Flux balance analysis in the era of metabolomics. - Jong Min Lee 002; Erwin P. Gianchandani; Jason A. Papin (Briefings Bioinform., 2006)

Multiscale biosystems integration: Coupling intracellular network analysis with tissue-patterning simulations. - Shayn M. Peirce; Thomas C. Skalak; Jason A. Papin (IBM J. Res. Dev., 2006)

Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. - Erwin P. Gianchandani; Jason A. Papin; Nathan D. Price 001; Andrew R. Joyce; Bernhard Ø. Palsson (PLoS Comput. Biol., 2006)

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. - 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 (BMC Syst. Biol., 2007)

Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. - Kristen A. Wieghaus; Erwin P. Gianchandani; Mikell A. Paige; Milton L. Brown; Edward A. Botchwey; Jason A. Papin (Bioinform., 2008)

Predicting biological system objectives de novo from internal state measurements. - Erwin P. Gianchandani; Matthew A. Oberhardt; Anthony P. Burgard; Costas D. Maranas; Jason A. Papin (BMC Bioinform., 2008)

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks. - Jong Min Lee 002; Erwin P. Gianchandani; James A. Eddy; Jason A. Papin (PLoS Comput. Biol., 2008)

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology. - Jacek Puchalka; Matthew A. Oberhardt; Miguel Godinho; Agata Bielecka; Daniela Regenhardt; Kenneth N. Timmis; Jason A. Papin; Vítor A. P. Martins dos Santos (PLoS Comput. Biol., 2008)

Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. - Seth B. Roberts; Jennifer L. Robichaux; Arvind K. Chavali; Patricio A. Manque; Vladimir Lee; Ana M. Lara; Jason A. Papin; Gregory A. Buck (BMC Syst. Biol., 2009)

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System. - Erwin P. Gianchandani; Andrew R. Joyce; Bernhard O. Palsson; Jason A. Papin (PLoS Comput. Biol., 2009)

Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation. - Brian J. Schmidt; Jason A. Papin; Michael B. Lawrence (PLoS Comput. Biol., 2009)

Functional integration of a metabolic network model and expression data without arbitrary thresholding. - Paul A. Jensen; Jason A. Papin (Bioinform., 2011)

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. - Paul A. Jensen; Kyla Lutz; Jason A. Papin (BMC Syst. Biol., 2011)

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis. - Matthew A. Oberhardt; Jacek Puchalka; Vítor A. P. Martins dos Santos; Jason A. Papin (PLoS Comput. Biol., 2011)

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. - Arvind K. Chavali; Anna S. Blazier; Jose L. Tlaxca; Paul A. Jensen; Richard D. Pearson; Jason A. Papin (BMC Syst. Biol., 2012)

Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. - 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 (BMC Syst. Biol., 2012)

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. - Paul A. Jensen; Jason A. Papin (Bioinform., 2014)

From "What Is?" to "What Isn't?" Computational Biology. - Ruth Nussinov; Sebastian Bonhoeffer; Jason A. Papin; Olaf Sporns (PLoS Comput. Biol., 2015)

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. - Steven N. Steinway; Matthew B. Biggs; Thomas P. Loughran Jr.; Jason A. Papin; Réka Albert (PLoS Comput. Biol., 2015)

Metabolic network-guided binning of metagenomic sequence fragments. - Matthew B. Biggs; Jason A. Papin (Bioinform., 2016)

Computing Biology. - Ruth Nussinov; Jason A. Papin (PLoS Comput. Biol., 2016)

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. - Matthew B. Biggs; Jason A. Papin (PLoS Comput. Biol., 2017)

How can computation advance microbiome research? - Ruth Nussinov; Jason A. Papin (PLoS Comput. Biol., 2017)

Computing the Dynamic Supramolecular Structural Proteome. - Ruth Nussinov; Jason A. Papin; Ilya A. Vakser (PLoS Comput. Biol., 2017)

One thousand simple rules. - Philip E. Bourne; Fran Lewitter; Scott Markel; Jason A. Papin (PLoS Comput. Biol., 2018)

Ten simple rules for biologists learning to program. - Maureen A. Carey; Jason A. Papin (PLoS Comput. Biol., 2018)

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies. - Ana M. Untaroiu; Maureen A. Carey; Jennifer L. Guler; Jason A. Papin (BMC Bioinform., 2019)

A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools. - 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 (Comput. Biol. Medicine, 2019)

Reconciling high-throughput gene essentiality data with metabolic network reconstructions. - Anna S. Blazier; Jason A. Papin (PLoS Comput. Biol., 2019)

Wisdom of crowds in computational biology. - Jason A. Papin; Feilim Mac Gabhann (PLoS Comput. Biol., 2019)

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. - Matthew L. Jenior; Thomas J. Moutinho Jr.; Bonnie V. Dougherty; Jason A. Papin (PLoS Comput. Biol., 2020)

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. - Gregory L. Medlock; Thomas J. Moutinho Jr.; Jason A. Papin (PLoS Comput. Biol., 2020)

Improving reproducibility in computational biology research. - Jason A. Papin; Feilim Mac Gabhann; Herbert M. Sauro; David P. Nickerson; Anand K. Rampadarath (PLoS Comput. Biol., 2020)

Collaborating with our community to increase code sharing. - Lauren Cadwallader; Jason A. Papin; Feilim Mac Gabhann; Rebecca Kirk (PLoS Comput. Biol., 2021)

Advancing code sharing in the computational biology community. - Lauren Cadwallader; Feilim Mac Gabhann; Jason A. Papin; Virginia E. Pitzer (PLoS Comput. Biol., 2022)

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. - Maureen A. Carey; Gregory L. Medlock; Michal Stolarczyk; William A. Petri Jr.; Jennifer L. Guler; Jason A. Papin (PLoS Comput. Biol., 2022)

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. - Thomas J. Moutinho Jr.; Benjamin C. Neubert; Matthew L. Jenior; Jason A. Papin (PLoS Comput. Biol., 2022)

Ten simple rules for launching an academic research career. - Jason A. Papin; Jessica Keim-Malpass; Sana Syed (PLoS Comput. Biol., 2022)

The blossoming of methods and software in computational biology. - Feilim Mac Gabhann; Virginia E. Pitzer; Jason A. Papin (PLoS Comput. Biol., 2023)

Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses. - Connor J. Moore; Christopher P. Holstege; Jason A. Papin (PLoS Comput. Biol., 2023)

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. - Deborah A. Powers; Matthew L. Jenior; Glynis L. Kolling; Jason A. Papin (PLoS Comput. Biol., 2023)

A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization. - Philip J. Tubergen; Gregory L. Medlock; Anni Moore; Xiaomu Zhang; Jason A. Papin; Cristian H. Danna (PLoS Comput. Biol., 2023)

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. - Tracy J. Kuper; Mohammad Mazharul Islam; Shayn M. Peirce-Cottler; Jason A. Papin; Roseanne M. Ford (PLoS Comput. Biol., 2024)

Celebrating a body of work. - Jason A. Papin; Feilim Mac Gabhann; Virginia E. Pitzer (PLoS Comput. Biol., 2024)

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. - 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 (PLoS Comput. Biol., 2024)

Ten simple rules for good model-sharing practices. - Ismael Kherroubi Garcia; Christopher Erdmann; Sandra Gesing; C. Michael Barton; Lauren Cadwallader; Geerten Hengeveld; Christine R. Kirkpatrick; Kathryn Knight; Carsten Lemmen; Rebecca Ringuette; Qing Zhan; Melissa Harrison; et al. (PLoS Comput. Biol., 2025)