Barski Lab

Publications

Felton, JM; Edsall, LE; Troutman, TD; Mack, L; Kotliar, M; Morgenstern, NB-B; Psaila, AM; Rochman, M; Klingler, AM; Osswald, GA; Barski, A; Quinlan, KGR; Weirauch, MT; Rothenberg, ME. Epigenetic and transcriptional programming of murine eosinophils in the esophagus. Nature Communications. 2025; 16(1):10454.

Rochman, Y; Kotliar, M; Klingler, AM; Rochman, M; Alameh, M-G; Melamed, JR; Osswald, GA; Caldwell, JM; Felton, JM; Mack, LE; Hargis, J; Lewkowich, IP; Barski, A; Weissman, D; Rothenberg, ME. Allergen-specific mRNA-lipid nanoparticle therapy for prevention and treatment of experimental allergy in mice. Journal of Clinical Investigation. 2025; 135(21).

Smith, S; Kotliar, M; Wunderlich, M; Wellendorf, A; Das, S; Mizukawa, B; Barski, A; Rai, S; Cancelas, J; Nayak, R. Chromatin remodeler SATB2 thorough Bmi1/PRC1 activity controls transformation and reprogramming of ph+ B-cell progenitors. Blood. 2025; 146(Supplement 1):5032-5032.

Peters, AL; Depasquale, EAK; Begum, G; Roskin, KM; Kotliar, M; Barski, A; Salomonis, N; Shi, T; Ranganathan, S; Woodle, ES; Hildeman, DA. Single-cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells. American Journal of Transplantation. 2025; 25(11):2345-2360.

Lin, S; Kotliar, M; Vallabh, S; Ptasinska, A; Assi, SA; Wunderlich, M; Bonifer, C; Barski, A; Mulloy, JC. Fusion-specific chromatin profiles mediate transcriptional heterogeneity in MLL-rearranged acute lymphoblastic leukemia. Blood advances. 2025; 9(4):856-861.

Johansen, AKZ; Kasam, RK; Vagnozzi, RJ; Lin, S-CJ; Gomez-Arroyo, J; Shittu, A; Bowers, SLK; Kuwabara, Y; Grimes, KM; Warrick, K; Sargent, MA; Baldwin, TA; Quaggin, SE; Barski, A; Molkentin, JD. Transcription Factor 21 Regulates Cardiac Myofibroblast Formation and Fibrosis. Circulation Research. 2025; 136(1):44-58.

Kotliar, M; Kartashov, A; Barski, A. Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach. Methods in Molecular Biology. 2025; 2880:255-292.

Brown, AP; Parameswaran, S; Cai, L; Elston, S; Pham, C; Barski, A; Weirauch, MT; Ji, H. Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells. Environmental Epigenetics. 2025; 11(1):dvaf007.

Ben-Baruch Morgenstern, N; Rochman, M; Kotliar, M; Dunn, JLM; Mack, L; Besse, J; Natale, MA; Klingler, AM; Felton, JM; Caldwell, JM; Barski, A; Rothenberg, ME. Single-cell RNA-sequencing of human eosinophils in allergic inflammation in the esophagus. Journal of Allergy and Clinical Immunology. 2024; 154(4):974-987.

Proper, SP; Dwyer, AT; Appiagyei, A; Felton, JM; Ben-Baruch Morgenstern, N; Marlman, JM; Kotliar, M; Barski, A; Troutman, TD; Rothenberg, ME; Mersha, TB; Azouz, NP. Aryl hydrocarbon receptor and IL-13 signaling crosstalk in human keratinocytes and atopic dermatitis. Frontiers in Allergy. 2024; 5:1323405.

Potter, SJ; Zhang, L; Kotliar, M; Wu, Y; Schafer, C; Stefan, K; Boukas, L; Qu'd, D; Bodamer, O; Simpson, BN; Barski, A; Lindsley, AW; Bjornsson, HT. KMT2D regulates activation, localization, and integrin expression by T-cells. Frontiers in Immunology. 2024; 15:1341745.

Rochman, Y; Kotliar, M; Ben-Baruch Morgenstern, N; Barski, A; Wen, T; Rothenberg, ME. TSLP shapes the pathogenic responses of memory CD4+ T cells in eosinophilic esophagitis. Science Signaling. 2023; 16(802):eadg6360.

Maezawa, S; Yukawa, M; Hasegawa, K; Sugiyama, R; Iizuka, M; Hu, M; Sakashita, A; Vidal, M; Koseki, H; Barski, A; Defalco, T; Namekawa, SH. PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. Cell Death and Disease. 2023; 14(8):501.

Stefan, K; Barski, A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics. 2023; 24(1):253.

Brusilovsky, M; Rochman, M; Shoda, T; Kotliar, M; Caldwell, JM; Mack, LE; Besse, JA; Chen, X; Weirauch, MT; Barski, A; Rothenberg, ME. Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling. Gut. 2023; 72(5):834-845.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Prasath, VBS; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19(1):e1010863.

Nayak, RC; Chang, KH; Singh, AK; Kotliar, M; Desai, M; Wellendorf, AM; Wunderlich, M; Bartram, J; Mizukawa, B; Cuadrado, M; Dexheimer, P; Barski, A; Bustelo, XR; Nassar, NN; Cancelas, JA. Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis. Nature Communications. 2022; 13(1):3056.

Korinfskaya, S; Kotliar, M; Katko, A; Hildeman, D; Miraldi, ER; Barski, A. Role of transcription factor RUNX1 in the maintenance of T helper cell epigenome and rapid recall response. Journal of Immunology. 2022; 208(Supplement_1):56.13-56.13.

Surumbayeva, A; Kotliar, M; Gabitova-Cornell, L; Kartashov, A; Peri, S; Salomonis, N; Barski, A; Astsaturov, I. Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. STAR Protocols. 2021; 2(4):100989.

Felton, JM; Bouffi, C; Schwartz, JT; Schollaert, KL; Malik, A; Vallabh, S; Wronowski, B; Magier, AZ; Merlin, L; Barski, A; Weirauch, MT; Fulkerson, PC; Rothenberg, ME. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. 2021; 14(6):1271-1281.

Felton, JM; Vallabh, S; Parameswaran, S; Edsall, LE; Ernst, K; Wronowski, B; Malik, A; Kotliar, M; Weirauch, MT; Barski, A; Fulkerson, PC; Rothenberg, ME. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of Immunology. 2021; 207(4):1044-1054.

Chidambaran, V; Zhang, X; Pilipenko, V; Chen, X; Wronowski, B; Geisler, K; Martin, LJ; Barski, A; Weirauch, MT; Ji, H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics. 2021; 13(8):613-630.

Milewski, D; Shukla, S; Gryder, BE; Pradhan, A; Donovan, J; Sudha, P; Vallabh, S; Pyros, A; Xu, Y; Barski, A; Millay, DP; Khan, J; Kalinichenko, VV; Kalin, TV. FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene. 2021; 40(12):2182-2199.

Korinfskaya, S; Parameswaran, S; Weirauch, MT; Barski, A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Frontiers in Immunology. 2021; 12:701924.