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Author Details

Jason A Papin
University of Virginia
2002
144
45
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36272885New perspectives into the vaginal microbiome with systems biology.Trends Microbiol2023
36272885New perspectives into the vaginal microbiome with systems biology.Trends Microbiol2023
37603574Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.PLoS Comput Biol2023
37590323The blossoming of methods and software in computational biology.PLoS Comput Biol2023
37873245Model-driven characterization of functional diversity of <i>Pseudomonas aeruginosa</i> clinical isolates with broadly representative phenotypes.bioRxiv2023
37609255Systems-ecology designed bacterial consortium protects from severe <i>Clostridioides difficile</i> infection.bioRxiv2023
37279743Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.Bioinformatics2023
36511689Metabolic Network Models of the <i>Gardnerella</i> Pangenome Identify Key Interactions with the Vaginal Environment.mSystems2023
37387581Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in <i>Neisseria gonorrhoeae</i> during neutrophil co-culture.mSystems2023
36798158Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses.bioRxiv2023
36604447Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models.Sci Rep2023
37099624Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.PLoS Comput Biol2023
37590323The blossoming of methods and software in computational biology.PLoS Comput Biol2023
37609255Systems-ecology designed bacterial consortium protects from severe <i>Clostridioides difficile</i> infection.bioRxiv2023
37873245Model-driven characterization of functional diversity of <i>Pseudomonas aeruginosa</i> clinical isolates with broadly representative phenotypes.bioRxiv2023
37603574Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.PLoS Comput Biol2023
37387581Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in <i>Neisseria gonorrhoeae</i> during neutrophil co-culture.mSystems2023
37279743Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.Bioinformatics2023
37099624Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.PLoS Comput Biol2023
36511689Metabolic Network Models of the <i>Gardnerella</i> Pangenome Identify Key Interactions with the Vaginal Environment.mSystems2023
36604447Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models.Sci Rep2023
36798158Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses.bioRxiv2023
34839237Computational approaches to understanding Clostridioides difficile metabolism and virulence.Curr Opin Microbiol2022
36307414Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae.NPJ Syst Biol Appl2022
35653366Advancing code sharing in the computational biology community.PLoS Comput Biol2022
35819731Leveraging metabolic modeling to identify functional metabolic alterations associated with COVID-19 disease severity.Metabolomics2022
35934064Histone Deacetylase Inhibition by Gut Microbe-Generated Short-Chain Fatty Acids Entrains Intestinal Epithelial Circadian Rhythms.Gastroenterology2022
36385534Enterococci enhance Clostridioides difficile pathogenesis.Nature2022
36520710Ten simple rules for launching an academic research career.PLoS Comput Biol2022
36549272How can systems approaches help us understand and treat infectious disease?Cell Syst2022
34839237Computational approaches to understanding Clostridioides difficile metabolism and virulence.Curr Opin Microbiol2022
35130271Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.PLoS Comput Biol2022
35285019Fecal sphingolipids predict parenteral nutrition-associated cholestasis in the neonatal intensive care unit.JPEN J Parenter Enteral Nutr2022
35196325Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.PLoS Comput Biol2022
35653366Advancing code sharing in the computational biology community.PLoS Comput Biol2022
35819731Leveraging metabolic modeling to identify functional metabolic alterations associated with COVID-19 disease severity.Metabolomics2022
36520710Ten simple rules for launching an academic research career.PLoS Comput Biol2022
36549272How can systems approaches help us understand and treat infectious disease?Cell Syst2022
35934064Histone Deacetylase Inhibition by Gut Microbe-Generated Short-Chain Fatty Acids Entrains Intestinal Epithelial Circadian Rhythms.Gastroenterology2022
36307414Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae.NPJ Syst Biol Appl2022
36385534Enterococci enhance Clostridioides difficile pathogenesis.Nature2022
35130271Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.PLoS Comput Biol2022
35285019Fecal sphingolipids predict parenteral nutrition-associated cholestasis in the neonatal intensive care unit.JPEN J Parenter Enteral Nutr2022
35196325Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.PLoS Comput Biol2022
33387578Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model.Toxicol Appl Pharmacol2021
34125127Mechanistic models of microbial community metabolism.Mol Omics2021
33691118Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model.Cell Rep2021
33684930Megasphaera in the Stool Microbiota Is Negatively Associated With Diarrheal Cryptosporidiosis.Clin Infect Dis2021
33784294Collaborating with our community to increase code sharing.PLoS Comput Biol2021
34156287Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus.mSystems2021
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Collaborators

Bernhard O Palsson
University of California San Diego
Co-authored papers 21
Nathan D Price
Institute for Systems Biology
Co-authored papers 14
Arvind K Chavali
Carnegie Institution for Science
Co-authored papers 11
Matthew L Jenior
University of Virginia
Co-authored papers 10
Edik M Blais
University of Virginia
Co-authored papers 7
Kalyan C Vinnakota
Gilbert Family Foundation
Co-authored papers 6
William A Petri
University of Virginia
Co-authored papers 5
Ruth Nussinov
Sackler School of Medicine, Tel Aviv University
Co-authored papers 4
Jens Nielsen
Chalmers University of Technology
Co-authored papers 4
Nathan E Lewis
University of California San Diego
Co-authored papers 3
John T Parsons
The School of Medicine, University of Virginia
Co-authored papers 3
Jeffrey J Saucerman
University of Virginia
Co-authored papers 3
Kevin A Janes
University of Virginia
Co-authored papers 2
David L Brautigan
Co-authored papers 2
Shankar Subramaniam
University of California
Co-authored papers 2
Jhansi L Leslie
University of Virginia
Co-authored papers 2
Adil Mardinoglu
Royal Institute of Technology Science for Life Laboratory Stockholm Sweden.
Co-authored papers 2
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 2
Jos?? P Faria
Argonne National Laboratory
Co-authored papers 2
Christopher S Henry
Argonne National Laboratory
Co-authored papers 2
Janaka N Edirisinghe
Computation Institute, University of Chicago
Co-authored papers 2
Jamey D Young
Co-authored papers 2
Jason H Yang
Rutgers New Jersey Medical School
Co-authored papers 2
Nicholas E Sherman
University of Virginia
Co-authored papers 2
Cheng Zhang
KTH-Royal Institute of Technology
Co-authored papers 2
Ani Manichaikul
Co-authored papers 2
Jae K Lee
Co-authored papers 2
Haiyuan Yu
Weill Institute for Cell and Molecular Biology, Cornell University
Co-authored papers 2
Sunjae Lee
Gwangju Institute of Science and Technology
Co-authored papers 2
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