default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDJason A. Papin
Person information
SPARQL queries 
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
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, 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)- [j44]Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce-Cottler, Jason A. Papin, Roseanne M. Ford:
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, Feilim Mac Gabhann, Virginia E. Pitzer:
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, 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
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-12-02 21:26 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
