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.
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.
Dufault-Thompson K, Jiang X.
2024.
Annotating microbial functions with ProkFunFind.
mSystems.
19:
e0003624.
DOI:
10.1128/msystems.00036-24.
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.
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.
See more…
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.
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.
Dufault-Thompson K, Jiang X.
2024.
Annotating microbial functions with ProkFunFind.
mSystems.
19:
e0003624.
DOI:
10.1128/msystems.00036-24.
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.
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.
See more…
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.
See more…