A photo of Artem Barski.

Artem Barski, PhD


  • Director, Epigenomics Data Analysis Core
  • Associate Professor, UC Department of Pediatrics

About

Biography

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.

Publications

Selected

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.

Selected

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

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

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

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

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

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.

From the Blog


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