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August 23 2023
  • Published Works

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

bioRxiv. 2023 Aug 10:2023.08.08.552483. doi: 10.1101/2023.08.08.552483. Preprint. ABSTRACT Fecal Microbiota Transplant (FMT) is an emerging therapy that has had remarkable success in treatment and prevention of recurrent Clostridioides difficile infection (rCDI). FMT has recently been associated with adverse outcomes such as inadvertent transfer of antimicrobial resistance, necessitating development of more targeted bacteriotherapies. To address this […]

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August 21 2023
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Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses

PLoS Comput Biol. 2023 Aug 21;19(8):e1010927. doi: 10.1371/journal.pcbi.1010927. Online ahead of print. ABSTRACT Male subjects in animal and human studies are disproportionately used for toxicological testing. This discrepancy is evidenced in clinical medicine where females are more likely than males to experience liver-related adverse events in response to xenobiotics. While previous work has shown gene […]

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August 17 2023
  • Published Works

The blossoming of methods and software in computational biology

PLoS Comput Biol. 2023 Aug 17;19(8):e1011390. doi: 10.1371/journal.pcbi.1011390. eCollection 2023 Aug. NO ABSTRACT PMID:37590323 | DOI:10.1371/journal.pcbi.1011390

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June 30 2023
  • Published Works

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

mSystems. 2023 Jun 30:e0126522. doi: 10.1128/msystems.01265-22. Online ahead of print. ABSTRACT The ability of bacterial pathogens to metabolically adapt to the environmental conditions of their hosts is critical to both colonization and invasive disease. Infection with Neisseria gonorrhoeae (the gonococcus, Gc) is characterized by the influx of neutrophils [polymorphonuclear leukocytes (PMNs)], which fail to clear […]

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June 6 2023
  • Published Works

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

Bioinformatics. 2023 Jun 5:btad367. doi: 10.1093/bioinformatics/btad367. Online ahead of print. ABSTRACT MOTIVATION: Genome-scale metabolic network reconstructions (GENREs) are valuable for understanding cellular metabolism in silico. Several tools exist for automatic GENRE generation. However, these tools frequently (1) do not readily integrate with some of the widely-used suites of packaged methods available for network analysis, (2) […]

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April 26 2023
  • Published Works

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

PLoS Comput Biol. 2023 Apr 26;19(4):e1011076. doi: 10.1371/journal.pcbi.1011076. Online ahead of print. ABSTRACT Clostridioides difficile pathogenesis is mediated through its two toxin proteins, TcdA and TcdB, which induce intestinal epithelial cell death and inflammation. It is possible to alter C. difficile toxin production by changing various metabolite concentrations within the extracellular environment. However, it is […]

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February 17 2023
  • Published Works

Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses

bioRxiv. 2023 Feb 7:2023.02.07.527430. doi: 10.1101/2023.02.07.527430. Preprint. ABSTRACT Male subjects in animal and human studies are disproportionately used for toxicological testing. This discrepancy is evidenced in clinical medicine where females are more likely than males to experience liver-related adverse events in response to xenobiotics. While previous work has shown gene expression differences between the sexes, […]

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January 5 2023
  • Published Works

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

Sci Rep. 2023 Jan 5;13(1):203. doi: 10.1038/s41598-022-26816-5. ABSTRACT Crohn’s disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. A clear gap in our existing CD diagnostics and current disease management approaches is the lack of highly specific biomarkers that can be used to streamline or personalize disease management. Comprehensive profiling of metabolites holds […]

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December 15 2022
  • Published Works

Ten simple rules for launching an academic research career

PLoS Comput Biol. 2022 Dec 15;18(12):e1010689. doi: 10.1371/journal.pcbi.1010689. eCollection 2022 Dec. NO ABSTRACT PMID:36520710 | DOI:10.1371/journal.pcbi.1010689

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December 13 2022
  • Published Works

Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment

mSystems. 2022 Dec 13:e0068922. doi: 10.1128/msystems.00689-22. Online ahead of print. NO ABSTRACT PMID:36511689 | DOI:10.1128/msystems.00689-22

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Recent Posts

  • Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection
  • Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses
  • The blossoming of methods and software in computational biology
  • Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture
  • Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling
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Computational Systems Biology Laboratory; The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia.

Related Links

  • PubMed
  • UVA Engineering

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The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia

  • Email: papinlab@virginia.edu
  • Phone (434) 924-8195

  • Home
  • Publications
  • Meet Our Team
  • Contact