Selected Publications
Development of an FKBP12-recruiting chemical-induced proximity DNA-encoded library and its application to discover an autophagy potentiator.
Cell Chem Biol. 2025;32(3):498-510.e35
Spatially restricted immune and microbiota-driven adaptation of the gut.
Nature. 2024;636(8042):447-456
Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
Cell Chem Biol. 2024;31(12):2138-2155.e32
Commensal consortia decolonize Enterobacteriaceae via ecological control.
Nature. 2024;633(8031):878-886
Emerging biochemical, microbial and immunological evidence in the search for why HLA-B∗27 confers risk for spondyloarthritis.
Cell Chem Biol. 2024;32(1):12-24
B cell tolerance and autoimmunity: Lessons from repertoires.
J Exp Med. 2024;221(9):ePub
Small-molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation.
Sci Adv. 2024;10(29):eadn2339
The centrosomal protein FGFR1OP controls myosin function in murine intestinal epithelial cells.
Dev Cell. 2024;59(18):2460-2476.e10
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission.
Nat Commun. 2024;15(1):3344
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
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
