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.

Jiang X, Hall AB, Xavier RJ, Alm EJ. 2019. Comprehensive Analysis of Chromosomal Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools. Plos One. 14: e0223680. DOI: 10.1371/journal.pone.0223680.

Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, Livny J, Vlamakis H, Clish C, Bullock K, Deik A, Scott J, Pierce KA, Xavier RJ, Alm EJ. 2019. A Library of Human Gut Bacterial Isolates Paired with Longitudinal Multiomics Data Enables Mechanistic Microbiome Research. Nature Medicine. 25: 1442-1452. DOI: 10.1038/s41591-019-0559-3.

Jiang X*, Hall AB*, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. 2019. Invertible Promoters Mediate Bacterial Phase Variation, Antibiotic Resistance, and Host Adaptation in the Gut. Science. 363: 181-187. DOI: 10.1126/science.aau5238.

Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. 2019. Analysis of 1135 Gut Metagenomes Identifies Sex-Specific Resistome Profiles. Gut Microbes. 10: 358-366. DOI: 10.1080/19490976.2018.1528822.

Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. 2018. Predictability and Persistence of Prebiotic Dietary Supplementation in a Healthy Human Cohort. Scientific Reports. 8: 12699. DOI: 10.1038/s41598-018-30783-1.

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. 2018. Gut Microbiota Composition and Functional Changes in Inflammatory Bowel Disease and Irritable Bowel Syndrome. Science Translational Medicine. 10: eaap8914. DOI: 10.1126/scitranslmed.aap8914.

Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. 2017. A Novel Ruminococcus Gnavus Clade Enriched in Inflammatory Bowel Disease Patients. Genome Medicine. 9: 103. DOI: 10.1186/s13073-017-0490-5.