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Jaiswal A, Kooistra T, Pokatayev V, Bastos HN, Santos RF, Sarraf TR, Segerstolpe Å, Lin C, Amir-Zilberstein L, Twardus S, Shannon K, Murphy SP, Knipe R, Ganzleben IK, Black KE, Delorey TM, Graham DB, Hung YP, Hariri LP, Deguine J, Carvalho A, Medoff BD, Xavier RJ

Spatial transcriptomics reveals altered communities and drivers of aberrant epithelia and pro-fibrotic fibroblasts in interstitial lung diseases.
Cell Genom. 2026;:101066 - PMID: 41576947 - DOI: 10.1016/j.xgen.2025.101066

Rush JS, Wertheimer JD, Goldberg SD, Raymond D, Szuchnicki M, Baltus AJ, Branson J, Stratton CF, Patrick AN, Steele R, Adhikary S, Del Rosario A, Liu A, Gomersall NJ, Chung M, Ranaghan MJ, Gu X, Brandt M, Cao Z, Bebenek A, Oliver BA, Hoebe K, Szewczuk LM, Venable JD, Graham DB, Towne J, Xavier RJ

Human genetics guides the discovery of CARD9 inhibitors with anti-inflammatory activity.
Cell. 2026;:ePub - PMID: 41547356 - PMCID: PMC12817910 - DOI: 10.1016/j.cell.2025.12.013

Ashenberg O, Xavier RJ

Bridging AI and biology: Foundation models meet human physiology and disease.
Med. 2026;7(1):100971 - PMID: 41519120 - DOI: 10.1016/j.medj.2025.100971

Pokatayev V, Jaiswal A, Shih AR, Segerstolpe Å, Li B, Creasey EA, Zhao Y, Lin C, Murphy S, Chou CH, Graham DB, Xavier RJ

Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit.
Nature. 2026;:ePub - PMID: 41501466 - PMCID: PMC12820784 - DOI: 10.1038/s41586-025-09907-x

Thurimella K, Mohamed AMT, Li C, Vatanen T, Graham DB, Owens RM, La Rosa SL, Plichta DR, Bacallado S, Xavier RJ

Protein language models uncover carbohydrate-active enzyme function in metagenomics.
BMC Bioinformatics. 2025;26(1):285 - PMID: 41299229 - PMCID: PMC12659350 - DOI: 10.1186/s12859-025-06286-y

Bond AN, Orzechowski M, Zhang S, Ben-Zion I, Lemmer A, Garry N, Lee K, Chen M, Delano K, Gath E, Golas AL, Nietupski R, Fitzgerald M, Ehrt S, Rubin EJ, Sassetti CM, Schnappinger D, Shoresh N, Hunt DK, Gomez JE, Hung DT

Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis.
Nat Commun. 2025;16(1):9673 - PMID: 41184262 - PMCID: PMC12583738 - DOI: 10.1038/s41467-025-64662-x

Tan P, Jaiswal A, Murphy SP, Brown EM, Wheeler H, Su CW, Finan EP, Jasso GJ, Shi HN, Graham DB, Delorey TM, Deguine J, Xavier RJ

Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation.
Science. 2025;390(6772):eadr3545 - PMID: 41166460 - DOI: 10.1126/science.adr3545

Jabbar KS, Priya S, Xu J, Das Adhikari U, Pishchany G, Mohamed ATM, Johansen J, Thurimella K, McCabe C, Vlamakis H, Okello S, Delorey TM, Lankowski A, Mosepele M, Siedner MJ, Plichta DR, Kwon DS, Xavier RJ

Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.
Nat Microbiol. 2025;10(11):2720-2735 - PMID: 41168431 - DOI: 10.1038/s41564-025-02157-7

Nie X, Sheen J, Ye R

The plant epigenome governed by nutrients and metabolism.
Curr Opin Plant Biol. 2025;88:102820 - PMID: 41167146 - DOI: 10.1016/j.pbi.2025.102820

Neo DM, Ben-Zion I, Bagnall J, Solomon MY, Bond AN, Gath E, Zhang S, Shoresh N, Gomez J, Hung DT

A Multiplexed, Target-Based Phenotypic Screening Platform Using CRISPR Interference in Mycobacterium abscessus.
ACS Infect Dis. 2025;11(11):3263-3275 - PMID: 41139833 - PMCID: PMC12624723 - DOI: 10.1021/acsinfecdis.5c00623

Goering ER, Clatworthy AE, Parada-Kusz M, Bagnall J, Hung DT

Kmo restricts Salmonella in a whole organism infection model by promoting macrophage lysosomal acidification through kainate receptor antagonism.
PLoS Pathog. 2025;21(10):e1013273 - PMID: 41129589 - PMCID: PMC12571273 - DOI: 10.1371/journal.ppat.1013273

Penaranda C, Brenner EP, Clatworthy AE, Cosimi LA, Ravi J, Hung DT

Mapping genetic and phenotypic diversity of Pseudomonas aeruginosa across clinical and environmental isolation sites.
bioRxiv. 2025;:ePub - PMID: 41040319 - PMCID: PMC12485682 - DOI: 10.1101/2025.09.22.677895

Chen X, Hwang HS, Li B, Zhao Y, Ghosh K, Deng L, Creasey EA, Ashenberg O, Graham DB, Xavier RJ

Nuclear receptor coregulator NRIP1 R448G modulates T cell gut homing to control intestinal inflammation.
Proc Natl Acad Sci U S A. 2025;122(38):e2508269122 - PMID: 40966276 - PMCID: PMC12478152 - DOI: 10.1073/pnas.2508269122

Xu J, Kong L, Creasey EA, Rath S, Deng L, Avila-Pacheco J, Li C, Oliver BA, Dao TT, Shih AR, Daly MJ, Shalek AK, Clish CB, Graham DB, Deguine J, Xavier RJ

Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation.
J Exp Med. 2025;222(11):ePub - PMID: 40932625 - DOI: 10.1084/jem.20250185

Sullivan JR, Ferrara K, Barrick R, Romano KP, Warrier T, Hung DT

An Inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa.
bioRxiv. 2025;:ePub - PMID: 40964384 - PMCID: PMC12439951 - DOI: 10.1101/2025.09.11.675340

Kniazeva M, Ruvkun G

A spurious fln-2 mutation in a wide variety of commonly used C. elegans strains.
MicroPubl Biol. 2025;2025:ePub - PMID: 40708994 - PMCID: PMC12287765 - DOI: 10.17912/micropub.biology.001684

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;57(7):1742-1753 - PMID: 40562913 - PMCID: PMC12709777 - DOI: 10.1038/s41588-025-02225-y

Zhu G, Yuan W, Wang K, Wu H, Lv K, Wang X, Tuffour A, Ren B, Zhang J, Jiang C, Jiang Y, Hsiang T, Yu PS, Ausubel FM, Zhang L, Dai H, Liu X

Feature-Based Molecular Networking Guided Characterization of Clonocoprogen Siderophores with Anti-Pseudomonas aeruginosa Activity in Nematodes through Immune Up-Regulating Effects.
ACS Chem Biol. 2025;20(7):1450-1456 - PMID: 40545628 - DOI: 10.1021/acschembio.5c00178

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;389(6757):260-267 - PMID: 40403128 - PMCID: PMC12632183 - 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

Mishra B, Basu A, Shehadeh F, Felix L, Kollala SS, Chhonker YS, Naik MT, Dellis C, Zhang L, Ganesan N, Murry DJ, Gu J, Sherman MB, Ausubel FM, Sotiriadis PP, Mylonakis E

Antimicrobial Peptide Developed with Machine Learning Sequence Optimization Targets Drug Resistant Staphylococcus aureus in Mice.
J Clin Invest. 2025;135(12):ePub - PMID: 40261713 - PMCID: PMC12165799 - DOI: 10.1172/JCI185430

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

Meirelles LA, Persat A.

Decoding host-microbe interactions with engineered human organoids
EMBO J. 2025;44:1569–1573 - PMID: 39984757 - PMCID: PMC11914615 - DOI: 10.1038/s44318-025-00387-3

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
Total: 2498