Publications for All Faculty

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Kong L, Subramanian S, Segerstolpe Å, Tran V, Shih AR, Carter GT, Kunitake H, Twardus SW, Li J, Gandhi S, Kaper ME, Cauley C, Chen EJ, Porter CBM, Delorey TM, Bordeianou L, Ricciardi R, Ananthakrishnan AN, Lau H, Graham DB, Hodin R, Deguine J, Smillie CS, Xavier RJ

Single-cell and spatial transcriptomics of stricturing Crohn's disease highlights a fibrosis-associated network.

Nat Genet. 2025;:ePub - PMID: 40562913 - DOI: 10.1038/s41588-025-02225-y
Brown EM, Temple ER, Jeanfavre S, Avila-Pacheco J, Taylor N, Liu K, Nguyen PNU, Mohamed AMT, Ung P, Walker RA, Graham DB, Clish CB, Xavier RJ

Bacteroides sphingolipids promote anti-inflammatory responses through the mevalonate pathway.

Cell Host Microbe. 2025;33(6):901-914.e6 - PMID: 40449488 - PMCID: PMC12169427 - DOI: 10.1016/j.chom.2025.05.007
Barilla RM, Berard C, Sun L, Sandhu S, Zaghouani S, Iyer KS, Altun G, Su CW, Deguine J, Singh V, Hou Y, Kusumakar K, Rutlin ML, Rao M, Zaghouani H, Shi HN, Xavier RJ, Kuchroo VK

Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense.

Science. 2025;:eadn9850 - PMID: 40403128 - DOI: 10.1126/science.adn9850
Halvorsen S, Thomas M, Mino-Kenudson M, Kinowaki Y, Burke KE, Morgan D, Miller KC, Williams KM, Gurung J, McGoldrick J, Hopton M, Hoppe B, Samanta N, Martin S, Tirard A, Arnold BY, Tantivit J, Yarze J, Staller K, Chung DC, Villani AC, Sassi S, Khalili H

Single-cell transcriptomic characterization of microscopic colitis

Nat Commun. 2025;16(1):4618 - PMID: 40383833 - PMCID: PMC12086216 - DOI: 10.1038/s41467-025-59648-8
Humeidi R, Oshiro-Rapley N, Gu X, An JS, Ananthakrishnan AN, Creasey EA, Daly MJ, Schreiber SL, Graham DB, Seyedsayamdost MR, Xavier RJ

The Ulcerative Colitis-Associated Gene NXPE1 Catalyzes Glycan Modifications on Colonic Mucin.

J Am Chem Soc. 2025;147(12):10618-10628 - PMID: 40067145 - PMCID: PMC12076216 - DOI: 10.1021/jacs.5c00769
Kniazeva M, Ruvkun G

Translation elongation defects activate the Caenorhabditis elegans ZIP-2 bZIP transcription factor-mediated toxin defense.

Proc Natl Acad Sci U S A. 2025;122(6):e2423578122 - PMID: 39899724 - PMCID: PMC11831180 - DOI: 10.1073/pnas.2423578122
Seetharaman A, Galagali H, Linarte E, Liu MHX, Cohen JD, Chetal K, Sadreyev R, Tate AJ, Montgomery TA, Ruvkun G

Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans.

PLoS Biol. 2025;23(1):e3002748 - PMID: 39879188 - PMCID: PMC11778786 - DOI: 10.1371/journal.pbio.3002748
Jimena B, Kazimierczyk D, Kazimierczyk S, Moya H, Shin E, Li L, Korgaonkar P, Porter C, Seed B, Cherayil BJ, Jain N

Prenatal maternal infection promotes maternal microchimeric cells to alter infection risk in male offspring.

bioRxiv. 2025;:ePub - PMID: 39896468 - PMCID: PMC11785123 - DOI: 10.1101/2025.01.17.633596
Patange O, Breen P, Arsuffi G, Ruvkun G

Hydrogen sulfide mediates the interaction between C. elegans and Actinobacteria from its natural microbial environment.

Cell Rep. 2025;44(1):115170 - PMID: 39786993 - DOI: 10.1016/j.celrep.2024.115170
Tan ZY, Adade JKA, Gu X, Hecht CJS, Salcius M, Tong B, Liu S, Hwang S, Zécri FJ, Graham DB, Schreiber SL, Xavier RJ

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 - PMID: 39753134 - PMCID: PMC11928285 - DOI: 10.1016/j.chembiol.2024.12.002
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