Xiaofang Jiang

Principal Investigator since 2019

Research areas

  • Microbial genomics
  • Microbiome metagenomics
  • SARS-CoV-2
  • Bioinformatics

Education

  • BS: Wuhan University, Life Science (2006-2010)
  • PhD: Virginia Tech, Genetics, Bioinformatics and Computational Biology (2011-2016)
  • Postdoc: Massachusetts Institute of Technology (2016-2019)
Xiaofang Jiang

Background

I have a broad interest in genomics and bioinformatics. During my Ph.D., I investigated the genomics and transcriptomics of mosquitoes. I tackled several interesting questions on mosquito biology including verifying dosage compensation, discovering trans-splicing in mosquitoes, disentangling the enigmatic Anopheline phylogeny, and identifying the gene determining the sex of mosquitoes. During my postdoctoral training at MIT and the Broad Institute, I developed a new tool to identify and quantify the orientations of invertible DNA regions, called PhaseFinder, and a new method to identify the exact edges of mobile genetic elements to better track the horizontal transfer of genes through the human microbiome.

I believe that the most important criterion of success for bioinformatics algorithms is being able to solve real biological problems. At the National Library of Medicine, we are particularly interested in the hypothesis-driven investigation of specific biological problems, such as the identification of key genes associated with phenotypic changes, tracking the spread and evolution of microbes and viruses, prediction of biological interactions, and modeling molecular pathways.

Papers from time in Jiang lab

  1. Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA 2nd, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. 2021. High-Throughput Sequencing of SARS-CoV-2 in Wastewater Provides Insights into Circulating Variants. Water Research. 205: 117710. DOI: 10.1016/j.watres.2021.117710.
  2. 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.
  3. 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.
  4. Yang Y, Yan W, Hall AB, Jiang X. 2021. Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination. Molecular Biology and Evolution. 38: 1241-1248. DOI: 10.1093/molbev/msaa281.
  5. 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.
  6. 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.
  7. 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.
  8. Yang Y, Dufault-Thompson K, Fontenele RS, Jiang X. 2022. Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants. mSystem. DOI: 10.1128/msystems.00179-22.
  9. 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.
  10. Dufault-Thompson K, Jiang X. 2022. Applications of de Bruijn Graphs in Microbiome Research. iMeta. 1: e4. DOI: 10.1002/imt2.4.
  11. 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.
  12. Fontenele RS, Yang Y, Driver EM, Magge A, Kraberger S, Custer JM, Dufault-Thompson K, Cox E, Newell ME, Varsani A, Halden RU, Scotch M, Jiang X. 2023. Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Sci Total Environ.. 877: 162862. DOI: 10.1016/j.scitotenv.2023.162862.
  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. 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.
  15. 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.
  16. 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.
  17. Hall B, Jiang X. 2024. Bacterial intragenic inversions a new layer of diversity. Trends in Genetics. DOI: 10.1016/j.tig.2024.12.002.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. Dufault-Thompson K, Jiang X. 2024. Annotating microbial functions with ProkFunFind. mSystems. 19: e0003624. DOI: 10.1128/msystems.00036-24.
  25. 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.