Jason A. Papin

Also affiliated with University of Virginia

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.649Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

npj Systems Biology and Applications(2021)10.1038/s41540-021-00198-2

Top 31%

0.649DataRank

Top 31%24 citations

Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, Jason A. Papin +1 more

Papers

Driven by 42 papers — median percentile 35. Top paper: “Megasphaera in the Stool Microbiota Is Negatively Associated With Diarrheal Cryptosporidiosis”.

Megasphaera in the Stool Microbiota Is Negatively Associated With Diarrheal Cryptosporidiosis

Clinical Infectious Diseases(2021)10.1093/cid/ciab207

N/A

1.8DataRank · unranked

62 citations

Gregory L. Medlock, Masud Alam, Mamun Kabir, Md. Jashim Uddin, Uma Nayak +6 more

Community standards to facilitate development and address challenges in metabolic modeling

Molecular Systems Biology(2020)10.15252/msb.20199235

N/A

1.3DataRank · unranked

60 citations

Andreas Dräger, Moritz E. Beber, Jason A. Papin, James T. Yurkovich, Maureen A. Carey

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

npj Systems Biology and Applications(2021)10.1038/s41540-021-00198-2

Top 31%

0.649DataRank

Top 31%24 citations

Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, Jason A. Papin +1 more

One thousand simple rules

PLOS Computational Biology(2018)10.1371/journal.pcbi.1006670

N/A

0.241DataRank · unranked

4 citations

Scott Markel, Jason A. Papin, Fran Lewitter, Philip E. Bourne

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007847

N/A

0DataRank · unranked

25 citations

Thomas J. Moutinho, Jason A. Papin, Gregory L. Medlock

Minimum bactericidal concentration of ciprofloxacin to Pseudomonas aeruginosa determined rapidly based on pyocyanin secretion

Sensors and Actuators B Chemical(2020)10.1016/j.snb.2020.127936

N/A

0DataRank · unranked

32 citations

John H. Moore, Glynis L. Kolling, John S. McGrath, Jason A. Papin, Nathan S. Swami +1 more

Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.01.323147

N/A

0DataRank · unranked

2 citations

Gregory L. Medlock, Masud Alam, Mamun Kabir, Md. Jashim Uddin, Uma Nayak +6 more

Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.09.143057

N/A

0DataRank · unranked

0 citations

Jibraan A. Fawad, Thomas J. Moutinho, Paul Mitchell, Kathleen Brown-Steinke, Jesse Zhao +7 more

Asynchronous influenza vaccination and adverse maternal-child health outcomes in the Brazilian semiarid, 2013 to 2018: the INFLUEN-SA Study

medRxiv(2020)10.1101/2020.08.24.20180455

N/A

0DataRank · unranked

0 citations

Saionara Cristina Francisco, Thaisy B.R. Lima, Vânia A.F. Viana, Jaqueline S.V. Burgoa, Alberto M. Soares +9 more

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli

UNC Libraries(2020)10.17615/e1p6-pm51

N/A

0DataRank · unranked

0 citations

Jason A. Papin, Steven M. Singer, David T. Bolick, Luther A. Bartelt, Jeffery Donowitz +9 more

Mechanistic models of microbial community metabolism

Molecular Omics(2021)10.1039/d0mo00154f

N/A

0DataRank · unranked

38 citations

Dawson Payne, Jason A. Papin, Lillian Dillard

Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model

Cell Reports(2021)10.1016/j.celrep.2021.108836

N/A

0DataRank · unranked

30 citations

Kristopher D. Rawls, Glynis L. Kolling, Kalyan C. Vinnakota, Anders Wallqvist, Jason A. Papin +1 more

Computational approaches to understanding Clostridioides difficile metabolism and virulence

Current Opinion in Microbiology(2021)10.1016/j.mib.2021.11.002

N/A

0DataRank · unranked

4 citations

Jason A. Papin, Matthew L. Jenior

Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.08.459555

N/A

0DataRank · unranked

1 citations

Mary E. Dickenson, Jason A. Papin, Matthew L. Jenior

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.10.434463

Top 100%

0DataRank

Top 100%0 citations

Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, Jason A. Papin +1 more

Histone Deacetylase Inhibition by Gut Microbe-Generated Short-Chain Fatty Acids Entrains Intestinal Epithelial Circadian Rhythms

Gastroenterology(2022)10.1053/j.gastro.2022.07.051

N/A

0DataRank · unranked

145 citations

Deborah Luzader, Gabriel F. Hanson, Thomas J. Moutinho, Craig A. McKinney, Paul Mitchell +15 more

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

PLoS Computational Biology(2022)10.1371/journal.pcbi.1009870

N/A

0DataRank · unranked

13 citations

Gregory L. Medlock, Michał Stolarczyk, William A. Petri Jr., Jennifer L. Güler, Jason A. Papin +1 more

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

PLoS Computational Biology(2022)10.1371/journal.pcbi.1009341

N/A

0DataRank · unranked

9 citations

Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin, Thomas J. Moutinho

Ten simple rules for launching an academic research career

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010689

N/A

0DataRank · unranked

1 citations

Jessica Keim‐Malpass, Sana Syed, Jason A. Papin

Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.17.508371

N/A

0DataRank · unranked

4 citations

Emma M. Glass, Jason A. Papin, Matthew L. Jenior

Transcriptome guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.19.521143

N/A

0DataRank · unranked

1 citations

Christopher M. Baiocco, Jason A. Papin, Alison K. Criss, Aimee D. Potter

Evolution shapes metabolic function and niche-specific antimicrobial targets in pathobionts

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.10.515998

N/A

0DataRank · unranked

0 citations

Lillian Dillard, Glynis L. Kolling, Andrew Warren, Jason A. Papin, Emma M. Glass

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

Bioinformatics(2023)10.1093/bioinformatics/btad367

N/A

0DataRank · unranked

21 citations

Emma M. Glass, Jason A. Papin, Matthew L. Jenior

Identifying metabolic shifts in Crohn's disease using 'omics-driven contextualized computational metabolic network models

Scientific Reports(2023)10.1038/s41598-022-26816-5

N/A

0DataRank · unranked

21 citations

Yash Sharma, Fatima Zulqarnain, Brooklyn McGrew, Aman Shrivastava, Lubaina Ehsan +11 more

Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

mSystems(2023)10.1128/msystems.01265-22

N/A

0DataRank · unranked

12 citations

Christopher M. Baiocco, Jason A. Papin, Alison K. Criss, Aimee D. Potter

Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses

PLoS Computational Biology(2023)10.1371/journal.pcbi.1010927

N/A

0DataRank · unranked

10 citations

Christopher P. Holstege, Jason A. Papin, Connor J. Moore

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011076

N/A

0DataRank · unranked

12 citations

Matthew L. Jenior, Glynis L. Kolling, Jason A. Papin, Deborah Powers

Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.08.552483

N/A

0DataRank · unranked

8 citations

Jhansi L. Leslie, Glynis L. Kolling, Laurie Archbald‐Pannone, Deborah Powers, William A. Petri Jr. +2 more

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.08.561426

N/A

0DataRank · unranked

1 citations

Glynis L. Kolling, Emma M. Glass, Joanna B. Goldberg, Jason A. Papin, Mohammad Mazharul Islam

Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation

mSphere(2024)10.1128/msphere.00081-24

N/A

0DataRank · unranked

16 citations

Lucas Plott, Matthew R. Markovetz, Deborah Powers, Hao Wang, David B. Hill +4 more

Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

PLoS Computational Biology(2024)10.1371/journal.pcbi.1012031

N/A

0DataRank · unranked

13 citations

Mohammad Mazharul Islam, Shayn M. Peirce, Jason A. Papin, Roseanne M. Ford, Tracy Kuper

Applying a polysaccharide lyase from Stenotrophomonas maltophilia to disrupt alginate exopolysaccharide produced by Pseudomonas aeruginosa clinical isolates

Applied and Environmental Microbiology(2024)10.1128/aem.01853-24

N/A

0DataRank · unranked

12 citations

Nikki Akula, Glynis L. Kolling, Parastoo Azadi, Ian Black, Ambrish Kumar +6 more

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism

PLoS Computational Biology(2024)10.1371/journal.pcbi.1011919

N/A

0DataRank · unranked

6 citations

Connor J. Moore, Kristopher D. Rawls, Matthew L. Jenior, Bryan Chun, Sarbajeet Nagdas +5 more

Niche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens

PLoS Biology(2024)10.1371/journal.pbio.3002907

N/A

0DataRank · unranked

6 citations

Lillian Dillard, Glynis L. Kolling, Andrew Warren, Jason A. Papin, Emma M. Glass

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes

Microbial Genomics(2024)10.1099/mgen.0.001259

N/A

0DataRank · unranked

4 citations

Glynis L. Kolling, Emma M. Glass, Joanna B. Goldberg, Jason A. Papin, Mohammad Mazharul Islam

Clostridioides difficile -mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.01.578425

N/A

0DataRank · unranked

4 citations

Lucas Plott, Matthew R. Markovetz, Deborah Powers, Hao Wang, David B. Hill +4 more

Reframing the role of the objective function in its proper context for metabolic network modeling

Cell Systems(2025)10.1016/j.cels.2025.101298

N/A

0DataRank · unranked

7 citations

William Shao, Mariska Batavia, Roseanne M. Ford, Bernhard Ø. Palsson, Jens Nielsen +4 more

Characterizing Spatiotemporal Expansion of Pseudomonas aeruginosa Communities in Polymer and Mucin Gel Environments

Biotechnology and Bioengineering(2025)10.1002/bit.70098

N/A

0DataRank · unranked

0 citations

Glynis L. Kolling, Katharina Ribbeck, Shayn M. Peirce, Jason A. Papin, Roseanne M. Ford +1 more

Metabolic network analysis of Crohn’s disease reveals sex- and age-specific cellular phenotypes

Cell Systems(2025)10.1016/j.cels.2025.101447

N/A

0DataRank · unranked

0 citations

Mariska Batavia, William Shao, Fatima Zulqarnain, Glynis L. Kolling, A. Greene +4 more

MEMOTE for standardized genome-scale metabolic model testing

Nature Biotechnology(2020)10.1038/s41587-020-0446-y

N/A

0DataRank · unranked

558 citations

Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meriç Ataman, Parizad Babaei +64 more

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

Cell Systems(2020)10.1016/j.cels.2019.11.006

N/A

0DataRank · unranked

66 citations

Jason A. Papin, Gregory L. Medlock

Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model

Toxicology and Applied Pharmacology(2020)10.1016/j.taap.2020.115390

N/A

0DataRank · unranked

36 citations

Bonnie V. Dougherty, Kalyan C. Vinnakota, Venkat R. Pannala, Anders Wallqvist, Glynis L. Kolling +2 more

Jason A. Papin

Indexed papers

Top data-sharing exemplar

Papers