Barski Lab

Publications

Yukawa, M; Jagannathan, S; Vallabh, S; Kartashov, AV; Chen, X; Weirauch, MT; Barski, A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. 2020; 217:e20182009.

Kotliar, M; Kartashov, AV; Barski, A. CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. GigaScience. 2019; 8:giz084.

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

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

Wayman, JA; Thomas, A; Bejjani, A; Katko, A; Almanan, M; Godarova, A; Korinfskaya, S; Cazares, TA; Yukawa, M; Kottyan, LC; et al. An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. 2023; 4:2023.03.07.531590.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; et al. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Editor, Przytycka TM. PLoS Computational Biology. 2023; 19:e1010863.

Nayak, RC; Chang, KH; Singh, AK; Kotliar, M; Desai, M; Wellendorf, AM; Wunderlich, M; Bartram, J; Mizukawa, B; Cuadrado, M; et al. Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis. Nature Communications. 2022; 13:3056.

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 (Baltimore, Md. : 1950). 2022; 208:56.13.

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; 2:100989.

Felton, JM; Bouffi, C; Schwartz, JT; Schollaert, KL; Malik, A; Vallabh, S; Wronowski, B; Magier, AZ; Merlin, L; Barski, A; et al. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. 2021; 14:1271-1281.

Felton, JM; Vallabh, S; Parameswaran, S; Edsall, LE; Ernst, K; Wronowski, B; Malik, A; Kotliar, M; Weirauch, MT; Barski, A; et al. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of immunology (Baltimore, Md. : 1950). 2021; 207:1044-1054.

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.

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; 13:613-630.

Milewski, D; Shukla, S; Gryder, BE; Pradhan, A; Donovan, J; Sudha, P; Vallabh, S; Pyros, A; Xu, Y; Barski, A; et al. FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene: Including Oncogene Reviews. 2021; 40:2182-2199.

Lavery, WJ; Barski, A; Wiley, S; Schorry, EK; Lindsley, AW. KMT2C/D COMPASS complex-associated diseases [KCDCOM-ADs]: an emerging class of congenital regulopathies. Clinical Epigenetics. 2020; 12:10.

Maezawa, S; Sakashita, A; Yukawa, M; Chen, X; Takahashi, K; Alavattam, KG; Nakata, I; Weirauch, MT; Barski, A; Namekawa, SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nature Structural and Molecular Biology. 2020; 27:978-988.

Sakashita, A; Maezawa, S; Takahashi, K; Alavattam, KG; Yukawa, M; Hu, Y; Kojima, S; Parrish, NF; Barski, A; Pavlicev, M; et al. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nature Structural and Molecular Biology. 2020; 27:967-977.

Barski, A. Epigenomics of T Cell Activation and Memory. Journal of immunology (Baltimore, Md. : 1950). 2020; 204:78.21.

Pilarowski, GO; Cazares, T; Zhang, L; Benjamin, JS; Liu, K; Jagannathan, S; Mousa, N; Kasten, J; Barski, A; Lindsley, AW; et al. Abnormal Peyer patch development and B-cell gut homing drive IgA deficiency in Kabuki syndrome. Journal of Allergy and Clinical Immunology. 2020; 145:982-992.

Yukawa, M; Jagannathan, S; Vallabh, S; Kartashov, AV; Chen, X; Weirauch, MT; Barski, A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. 2020; 217:e20182009.

Vanoni, S; Zeng, C; Marella, S; Uddin, J; Wu, D; Arora, K; Ptaschinski, C; Que, J; Noah, T; Waggoner, L; et al. Identification of anoctamin 1 (ANO1) as a key driver of esophageal epithelial proliferation in eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2020; 145:239-254.e2.

Kotliar, M; Kartashov, AV; Barski, A. CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. GigaScience. 2019; 8:giz084.

Barski, A; Yukawa, M; Jagannathan, S; Kartashov, AV; Chen, X; Weirauch, MT. Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation. Journal of immunology (Baltimore, Md. : 1950). 2019; 202:125.13.

Miller, DE; Forney, C; Rochman, M; Cranert, S; Habel, J; Rymer, J; Lynch, A; Schroeder, C; Lee, J; Sauder, A; et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3-Genes Genomes Genetics. 2019; 9:729-736.

Alavattam, KG; Maezawa, S; Sakashita, A; Khoury, H; Barski, A; Kaplan, N; Namekawa, SH. Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. Nature Structural and Molecular Biology. 2019; 26:175-184.

Miller, DE; Forney, C; Rochman, M; Cranert, S; Habel, J; Rymer, J; Lynch, A; Schroeder, C; Lee, J; Sauder, A; et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3-Genes Genomes Genetics. 2019; 9:729-736.

Maezawa, S; Alavattam, KG; Tatara, M; Nagai, R; Barski, A; Namekawa, SH. A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. Biology of Reproduction. 2019; 100:409-419.