Research

Microbial Genomics

We are interested in characterizing medically-relevant features in microbiome data. We have utilized the vast amount of publicly available microbiome data to investigate a variety of different topics. The focus of these projects have ranged from the production of metabolites by microbes in the gastrointestinal tract to the evolution and regulation of antibiotic resistance genes, but have all been linked by their relevance to different aspects of human health and disease.

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.
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.
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.
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.

SARS-CoV-2 Research

Our labs interest in genomics also extends to viral genomics, where we have applied our skills and expertise in SARS-CoV-2 research. Through this work we have developed new computational tools and approaches to aide in wastewater-based epidemiology, which we hope will aide in the monitoring of SARS-CoV-2 spread and evolution. We have also investigated the evolution of the SARS-CoV-2 genome through analyses of large genomic insertions and transcriptional regulatory sequences. Through this work we aim to contribute to the scientific effort to understand and manage SARS-CoV-2, and develop tools and approaches that can be applied more generally to other viruses.

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.
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.
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.
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.

Microbiome Research

We are also interested in studying the microbiome more generally through the analysis of microbiome data and the development of new tools. These projects have included analyses of microbiome changes in different diseases, the development of new approaches to identify mobile genetic elements in bacterial genomes, and the characterization of specific regulatory mechanisms in microbial genomes.

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.
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.
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.
Dufault-Thompson K, Jiang X. 2022. Applications of de Bruijn Graphs in Microbiome Research. iMeta. 1: e4. DOI: 10.1002/imt2.4.

Computational Genomics

We are also interested in collaborative projects on the development and application of computational genomics methods for analyzing and interpreting complex biological data sets.

Artemov GN, Peery AN, Jiang X, Tu Z, Stegniy VN, Sharakhova MV, Sharakhov IV. 2017. The Physical Genome Mapping of Anopheles Albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles. G3 Genes|Genomes|Genetics. 7: 155-164. DOI: 10.1534/g3.116.034959.
Prasad TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. 2017. Integrating Transcriptomic and Proteomic Data for Accurate Assembly and Annotation of Genomes. Genome Research. 27: 133-144. DOI: 10.1101/gr.201368.115.
Jiang X, Hall AB, Biedler JK, Tu Z. 2017. Single Molecule RNA Sequencing Uncovers Trans -Splicing and Improves Annotations in Anopheles Stephensi: SMRT Sequencing Uncovers Trans-Splicing. Insect Molecular Biology. 26: 298-307. DOI: 10.1111/imb.12294.
Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. 2016. Radical Remodeling of the Y Chromosome in a Recent Radiation of Malaria Mosquitoes. Proceedings of the National Academy of Sciences. 113: E2114-23. DOI: 10.1073/pnas.1525164113.