A photo of Artem Barski.

Director, Epigenomics Data Analysis Core

Associate Professor, UC Department of Pediatrics


Biography & Affiliation


My research areas are epigenetics, epigenomics, immunology, T cell memory and T cell mechanisms in food allergies. I’m working to understand how T cells remember previous encounters with antigens and how this leads to an enhanced immune response.

During my post-doctoral training in the Keji Zhao lab at the National Institutes of Health (NIH), I participated in the development of ChIP-Seq. This revolutionary method combines ChIP with next-generation sequencing. ChIP-Seq allows for genome-wide mapping of chromatin modifications and transcription factor binding sites with enhanced resolution and sensitivity that far exceed older methods. Since my arrival to Cincinnati Children’s in 2011, my laboratory has been working on epigenomics of immunological memory. In 2017, we described the relationship between epigenetic gene poising and the rapid recall ability of memory T cells. We also reported on the role AP-1 transcription factor plays in chromatin remodeling during T cell activation.

Our laboratory is developing both wet lab and computational approaches for the study of epigenomics. We have created Biowardrobe, a user-friendly platform for processing next-generation sequencing-based data. In order to make data analysis more reproducible, we are using Common Workflow Language (CWL) and developed CWL-Airflow, a pipeline manager for CWL-based workflows. We also run the BioWardrobe/SciDAP bioinformatics server as the Cincinnati Children’s Epigenomics Data Analysis Core.

I am a recipient of the 2011 National Heart, Lung, and Blood Institute’s (NHLBI) Career Transition Award (K22) and 2015 NIH Director’s New Innovator Award (DP2). My work has been published in prestigious journals, including Cell, Nature Structural and Molecular Biology, The Journal of Experimental Medicine, GigaScience, Genome Research and Genome Biology. I have been a researcher for more than 20 years and began working at Cincinnati Children’s in 2011.

Research Interests

Epigenetics; epigenomics; immunology; T cell memory

Academic Affiliation

Associate Professor, UC Department of Pediatrics

Research Divisions

Allergy and Immunology, Human Genetics

Blog Posts

Healthy T Cell Formation Depends on Transcription Factor AP-1 to Open Chromatin

Genomics and Development

Healthy T Cell Formation Depends on Transcription Factor AP-1 to Open Chromatin

Artem Barski, PhD12/2/2020


BS/MS: Moscow State University, Department of Chemistry, Moscow, Russia, 2000.

PhD: University of Southern California, Los Angeles, CA, 2006.

Fellowship: National Institutes of Health (NIH), National Heart Lung, and Blood Institute (NHLBI), Bethesda, MD, 2011.


Selected Publication

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

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

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

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

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

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

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

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

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

Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation. Yukawa, M; Jagannathan, S; Kartashov, A; Chen, X; Weirauch, M; Barski, A. 2019.