Martin Aryee

Detection of allele-specific expression in spatial transcriptomics with spASE.

Zou LS, Cable DM, Barrera-Lopez IA, Zhao T, Murray E, Aryee MJ, Chen F, Irizarry RA.

Genome Biol. 2024 Jul 08. 25(1):180. PMID: 38978101

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.

Liu C, Nagashima H, Fernando N, Bass V, Gopalakrishnan J, Signorella S, Montgomery W, Lim AI, Harrison O, Reich L, Yao C, Sun HW, Brooks SR, Jiang K, Nagarajan V, Zhao Y, Jung S, Phillips R, Mikami Y, Lareau CA, Kanno Y, Jankovic D, Aryee MJ, Pekowska A, Belkaid Y, O'Shea J, Shih HY.

Immunity. 2024 May 14. 57(5):1005-1018.e7. PMID: 38697116

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.

Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N.

Nat Immunol. 2024 Apr. 25(4):644-658. PMID: 38503922

Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma.

Coley AK, Lu C, Pankaj A, Emmett MJ, Lang ER, Song Y, Xu KH, Xu N, Patel BK, Chougule A, Nieman LT, Aryee MJ, Ferrone CR, Deshpande V, Franses JW, Ting DT.

bioRxiv. 2023 Dec 05. PMID: 38105940

Spatial transcriptomics reveals distinct tissue niches linked with steroid responsiveness in acute gastrointestinal GVHD.

Patel BK, Raabe MJ, Lang ER, Song Y, Lu C, Deshpande V, Nieman LT, Aryee MJ, Chen YB, Ting DT, DeFilipp Z.

Blood. 2023 11 23. 142(21):1831-1844. PMID: 37699201

High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics.

Sept CE, Tak YE, Cerda-Smith CG, Hutchinson HM, Goel V, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone S, Eyler CE, Aryee MJ.

bioRxiv. 2023 Oct 28. PMID: 37961446

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization.

Cerda-Smith CG, Hutchinson HM, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE, Wood KC.

bioRxiv. 2023 Sep 21. PMID: 37786671

Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.

Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG.

Nat Biotechnol. 2023 Sep. 41(9):1345. PMID: 37653227

DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs.

Guo H, Vuille JA, Wittner BS, Lachtara EM, Hou Y, Lin M, Zhao T, Raman AT, Russell HC, Reeves BA, Pleskow HM, Wu CL, Gnirke A, Meissner A, Efstathiou JA, Lee RJ, Toner M, Aryee MJ, Lawrence MS, Miyamoto DT, Maheswaran S, Haber DA.

Cell. 2023 06 22. 186(13):2765-2782.e28. PMID: 37327786

Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response.

Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N.

bioRxiv. 2023 Apr 06. PMID: 37066412