Jason A. Papin

48 papers Journal 48
YearRankTypeTitle / Venue / Authors
2025 J jnl
Ten simple rules for developing a training program.
PLoS Comput. Biol.
Leanna B. Blevins, Amy M. Harrigan, Kevin A. Janes, Jason A. Papin
2025 J jnl
Ten simple rules for good model-sharing practices.
PLoS Comput. Biol.
Ismael Kherroubi Garcia, Christopher Erdmann, Sandra Gesing, C. Michael Barton, Lauren Cadwallader, Geerten M. Hengeveld, Christine R. Kirkpatrick, Kathryn Knight, Carsten Lemmen, Rebecca Ringuette, Qing Zhan, Melissa Harrison, Feilim Mac Gabhann, Natalie Meyers, Cailean Osborne, Charlotte Till, Paul R. Brenner, Matt Buys, Min Chen, Allen Lee, Jason A. Papin, Yuhan Rao
2024 J jnl
Celebrating a body of work.
PLoS Comput. Biol.
Jason A. Papin, Feilim Mac Gabhann, Virginia E. Pitzer
2024 J jnl
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism.
PLoS Comput. Biol.
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
2024 J jnl
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment.
PLoS Comput. Biol.
Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce-Cottler, Jason A. Papin, Roseanne M. Ford
2023 J jnl
A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization.
PLoS Comput. Biol.
Philip J. Tubergen, Gregory L. Medlock, Anni Moore, Xiaomu Zhang, Jason A. Papin, Cristian H. Danna
2023 J jnl
Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.
PLoS Comput. Biol.
Connor J. Moore, Christopher P. Holstege, Jason A. Papin
2023 J jnl
Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies.
PLoS Comput. Biol.
Deborah A. Powers, Matthew L. Jenior, Glynis L. Kolling, Jason A. Papin
2023 J jnl
Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.
Bioinform.
Matthew L. Jenior, Emma M. Glass, Jason A. Papin
2023 J jnl
The blossoming of methods and software in computational biology.
PLoS Comput. Biol.
Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin
2022 J jnl
Advancing code sharing in the computational biology community.
PLoS Comput. Biol.
Lauren Cadwallader, Feilim Mac Gabhann, Jason A. Papin, Virginia E. Pitzer
2022 J jnl
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.
PLoS Comput. Biol.
Maureen A. Carey, Gregory L. Medlock, Michal Stolarczyk, William A. Petri Jr., Jennifer L. Guler, Jason A. Papin
2022 J jnl
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions.
PLoS Comput. Biol.
Thomas J. Moutinho Jr., Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin
2022 J jnl
Ten simple rules for launching an academic research career.
PLoS Comput. Biol.
Jason A. Papin, Jessica Keim-Malpass, Sana Syed
2021 J jnl
Collaborating with our community to increase code sharing.
PLoS Comput. Biol.
Lauren Cadwallader, Jason A. Papin, Feilim Mac Gabhann, Rebecca Kirk
2020 J jnl
Improving reproducibility in computational biology research.
PLoS Comput. Biol.
Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath
2020 J jnl
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions.
PLoS Comput. Biol.
Gregory L. Medlock, Thomas J. Moutinho Jr., Jason A. Papin
2020 J jnl
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments.
PLoS Comput. Biol.
Matthew L. Jenior, Thomas J. Moutinho Jr., Bonnie V. Dougherty, Jason A. Papin
2019 J jnl
A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.
Comput. Biol. Medicine
Kristopher D. Rawls, Bonnie V. Dougherty, Edik M. Blais, Ethan Stancliffe, Glynis L. Kolling, Kalyan C. Vinnakota, Venkat R. Pannala, Anders Wallqvist, Jason A. Papin
2019 J jnl
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies.
BMC Bioinform.
Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler, Jason A. Papin
2019 J jnl
Reconciling high-throughput gene essentiality data with metabolic network reconstructions.
PLoS Comput. Biol.
Anna S. Blazier, Jason A. Papin
2019 J jnl
Wisdom of crowds in computational biology.
PLoS Comput. Biol.
Jason A. Papin, Feilim Mac Gabhann
2018 J jnl
One thousand simple rules.
PLoS Comput. Biol.
Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin
2018 J jnl
Ten simple rules for biologists learning to program.
PLoS Comput. Biol.
Maureen A. Carey, Jason A. Papin
2017 J jnl
Computing the Dynamic Supramolecular Structural Proteome.
PLoS Comput. Biol.
Ruth Nussinov, Jason A. Papin, Ilya A. Vakser
2017 J jnl
How can computation advance microbiome research?
PLoS Comput. Biol.
Ruth Nussinov, Jason A. Papin
2017 J jnl
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.
PLoS Comput. Biol.
Matthew B. Biggs, Jason A. Papin
2016 J jnl
Computing Biology.
PLoS Comput. Biol.
Ruth Nussinov, Jason A. Papin
2016 J jnl
Metabolic network-guided binning of metagenomic sequence fragments.
Bioinform.
Matthew B. Biggs, Jason A. Papin
2015 J jnl
From "What Is?" to "What Isn't?" Computational Biology.
PLoS Comput. Biol.
Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns
2015 J jnl
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome.
PLoS Comput. Biol.
Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran Jr., Jason A. Papin, Réka Albert
2014 J jnl
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Bioinform.
Paul A. Jensen, Jason A. Papin
2012 J jnl
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.
BMC Syst. Biol.
Arvind K. Chavali, Anna S. Blazier, Jose L. Tlaxca, Paul A. Jensen, Richard D. Pearson, Jason A. Papin
2012 J jnl
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control.
BMC Syst. Biol.
Kevin M. D'Auria, Gina M. Donato, Mary C. Gray, Glynis L. Kolling, Cirle A. Warren, Lauren M. Cave, Michael D. Solga, Joanne A. Lannigan, Jason A. Papin, Erik L. Hewlett
2011 J jnl
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Bioinform.
Paul A. Jensen, Jason A. Papin
2011 J jnl
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis.
PLoS Comput. Biol.
Matthew A. Oberhardt, Jacek Puchalka, Vítor A. P. Martins dos Santos, Jason A. Papin
2011 J jnl
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
BMC Syst. Biol.
Paul A. Jensen, Kyla Lutz, Jason A. Papin
2009 J jnl
Functional States of the Genome-Scale
PLoS Comput. Biol.
Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin
2009 J jnl
Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation.
PLoS Comput. Biol.
Brian J. Schmidt, Jason A. Papin, Michael B. Lawrence
2009 J jnl
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi.
BMC Syst. Biol.
Seth B. Roberts, Jennifer L. Robichaux, Arvind K. Chavali, Patricio A. Manque, Vladimir Lee, Ana M. Lara, Jason A. Papin, Gregory A. Buck
2008 J jnl
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks.
PLoS Comput. Biol.
Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin
2008 J jnl
Genome-Scale Reconstruction and Analysis of the
PLoS Comput. Biol.
Jacek Puchalka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos
2008 J jnl
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule.
Bioinform.
Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, Jason A. Papin
2008 J jnl
Predicting biological system objectives de novo from internal state measurements.
BMC Bioinform.
Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin
2007 J jnl
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior.
BMC Syst. Biol.
Scott H. Robertson, Chris K. Smith, Anna L. Langhans, Sara E. McLinden, Matthew A. Oberhardt, Karoly R. Jakab, Bette Dzamba, Douglas W. DeSimone, Jason A. Papin, Shayn M. Peirce
2006 J jnl
Flux balance analysis in the era of metabolomics.
Briefings Bioinform.
Jong Min Lee, Erwin P. Gianchandani, Jason A. Papin
2006 J jnl
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems.
PLoS Comput. Biol.
Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson
2006 J jnl
Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations.
IBM J. Res. Dev.
Shayn M. Peirce, Thomas C. Skalak, Jason A. Papin