microbial genomics

  1. 1. Dufault-Thompson K, Levy S, Hall B, Jiang X. 2025. Bilirubin reductase shows host-specific associations in animal large intestines. The ISME Journal. S0168-9525: 00296-8. DOI: 10.1093/ismejo/wrae242.
  2. Dufault-Thompson K, Jiang X. 2024. Annotating microbial functions with ProkFunFind. mSystems. 19: e0003624. DOI: 10.1128/msystems.00036-24.
  3. Ndjite GM, Jiang A, Ravel C, Grant M, Jiang X, Hall B. 2024. Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE. bioRxiv. DOI: 10.1101/2024.11.07.622513.
  4. Yang Y, Yan J, Olson R, Jiang X. 2024. Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus. bioRxiv. DOI: 10.1101/2024.08.19.608685.
  5. Kim SK, Orr MW, Turdiev H, Jenkins CC, Lormand JD, Myers TM, Burnim AA, Carter JA, Kung WC, Jiang X, Sondermann H, Winkler WC, Lee VT. 2024. Diribonuclease activity eliminates toxic diribonucleotide accumulation. Cell Reports. 43: . DOI: 10.1016/j.celrep.2024.114759.
  6. Yang Y, Dufault-Thompson K, Yan W, Cai T, Xie L, Jiang X. 2024. Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants. GigaScience. 13: . DOI: 10.1093/gigascience/giae017.
  7. Burnim A, Dufault-Thompson K, Jiang X. 2024. The three-sided right-handed β-helix is a versatile fold for glycan interactions. Glycobiology. 26: cwaw\e037. DOI: 10.1093/glycob/cwae037.
  8. Arp G, Jiang A, Dufault-Thompson K, Levy S, Zhong A, Wassan JT, Grant M, Li Y, Hall B, Jiang X. 2024. Gut Bacteria Encode Reductases that Biotransform Steroid Hormones. bioRxiv. DOI: 10.1101/2024.10.04.616736.
  9. Hall B, Levy S, Dufault-Thompson K, Arp G, Zhong A, Ndjite GM, Weiss A, Braccia D, Jenkins C, Yang Y, Arp G, Abeysinghe S, Jermain M, Wu CH, Jiang X. 2024. BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. Nature Microbiology. 9: 173-184. DOI: 10.1038/s41564-023-01549-x.
  10. Jacoby C, Scorza K, Ecker L, McMillin M, Ramaswamy R, Sundararajan A, Sidebottom AM, Lin H, Dufault-Thompson K, Hall B, Jiang X, Light SH. 2024. Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway. bioRxiv. DOI: 10.1101/2024.10.08.617280.
  11. Hall B, Jiang X. 2024. Bacterial intragenic inversions a new layer of diversity. Trends in Genetics. DOI: 10.1016/j.tig.2024.12.002.
  12. Zhong A, Jiang X, Hickman AB, Klier K, Teodoro GIC, Dyda F, Laub TM, Storz S. 2023. Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins. Proceedings of the National Academy of Sciences. 120: e2307382120. DOI: 10.1073/pnas.2307382120.
  13. Yang Y, Jiang X. 2023. Evolink: A Phylogenetic Approach for Rapid Identification of Genotype-Phenotype Associations in Large-scale Microbial Multi-Species Data. Bioinformatics. DOI: 10.1093/bioinformatics/btad215.
  14. Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A M, Cui Y, Jiang X, Peng S, Li S, Tong Y. 2022. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR genomics and bioinformatics. 4: lqac057. DOI: 10.1093/nargab/lqac057.
  15. Dufault-Thompson K, Hall AB, Jiang X. 2022. Taxonomic Distribution and Evolutionary Analysis of the Equol Biosynthesis Gene Cluster. BMC Genomics. 23: 1. DOI: 10.1186/s12864-022-08426-7.
  16. Olejniczak M, Jiang X, Basczok MM, Storz G. 2022. KH Domain Proteins: Another Family of Bacterial RNA Matchmakers. Molecular Microbiology. 117: 10-19. DOI: 10.1111/mmi.14842.
  17. Braccia D J, Ndjite G M, Weiss A, Levy S, Abeysinghe S, Jiang X, Pop M, Hall B. 2022. Gut microbiome-wide search for bacterial azoreductases reveals potentially uncharacterized azoreductases encoded in the human gut microbiome. Drug Metabolism and Disposition. DOI: 10.1124/dmd.122.000898.
  18. Yan W, Hall AB, Jiang X. 2022. Bacteroidales Species in the Human Gut Are a Reservoir of Antibiotic Resistance Genes Regulated by Invertible Promoters. Npj Biofilms and Microbiomes. 8: 1. DOI: 10.1038/s41522-021-00260-1.
  19. Braccia DJ, Jiang X, Pop M, Hall AB. 2021. The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome. Frontiers in Microbiology. 12: 705583. DOI: 10.3389/fmicb.2021.705583.
  20. Mou Z, Yang Y, Hall AB, Jiang X. 2021. The Taxonomic Distribution of Histamine-Secreting Bacteria in the Human Gut Microbiome. BMC Genomics. 22: 695. DOI: 10.1186/s12864-021-08004-3.

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