Jason A. Papin

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 26

Top Topics

Computational Biology

Network Dynamics

Top Venues

PLoS Comput. Biol.

Comput. Biol. Medicine

Publications

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 Comput. Biol. 20 (2) (2024)
Philip J. Tubergen, Gregory L. Medlock, Anni Moore, Xiaomu Zhang, Jason A. Papin, Cristian H. Danna
A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization. PLoS Comput. Biol. 19 (12) (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 Comput. Biol. 19 (8) (2023)
Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin
The blossoming of methods and software in computational biology. PLoS Comput. Biol. 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 Comput. Biol. 19 (4) (2023)
Maureen A. Carey, Gregory L. Medlock, Michal Stolarczyk, William A. Petri Jr., Jennifer L. Guler, Jason A. Papin
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PLoS Comput. Biol. 18 (2) (2022)
Thomas J. Moutinho Jr., Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PLoS Comput. Biol. 18 (2) (2022)
Lauren Cadwallader, Feilim Mac Gabhann, Jason A. Papin, Virginia E. Pitzer
Advancing code sharing in the computational biology community. PLoS Comput. Biol. 18 (6) (2022)
Jason A. Papin, Jessica Keim-Malpass, Sana Syed
Ten simple rules for launching an academic research career. PLoS Comput. Biol. 18 (12) (2022)
Lauren Cadwallader, Jason A. Papin, Feilim Mac Gabhann, Rebecca Kirk
Collaborating with our community to increase code sharing. PLoS Comput. Biol. 17 (3) (2021)
Matthew L. Jenior, Thomas J. Moutinho Jr., Bonnie V. Dougherty, Jason A. Papin
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput. Biol. 16 (4) (2020)
Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand Rampadarath
Improving reproducibility in computational biology research. PLoS Comput. Biol. 16 (5) (2020)
Gregory L. Medlock, Thomas J. Moutinho Jr., Jason A. Papin
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. PLoS Comput. Biol. 16 (4) (2020)
Anna S. Blazier, Jason A. Papin
Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PLoS Comput. Biol. 15 (4) (2019)
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
A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools. Comput. Biol. Medicine 105 (2019)
Jason A. Papin, Feilim Mac Gabhann
Wisdom of crowds in computational biology. PLoS Comput. Biol. 15 (5) (2019)
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 Bioinform. 20 (1) (2019)
Maureen A. Carey, Jason A. Papin
Ten simple rules for biologists learning to program. PLoS Comput. Biol. 14 (1) (2018)
Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin
One thousand simple rules. PLoS Comput. Biol. 14 (12) (2018)
Matthew B. Biggs, Jason A. Papin
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput. Biol. 13 (3) (2017)
Ruth Nussinov, Jason A. Papin, Ilya A. Vakser
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13 (1) (2017)
Ruth Nussinov, Jason A. Papin
How can computation advance microbiome research? PLoS Comput. Biol. 13 (9) (2017)
Ruth Nussinov, Jason A. Papin
Computing Biology. PLoS Comput. Biol. 12 (7) (2016)
Matthew B. Biggs, Jason A. Papin
Metabolic network-guided binning of metagenomic sequence fragments. Bioinform. 32 (6) (2016)
Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns
From "What Is?" to "What Isn't?" Computational Biology. PLoS Comput. Biol. 11 (7) (2015)
Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran Jr., Jason A. Papin, Réka Albert
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. PLoS Comput. Biol. 11 (6) (2015)
Paul A. Jensen, Jason A. Papin
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinform. 30 (9) (2014)
Arvind K. Chavali, Anna S. Blazier, Jose L. Tlaxca, Paul A. Jensen, Richard D. Pearson, Jason A. Papin
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. BMC Syst. Biol. 6 (2012)
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
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. BMC Syst. Biol. 6 (2012)
Matthew A. Oberhardt, Jacek Puchalka, Vítor A. P. Martins dos Santos, Jason A. Papin
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis. PLoS Comput. Biol. 7 (3) (2011)
Paul A. Jensen, Kyla Lutz, Jason A. Papin
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst. Biol. 5 (2011)
Paul A. Jensen, Jason A. Papin
Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinform. 27 (4) (2011)
Seth B. Roberts, Jennifer L. Robichaux, Arvind K. Chavali, Patricio A. Manque, Vladimir Lee, Ana M. Lara, Jason A. Papin, Gregory A. Buck
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. BMC Syst. Biol. 3 (2009)
Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin
Transcriptional Regulatory System. PLoS Comput. Biol. 5 (6) (2009)
Brian J. Schmidt, Jason A. Papin, Michael B. Lawrence
Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation. PLoS Comput. Biol. 5 (12) (2009)
Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin
Predicting biological system objectives de novo from internal state measurements. BMC Bioinform. 9 (2008)
Kristen A. Wieghaus, Erwin P. Gianchandani, Mikell A. Paige, Milton L. Brown, Edward A. Botchwey, Jason A. Papin
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. Bioinform. 24 (20) (2008)
Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks. PLoS Comput. Biol. 4 (5) (2008)
Jacek Puchalka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos
a KT2440 Metabolic Network Facilitates Applications in Biotechnology. PLoS Comput. Biol. 4 (10) (2008)
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
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Syst. Biol. 1 (2007)
Jong Min Lee, Erwin P. Gianchandani, Jason A. Papin
Flux balance analysis in the era of metabolomics. Briefings Bioinform. 7 (2) (2006)
Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard Ø. Palsson
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. PLoS Comput. Biol. 2 (8) (2006)
Shayn M. Peirce, Thomas C. Skalak, Jason A. Papin
Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations. IBM J. Res. Dev. 50 (6) (2006)