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.
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.
Epigenetics; epigenomics; immunology; T cell memory
Allergy and Immunology, Human Genetics
AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. 2020; 217:e20182009.
CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. GigaScience. 2019; 8:giz084.
PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. Cell Death and Disease. 2023; 14:501.
An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. 2023; 4:2023.03.07.531590.
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19:e1010863.
Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis. Nature Communications. 2022; 13:3056.
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.
Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. STAR Protocols. 2021; 2:100989.
Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. 2021; 14:1271-1281.