Selected Publications

  • Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun. 2021;12(1):4845

  • Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe. 2021;29(9):1351-1365.e11

  • Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458-464

  • SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance. Cell Reports. 2021;36(4):109434

  • Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021;29(8):1294-1304.e4

  • B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021;184(12):3205-3221.e24

  • Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions. Nat Commun. 2021;12(1):1921

  • Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021;184(8):2053-2067.e18

  • QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis. Science. 2021;371(6524):ePub

  • Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature. 2021;589(7842):456-461

  • TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep. 2020;33(6):108371

  • A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity. Proc Natl Acad Sci U S A. 2020;117(46):28930-28938

  • The Human and Mouse Enteric Nervous System at Single-Cell Resolution. Cell. 2020;182(6):1606-1622.e23

  • Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. Cell Host Microbe. 2020;28(2):245-257.e6

  • Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity. 2019;51(4):696-708.e9

  • Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell. 2019;178(3):714-730.e22

  • Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655-662

  • The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. Elife. 2019;8:ePub

  • Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science. 2019;363, Issue 6423:181-187

  • Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019;4(2):293-305

  • T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. 2018;175(5):1307-1320.e22

  • The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018;562(7728):589-594

  • Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med. 2018;24(11):1762-1772

  • C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Science. 2018;359(6380):1161-1166

  • A single-cell survey of the small intestinal epithelium. Nature. 2017;551(7680):333-339

  • Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell. 2016;167(4):1125-1136.e8

  • Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk. Immunity. 2016;44(6):1392-1405

  • Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell. 2016;165(4):842-53

  • Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation. Immunity. 2015;43(4):715-726

  • Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci U S A. 2014;111(21):7741-7746

  • The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15(3):382-92