Author

J. A. Papin

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 9 Bioengineering· 3 Cell Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 11 Assay:bulk RNA-seq· 7 Organism:human· 7 Research Focus:metabolism & bioenergetics· 5 Assay:metabolomics· 5 Research Focus:host-pathogen & immune response· 3 Research Focus:chromatin & epigenetic regulation· 2 Organism:mouse· 2

Frequent Co-Authors

G. L. Medlock· 5 shared M. A. Carey· 4 shared G. L. Kolling· 3 shared M. L. Jenior· 3 shared A. Wallqvist· 2 shared D. A. Powers· 2 shared J. L. Guler· 2 shared K. D. Rawls· 2 shared

Activity by Year

2017-2024 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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5 shared papersMicrobiology

G. L. Medlock

Mutual co-authors in cluster

Author profile →

13 papers

Recent·Most cited

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

K. L. Furtado, L. M. Plott, M. R. Markovetz, D. A. Powers, H. Wang, D. B. Hill, J. A. Papin, N. L. Allbritton, R. Tamayo

This study investigates how C. difficile uses host-derived mucus for growth, metabolism, and biofilm formation, revealing metabolic shifts and potential pathogenic mechanisms.

mSphere · Jun 25, 2024Peer-reviewedMicrobiology

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

A. D. Potter, C. M. Baiocco, J. A. Papin, A. K. Criss

This paper uses transcriptome data and metabolic modeling to show Neisseria gonorrhoeae reorganizes its carbon flux during co-culture with neutrophils, enhancing its survival.

bioRxiv · Dec 19, 2022 · PreprintMicrobiology

A computational model of Pseudomonas syringae metabolism unveils the role of branched-chain amino acids in virulence expression at the early stages of Arabidopsis colonization

P. Tubergen, G. L. Medlock, A. Moore, J. A. Papin, C. H. Danna

This study uses a computational model to show that branched-chain amino acids suppress virulence in Pseudomonas syringae during early plant infection.

bioRxiv · Dec 16, 2022 · PreprintMicrobiology

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

M. L. Jenior, M. E. Dickenson, J. A. Papin

The paper uses transcriptomic and metabolic modeling to show clinical isolates of Klebsiella pneumoniae rely more on valine catabolism, suggesting a potential immunosuppressive strategy.

npj Systems Biology and Applications · Oct 28, 2022Peer-reviewedMicrobiology

Identifying metabolic adaptations during cardiotoxicity using paired transcriptomics andmetabolomics data integrated with a model of heart metabolism

B. Dougherty, K. D. Rawls, M. L. Jenior, B. Chun, S. Nagdas, J. J. Saucerman, G. L. Kolling, A. Wallqvist, J. A. Papin

The paper integrates transcriptomics and metabolomics data with a heart metabolic model to identify metabolic adaptations during cardiotoxicity from three compounds.

bioRxiv · Oct 31, 2021 · PreprintBioengineering

Novel drivers of virulence in Clostridioides difficile identified via context-specific metabolic network analysis

M. L. Jenior, J. L. Leslie, D. A. Powers, E. M. Garrett, K. A. Walker, M. E. Dickenson, W. A. Petri, R. Tamayo, J. A. Papin

This paper identifies novel metabolic drivers of virulence in C. difficile using genome-scale metabolic network analysis of two strains under different conditions.

bioRxiv · Nov 9, 2020Bioengineering

Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

M. A. Carey, G. L. Medlock, M. Alam, M. Kabir, M. J. Uddin, U. Nayak, J. A. Papin, A. S. G. Faruque, R. Haque, W. A. Petri, C. A. Gilchrist

The paper finds that lower Megasphaera abundance in stool microbiota is associated with diarrheal symptoms in infants infected with Cryptosporidium.

bioRxiv · Oct 1, 2020Microbiology

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

B. V. Dougherty, K. D. Rawls, G. L. Kolling, K. C. Vinnakota, A. Wallqvist, J. A. Papin

This study uses a cardiomyocyte-specific genome-scale model to identify common metabolic shifts in heart failure across omics datasets, finding decreased NO and Neu5Ac synthesis as common markers.

bioRxiv · Jul 20, 2020Bioengineering

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

D. H. Luzader, J. A. Fawad, T. J. Moutinho, P. G. Mitchell, K. Brown-Steinke, J. Y. Zhao, A. E. Rosselot, C. A. McKinney, C. I. Hong, C. J. Chou, J. A. Papin, S. R. Moore

The paper shows gut microbe-generated short chain fatty acids (SCFAs) delay intestinal epithelial circadian rhythms via an HDAC inhibitor-dependent mechanism.

bioRxiv · Jun 9, 2020 · PreprintCell Biology

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

M. A. Carey, A. M. Untaroiu, J. L. Guler, J. A. Papin

This study identifies metabolic weaknesses in chloroquine-resistant malaria parasites and proposes combination therapies using chloroquine with sulfadoxine-pyrimethamine or fosmidomycin.

bioRxiv · Sep 26, 2018Microbiology

Influential parameters for the analysis of intracellular parasite metabolomics

M. A. Carey, V. Covelli, A. Brown, G. L. Medlock, M. Haaren, J. G. Cooper, J. A. Papin, J. L. Guler

This study identifies normalization parameters that significantly affect differential abundance analysis in metabolomics of intracellular parasites, highlighting the impact of host contamination.

bioRxiv · Feb 22, 2018Microbiology

Metabolic mechanisms of interaction within a defined gut microbiota

G. L. Medlock, M. A. Carey, D. G. McDuffie, M. B. Mundy, N. Giallourou, J. R. Swann, G. Kolling, J. A. Papin

This paper develops and tests a framework to identify metabolic interactions in a defined gut microbiota, revealing an amino acid cross-feeding interaction that benefits one strain in co-culture.

bioRxiv · Jan 27, 2018Microbiology

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions

T. J. Moutinho, J. C. Panagides, M. B. Biggs, G. L. Medlock, G. L. Kolling, J. A. Papin

This paper introduces a co-culture plate to assess contact-independent microbial interactions using real-time optical density measurements between separated bacterial species.

bioRxiv · Jun 2, 2017Microbiology