Jason A Papin (Jason Papin)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 52

Top Venues

PLoS computational biology

mSystems

bioRxiv : the preprint server for biology

mSphere

University of Virginia

University of California San Diego (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Virginia

United States

Professor :: Biomedical Engineering

Education History

University of California San Diego

United States

PHD :: Bioengineering

Publications

Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 9 (6) (2024)
Bonnie V Dougherty, Connor J Moore, Kristopher D Rawls, Matthew L Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J Saucerman, Glynis L Kolling, Anders Wallqvist, Jason A Papin
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS computational biology 20 (2) (2024)
Bonnie V Dougherty, Connor J Moore, Kristopher D Rawls, Matthew L Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J Saucerman, Glynis L Kolling, Anders Wallqvist, Jason A Papin
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS computational biology 20 (2) (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. bioRxiv : the preprint server for biology (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. bioRxiv : the preprint server for biology (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. bioRxiv : the preprint server for biology (2024)
Bonnie V Dougherty, Connor J Moore, Kristopher D Rawls, Matthew L Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J Saucerman, Glynis L Kolling, Anders Wallqvist, Jason A Papin
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS computational biology 20 (2) (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 9 (6) (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. bioRxiv : the preprint server for biology (2024)
Bonnie V Dougherty, Connor J Moore, Kristopher D Rawls, Matthew L Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J Saucerman, Glynis L Kolling, Anders Wallqvist, Jason A Papin
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS computational biology 20 (2) (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 9 (6) (2024)
Kathleen L Furtado, Lucas Plott, Matthew Markovetz, Deborah Powers, Hao Wang, David B Hill, Jason A Papin, Nancy L Allbritton, Rita Tamayo
Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. bioRxiv : the preprint server for biology (2024)
Feilim Mac Gabhann, Virginia E Pitzer, Jason A Papin
The blossoming of methods and software in computational biology. PLoS computational biology 19 (8) (2023)
Deborah A Powers, Matthew L Jenior, Glynis L Kolling, Jason A Papin
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. PLoS computational biology 19 (4) (2023)
Deborah A Powers, Matthew L Jenior, Glynis L Kolling, Jason A Papin
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. PLoS computational biology 19 (4) (2023)
Connor J Moore, Christopher P Holstege, Jason A Papin
Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses. bioRxiv : the preprint server for biology (2023)
Connor J Moore, Christopher P Holstege, Jason A Papin
Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses. PLoS computational biology 19 (8) (2023)
Deborah A Powers, Matthew L Jenior, Glynis L Kolling, Jason A Papin
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. PLoS computational biology 19 (4) (2023)
Deborah A Powers, Matthew L Jenior, Glynis L Kolling, Jason A Papin
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. PLoS computational biology 19 (4) (2023)
Connor J Moore, Christopher P Holstege, Jason A Papin
Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses. bioRxiv : the preprint server for biology (2023)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Maureen A Carey, Gregory L Medlock, Michał Stolarczyk, William A Petri, Jennifer L Guler, Jason A Papin
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PLoS computational biology 18 (2) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 8 (1) (2022)
Alexander B Smith, Matthew L Jenior, Orlaith Keenan, Jessica L Hart, Jonathan T Specker, Arwa Abbas, Paula C Rangel, Chao Di, Jamal Green, Katelyn A Bustin, Jennifer A Gaddy, Maribeth R Nicholson, Clare Laut, Brendan J Kelly, Megan L Matthews, Daniel R Evans, Daria Van Tyne, Emma E Furth, Jason A Papin, Frederic D Bushman, Jessi Erlichman, Robert N Baldassano, Michael A Silverman, Gary M Dunny, Boone M Prentice, Eric P Skaar, Joseph P Zackular
Enterococci enhance Clostridioides difficile pathogenesis. Nature 611 (7937) (2022)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 8 (1) (2022)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Matthew L Jenior, Mary E Dickenson, Jason A Papin
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae. NPJ systems biology and applications 8 (1) (2022)
Lauren Cadwallader, Feilim Mac Gabhann, Jason A Papin, Virginia E Pitzer
Advancing code sharing in the computational biology community. PLoS computational biology 18 (6) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems (2022)
Thomas J Moutinho, Benjamin C Neubert, Matthew L Jenior, Jason A Papin
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PLoS computational biology 18 (2) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 8 (1) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 8 (1) (2022)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Lillian R Dillard, Emma M Glass, Amanda L Lewis, Krystal Thomas-White, Jason A Papin
Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment. mSystems 8 (1) (2022)
Jason A Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS computational biology 18 (12) (2022)
Dawson D Payne, Alina Renz, Laura J Dunphy, Taylor Lewis, Andreas Dräger, Jason A Papin
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. NPJ systems biology and applications 7 (1) (2021)
Matthew L Jenior, Jhansi L Leslie, Deborah A Powers, Elizabeth M Garrett, Kimberly A Walker, Mary E Dickenson, William A Petri, Rita Tamayo, Jason A Papin
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. mSystems 6 (5) (2021)
Maureen A Carey, Andreas Dräger, Moritz Emanuel Beber, Jason A Papin, Bernhard O Palsson
Community standards to facilitate development and address challenges in metabolic modeling. Molecular systems biology 16 (8) (2021)
Lauren Cadwallader, Jason A Papin, Feilim Mac Gabhann, Rebecca Kirk
Collaborating with our community to increase code sharing. PLoS computational biology 17 (3) (2021)
Matthew L Jenior, Thomas J Moutinho, Bonnie V Dougherty, Jason A Papin
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS computational biology 16 (4) (2020)
Gregory L Medlock, Thomas J Moutinho, Jason A Papin
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. PLoS computational biology 16 (4) (2020)
Ana M Untaroiu, Maureen A Carey, Jennifer L Guler, Jason A Papin
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies. BMC bioinformatics 20 (1) (2019)
Anna S Blazier, Jason A Papin
Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PLoS computational biology 15 (4) (2019)
Thomas J Moutinho, John C Panagides, Matthew B Biggs, Gregory L Medlock, Glynis L Kolling, Jason A Papin
Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions. PloS one 12 (8) (2017)
Luther A Bartelt, David T Bolick, Jordi Mayneris-Perxachs, Glynis L Kolling, Gregory L Medlock, Edna I Zaenker, Jeffery Donowitz, Rose Viguna Thomas-Beckett, Allison Rogala, Ian M Carroll, Steven M Singer, Jason A Papin, Jonathan R Swann, Richard L Guerrant
Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli. PLoS pathogens 13 (7) (2017)
Matthew B Biggs, Jason A Papin
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS computational biology 13 (3) (2017)
Angela Liu, Anne M Archer, Matthew B Biggs, Jason A Papin
Growth-altering microbial interactions are responsive to chemical context. PloS one 12 (3) (2017)
Ruth Nussinov, Jason A Papin
Computing Biology. PLoS computational biology 12 (7) (2016)

Jason A Papin.css-eqlu8i{font-size:small;padding-left:4px;} (Jason Papin)

Publication Activity (10 Years)

Top Topics

Top Venues

Jason A Papin (Jason Papin)