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 […]
Read MoreMetabolic 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 […]
Read MoreThe 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
Read MoreTranscriptome-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 […]
Read MoreReconstructor: 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) […]
Read MoreNetwork 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 […]
Read MoreMetabolic 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, […]
Read MoreIdentifying 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 […]
Read MoreTen 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
Read MoreMetabolic 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
Read More