bioRxiv},
  year = {2023},
}

2022

Curr. Opin. Plant Biol.

Genome-scale modeling of the primary–specialized metabolism interface

Kathleen Beilsmith, Christopher S. Henry, and Samuel M. D. Seaver

Current Opinion in Plant Biology, 2022

Bib

@article{beilsmith2022interface,
  title = {Genome-scale modeling of the primary--specialized metabolism interface},
  author = {Beilsmith, Kathleen and Henry, Christopher S. and Seaver, Samuel M. D.},
  journal = {Current Opinion in Plant Biology},
  volume = {68},
  year = {2022},
}

J. Exp. Bot.

Systems-level analysis of the plasticity of the maize metabolic network

Samuel M. D. Seaver

Journal of Experimental Botany, 2022

Bib

@article{seaver2022maizeplasticity,
  title = {Systems-level analysis of the plasticity of the maize metabolic network},
  author = {Seaver, Samuel M. D.},
  journal = {Journal of Experimental Botany},
  volume = {73},
  number = {1},
  year = {2022},
}

2021

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},
}

Curr. Plant Biol.

A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum

Sunita Kumari, Vivek Kumar, Kathleen Beilsmith, and 3 more authors

Current Plant Biology, 2021

Bib

@article{kumari2021sorghum,
  title = {A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum},
  author = {Kumari, Sunita and Kumar, Vivek and Beilsmith, Kathleen and Seaver, Samuel M. D. and others and Ware, Doreen},
  journal = {Current Plant Biology},
  volume = {28},
  pages = {100229},
  year = {2021},
}

2018

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},
}

Plant Sci.

A pathway for every product? Tools to discover and design plant metabolism

James G. Jeffryes, Samuel M. D. Seaver, José P. Faria, and 1 more author

Plant Science, 2018

Bib

@article{jeffryes2018pathway,
  title = {A pathway for every product? Tools to discover and design plant metabolism},
  author = {Jeffryes, James G. and Seaver, Samuel M. D. and Faria, Jos{\'e} P. and Henry, Christopher S.},
  journal = {Plant Science},
  volume = {273},
  year = {2018},
}

Methods

Integration of plant metabolomics data with metabolic networks: progresses and challenges

Nadine Töpfer, Samuel M. D. Seaver, and Asaph Aharoni

In Plant Metabolomics: Methods and Protocols, 2018

Bib

@incollection{topfer2018integration,
  title = {Integration of plant metabolomics data with metabolic networks: progresses and challenges},
  author = {T{\"o}pfer, Nadine and Seaver, Samuel M. D. and Aharoni, Asaph},
  booktitle = {Plant Metabolomics: Methods and Protocols},
  year = {2018},
}

2015

Front. Plant Sci.

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

Samuel M. D. Seaver, Louis M. T. Bradbury, Océane Frelin, and 1 more author

Frontiers in Plant Science, 2015

Bib

@article{seaver2015maize,
  title = {Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm},
  author = {Seaver, Samuel M. D. and Bradbury, Louis M. T. and Frelin, Oc{\'e}ane and others},
  journal = {Frontiers in Plant Science},
  volume = {6},
  year = {2015},
}

2014

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},
}

2012

J. Exp. Bot.

Plant B vitamin pathways and their compartmentation: a guide for the perplexed

Svetlana Gerdes, Claudia Lerma-Ortiz, Océane Frelin, and 3 more authors

Journal of Experimental Botany, 2012

Bib

@article{gerdes2012bvitamin,
  title = {Plant B vitamin pathways and their compartmentation: a guide for the perplexed},
  author = {Gerdes, Svetlana and Lerma-Ortiz, Claudia and Frelin, Oc{\'e}ane and Seaver, Samuel M. D. and others and Henry, Christopher S.},
  journal = {Journal of Experimental Botany},
  volume = {63},
  number = {15},
  year = {2012},
}

J. Exp. Bot.

Frontiers in metabolic reconstruction and modeling of plant genomes

Samuel M. D. Seaver, Christopher S. Henry, and Andrew D. Hanson

Journal of Experimental Botany, 2012

Bib

@article{seaver2012frontiers,
  title = {Frontiers in metabolic reconstruction and modeling of plant genomes},
  author = {Seaver, Samuel M. D. and Henry, Christopher S. and Hanson, Andrew D.},
  journal = {Journal of Experimental Botany},
  volume = {63},
  number = {6},
  pages = {2247--2258},
  year = {2012},
}

PLoS Comput. Biol.

Phenomenological model for predicting the catabolic potential of an arbitrary nutrient

Samuel M. Seaver, Marta Sales-Pardo, Roger Guimerà, and 1 more author

PLoS Computational Biology, 2012

Bib HTML

@article{seaver2012catabolic,
  title = {Phenomenological model for predicting the catabolic potential of an arbitrary nutrient},
  author = {Seaver, Samuel M. and Sales-Pardo, Marta and Guimer{\`a}, Roger and Amaral, Lu{\'i}s A. N.},
  journal = {PLoS Computational Biology},
  volume = {8},
  number = {11},
  pages = {e1002762},
  year = {2012},
}

2011

PhD

Modeling of gene regulation and metabolism in microbial organisms

Samuel M. D. Seaver

Northwestern University, 2011

Bib

@phdthesis{seaver2011thesis,
  title = {Modeling of gene regulation and metabolism in microbial organisms},
  author = {Seaver, Samuel M. D.},
  school = {Northwestern University},
  year = {2011},
}

2009

Eur. Phys. J. B

Micro-bias and macro-performance

Samuel M. D. Seaver, André A. Moreira, Marta Sales-Pardo, and 3 more authors

The European Physical Journal B, 2009

Bib

@article{seaver2009microbias,
  title = {Micro-bias and macro-performance},
  author = {Seaver, Samuel M. D. and Moreira, Andr{\'e} A. and Sales-Pardo, Marta and Malmgren, Rasmus D. and Diermeier, Daniel and others},
  journal = {The European Physical Journal B},
  volume = {67},
  number = {3},
  pages = {369--375},
  year = {2009},
}

2004

NAR

MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data

William J. Salerno, Samuel M. Seaver, Brent R. Armstrong, and 1 more author

Nucleic Acids Research, 2004

Bib HTML

@article{salerno2004monster,
  title = {MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data},
  author = {Salerno, William J. and Seaver, Samuel M. and Armstrong, Brent R. and Radhakrishnan, Ishwar},
  journal = {Nucleic Acids Research},
  volume = {32},
  number = {Web Server issue},
  pages = {W566--W568},
  year = {2004},
}