Selected Publications
Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.
Cell. 2024;187(8):1834-1852.e19
Translational genetics identifies a phosphorylation switch in CARD9 required for innate inflammatory responses.
Cell Rep. 2024;43(3):113944
Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm.
Gut. 2024;:ePub
Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.
Cell Host Microbe. 2024;32(2):209-226.e7
Host genetic regulation of human gut microbial structural variation.
Nature. 2024;625(7996):813-821
Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation.
Proc Natl Acad Sci U S A. 2023;121(1):e2307086120
Reverse metabolomics for the discovery of chemical structures from humans.
Nature. 2023;626(7998):419-426
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis.
bioRxiv. 2023;:ePub
Genetic vulnerability to Crohn's disease reveals a spatially resolved epithelial restitution program.
Sci Transl Med. 2023;15(719):eadg5252
Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics.
bioRxiv. 2023;:ePub
Revisiting Coley's Toxins: Immunogenic Cardiolipins from Streptococcus pyogenes.
J Am Chem Soc. 2023;145(39):21183-21188
Constitutively active autophagy in macrophages dampens inflammation through metabolic and post-transcriptional regulation of cytokine production.
Cell Rep. 2023;42(7):112708
HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.
Immunity. 2023;56(7):1681-1698.e13
Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence.
Cell Host Microbe. 2023;31(6):978-992.e5
Conditioning of the immune system by the microbiome.
Trends Immunol. 2023;44(7):499-511
Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.
Nat Microbiol. 2023;8(6):1064-1078
Association of distinct microbial signatures with premalignant colorectal adenomas.
Cell Host Microbe. 2023;31(5):827-838.e3
Remodeling of colon plasma cell repertoire within ulcerative colitis patients.
J Exp Med. 2023;220(4):ePub
Gut microbiome lipid metabolism and its impact on host physiology.
Cell Host Microbe. 2023;31(2):173-186
The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon.
Immunity. 2023;56(2):444-458.e5
Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.
Cell. 2022;185(26):4921-4936.e15
A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.
Cell. 2022;185(23):4280-4297.e12
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine.
Nat Microbiol. 2022;7(10):1673-1685
The CD4+ T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease.
Immunity. 2022;55(10):1909-1923.e6
Identification of trypsin-degrading commensals in the large intestine.
Nature. 2022;609(7927):582-589
Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling.
Immunity. 2022;55(9):1663-1679.e6
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.
Nat Genet. 2022;54(9):1275-1283
Akkermansia muciniphila phospholipid induces homeostatic immune responses.
Nature. 2022;608(7921):168-173
pH sensing controls tissue inflammation by modulating cellular metabolism and endo-lysosomal function of immune cells.
Nat Immunol. 2022;23(7):1063-1075
Lyme Disease, Borrelia burgdorferi, and Lipid Immunogens.
J Am Chem Soc. 2022;144(6):2474-2478
Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing.
PLoS Biol. 2022;20(1):e3001532
Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Nat Biotechnol. 2021;40(3):374-381
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
