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Jason A. Papin
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2020 – today
- 2024
- [j45]Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls
, Matthew L. Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J. Saucerman, Glynis L. Kolling, Anders Wallqvist
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) - [j44]Tracy J. Kuper
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. PLoS Comput. Biol. 20(4): 1012031 (2024) - [j43]Jason A. Papin
Celebrating a body of work. PLoS Comput. Biol. 20(9): 1012441 (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
The blossoming of methods and software in computational biology. PLoS Comput. Biol. 19(8) (2023) - [j40]Connor J. Moore
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
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
Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PLoS Comput. Biol. 18(2) (2022) - [j37]Thomas J. Moutinho Jr.
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. PLoS Comput. Biol. 18(2) (2022) - [j36]Lauren Cadwallader
Advancing code sharing in the computational biology community. PLoS Comput. Biol. 18(6) (2022) - [j35]Jason A. Papin
Ten simple rules for launching an academic research career. PLoS Comput. Biol. 18(12): 1010689 (2022) - 2021
- [j34]Lauren Cadwallader
Collaborating with our community to increase code sharing. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j33]Matthew L. Jenior
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput. Biol. 16(4) (2020) - [j32]Gregory L. Medlock
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
Improving reproducibility in computational biology research. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j30]Ana M. Untaroiu, Maureen A. Carey
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
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
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
Ten simple rules for biologists learning to program. PLoS Comput. Biol. 14(1) (2018) - [j25]Philip E. Bourne
One thousand simple rules. PLoS Comput. Biol. 14(12) (2018) - 2017
- [j24]Ruth Nussinov
Computing the Dynamic Supramolecular Structural Proteome. PLoS Comput. Biol. 13(1) (2017) - [j23]Matthew B. Biggs
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PLoS Comput. Biol. 13(3) (2017) - [j22]Ruth Nussinov
How can computation advance microbiome research? PLoS Comput. Biol. 13(9) (2017) - 2016
- [j21]Matthew B. Biggs
Metabolic network-guided binning of metagenomic sequence fragments. Bioinform. 32(6): 867-874 (2016) - [j20]Ruth Nussinov
Computing Biology. PLoS Comput. Biol. 12(7) (2016) - 2015
- [j19]Steven N. Steinway
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. PLoS Comput. Biol. 11(6) (2015) - [j18]Ruth Nussinov
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
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
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
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
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
Predicting biological system objectives de novo from internal state measurements. BMC Bioinform. 9 (2008) - [j6]Jong Min Lee
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
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
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
Flux balance analysis in the era of metabolomics. Briefings Bioinform. 7(2): 140-150 (2006) - [j2]Shayn M. Peirce
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
Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems. PLoS Comput. Biol. 2(8) (2006)
Coauthor Index
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last updated on 2024-12-02 21:26 CET by the dblp team
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