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2020 – today
- 2024
[j43]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)- 2023
- [j42]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) - [j41]Feilim Mac Gabhann, Virginia E. Pitzer, Jason A. Papin:
The blossoming of methods and software in computational biology. PLoS Comput. Biol. 19(8) (2023) - [j40]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) - [j39]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) - 2022
- [j38]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) - [j37]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) - [j36]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) - [j35]Jason A. Papin, Jessica Keim-Malpass, Sana Syed:
Ten simple rules for launching an academic research career. PLoS Comput. Biol. 18(12): 1010689 (2022) - 2021
- [j34]Lauren Cadwallader, Jason A. Papin, Feilim Mac Gabhann, Rebecca Kirk:
Collaborating with our community to increase code sharing. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j33]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) - [j32]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) - [j31]Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath:
Improving reproducibility in computational biology research. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j30]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): 186:1-186:9 (2019) - [j29]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: 64-71 (2019) - [j28]Anna S. Blazier, Jason A. Papin:
Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PLoS Comput. Biol. 15(4) (2019) - [j27]Jason A. Papin, Feilim Mac Gabhann:
Wisdom of crowds in computational biology. PLoS Comput. Biol. 15(5) (2019) - 2018
- [j26]Maureen A. Carey, Jason A. Papin:
Ten simple rules for biologists learning to program. PLoS Comput. Biol. 14(1) (2018) - [j25]Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin:
One thousand simple rules. PLoS Comput. Biol. 14(12) (2018) - 2017
- [j24]Ruth Nussinov, Jason A. Papin, Ilya A. Vakser:
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13(1) (2017) - [j23]Matthew B. Biggs, Jason A. Papin:
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput. Biol. 13(3) (2017) - [j22]Ruth Nussinov, Jason A. Papin:
How can computation advance microbiome research? PLoS Comput. Biol. 13(9) (2017) - 2016
- [j21]Matthew B. Biggs, Jason A. Papin:
Metabolic network-guided binning of metagenomic sequence fragments. Bioinform. 32(6): 867-874 (2016) - [j20]Ruth Nussinov, Jason A. Papin:
Computing Biology. PLoS Comput. Biol. 12(7) (2016) - 2015
- [j19]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) - [j18]Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns:
From "What Is?" to "What Isn't?" Computational Biology. PLoS Comput. Biol. 11(7) (2015) - 2014
- [j17]Paul A. Jensen, Jason A. Papin:
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinform. 30(9): 1327-1328 (2014) - 2012
- [j16]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: 2 (2012) - [j15]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: 27 (2012) - 2011
- [j14]Paul A. Jensen, Jason A. Papin:
Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinform. 27(4): 541-547 (2011) - [j13]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: 147 (2011) - [j12]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)
2000 – 2009
- 2009
- [j11]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: 52 (2009) - [j10]Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin:
Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System. PLoS Comput. Biol. 5(6) (2009) - [j9]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) - 2008
- [j8]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): 2384-2390 (2008) - [j7]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) - [j6]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) - [j5]Jacek Puchalka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos:
Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology. PLoS Comput. Biol. 4(10) (2008) - 2007
- [j4]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: 46 (2007) - 2006
- [j3]Jong Min Lee, Erwin P. Gianchandani, Jason A. Papin:
Flux balance analysis in the era of metabolomics. Briefings Bioinform. 7(2): 140-150 (2006) - [j2]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): 601-616 (2006) - [j1]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)
Coauthor Index
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