Jason A. Papin
Orcid: 0000-0002-2769-5805
According to our database1,
Jason A. Papin
authored at least 43 papers
between 2006 and 2024.
Collaborative distances:
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Bibliography
2024
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism.
PLoS Comput. Biol., February, 2024
2023
A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization.
PLoS Comput. Biol., December, 2023
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.
PLoS Comput. Biol., 2023
Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.
PLoS Comput. Biol., 2023
PLoS Comput. Biol., 2023
2022
PLoS Comput. Biol., December, 2022
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.
PLoS Comput. Biol., 2022
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.
PLoS Comput. Biol., 2022
PLoS Comput. Biol., 2022
2021
2020
PLoS Comput. Biol., 2020
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions.
PLoS Comput. Biol., 2020
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments.
PLoS Comput. Biol., 2020
2019
Reconciling high-throughput gene essentiality data with metabolic network reconstructions.
PLoS Comput. Biol., 2019
A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.
Comput. Biol. Medicine, 2019
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies.
BMC Bioinform., 2019
2018
2017
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.
PLoS Comput. Biol., 2017
2016
2015
PLoS Comput. Biol., 2015
2014
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Bioinform., 2014
2012
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control.
BMC Syst. Biol., 2012
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.
BMC Syst. Biol., 2012
2011
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis.
PLoS Comput. Biol., 2011
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
BMC Syst. Biol., 2011
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Bioinform., 2011
2009
Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation.
PLoS Comput. Biol., 2009
Functional States of the Genome-Scale <i>Escherichia Coli</i> Transcriptional Regulatory System.
PLoS Comput. Biol., 2009
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi.
BMC Syst. Biol., 2009
2008
Genome-Scale Reconstruction and Analysis of the <i>Pseudomonas putid</i>a KT2440 Metabolic Network Facilitates Applications in Biotechnology.
PLoS Comput. Biol., 2008
PLoS Comput. Biol., 2008
BMC Bioinform., 2008
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule.
Bioinform., 2008
2007
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior.
BMC Syst. Biol., 2007
2006
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
PLoS Comput. Biol., 2006
Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations.
IBM J. Res. Dev., 2006