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Sam Seaver
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KBase: the United States department of energy systems biology knowledgebase
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ...
Nature biotechnology 36 (7), 566-569, 2018
11962018
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, ...
Nucleic acids research 49 (D1), D575-D588, 2021
1742021
Plant B vitamin pathways and their compartmentation: a guide for the perplexed
S Gerdes, C Lerma-Ortiz, O Frelin, SMD Seaver, CS Henry, ...
Journal of experimental botany 63 (15), 5379-5395, 2012
1032012
Frontiers in metabolic reconstruction and modeling of plant genomes
SMD Seaver, CS Henry, AD Hanson
Journal of experimental botany 63 (6), 2247-2258, 2012
882012
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
SMD Seaver, S Gerdes, O Frelin, C Lerma-Ortiz, LMT Bradbury, R Zallot, ...
Proceedings of the National Academy of Sciences 111 (26), 9645-9650, 2014
842014
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
SMD Seaver, LMT Bradbury, O Frelin, R Zarecki, E Ruppin, AD Hanson, ...
Frontiers in plant science 6, 142, 2015
612015
Monster: inferring non-covalent interactions in macromolecular structures from atomic coordinate data
WJ Salerno, SM Seaver, BR Armstrong, I Radhakrishnan
Nucleic acids research 32 (suppl_2), W566-W568, 2004
472004
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency
SMD Seaver, C Lerma‐Ortiz, N Conrad, A Mikaili, A Sreedasyam, ...
The Plant Journal 95 (6), 1102-1113, 2018
322018
Metabolomic profiling of the nectars of Aquilegia pubescens and A. canadensis
C Noutsos, AM Perera, BJ Nikolau, SMD Seaver, DH Ware
PLoS One 10 (5), e0124501, 2015
262015
A pathway for every product? Tools to discover and design plant metabolism
JG Jeffryes, SMD Seaver, JP Faria, CS Henry
Plant Science 273, 61-70, 2018
252018
Integration of plant metabolomics data with metabolic networks: progresses and challenges
N Töpfer, SMD Seaver, A Aharoni
Plant Metabolomics: Methods and Protocols, 297-310, 2018
162018
Constructing and analyzing metabolic flux models of microbial communities
JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, SMD Seaver, ...
Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System …, 2017
152017
Micro-bias and macro-performance
SMD Seaver, AA Moreira, M Sales-Pardo, RD Malmgren, D Diermeier, ...
The European Physical Journal B 67, 369-375, 2009
102009
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.
S Kumari, V Kumar, K Beilsmith, SMD Seaver, S Canon, P Dehal, T Gu, ...
Current plant biology 28, 100229, 2021
62021
ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
JP Faria, F Liu, JN Edirisinghe, N Gupta, SMD Seaver, AP Freiburger, ...
bioRxiv, 2023.10. 04.556561, 2023
42023
Genome-scale modeling of the primary-specialized metabolism interface
K Beilsmith, CS Henry, SMD Seaver
Current Opinion in Plant Biology 68, 102244, 2022
32022
Systems-level analysis of the plasticity of the maize metabolic network reveals novel hypotheses in the nitrogen-use efficiency of maize roots
SMD Seaver
Journal of Experimental Botany 73 (1), 5-7, 2022
22022
Phenomenological model for predicting the catabolic potential of an arbitrary nutrient
SMD Seaver, M Sales-Pardo, R Guimerà, LAN Amaral
PLoS computational biology 8 (11), e1002762, 2012
22012
Social cognition in complex team networks
SMD Seaver, RD Malmgren, AA Moreira, M Sales-Pardo, D Diermeier, ...
Proceedings of the 2005 workshop on social agents, Argonne National …, 2006
22006
Improving Automated Model Reconstruction across Phylogenetically Diverse Genome-Scale Metabolic Models.
JP Faria, JN Edirisinghe, S Liu, SMD Seaver, P Weisenhorn, JG Jeffryes, ...
2017 AIChE Annual Meeting, 2017
2017
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Articles 1–20