Artem Barski

This study identifies gene regulatory networks in human memory CD4+ T cells that drive rapid recall, linking specific transcription factors to immune-mediated disease risk.

The paper identifies memory-specific AP-1 recruitment in T cells, driven by epigenetic changes and co-factor interactions, and links it to disease risk variants.

This study defines the transcriptional landscape of CD8+ T cells in pediatric liver transplant rejection using single-cell sequencing and identifies persistent CD8+ clones associated with graft failure.

The paper shows that DNA demethylation during spermatogenesis occurs before nucleosome retention in sperm, contributing to epigenetic reprogramming for embryonic gene regulation.

The paper introduces SciDAP, a platform enabling biologists to analyze single-cell sequencing data without coding expertise using reproducible pipelines.

This paper demonstrates that targeting islet-reactive T effector cells with a combination therapy improves long-term islet graft acceptance in T1D mice.

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

The paper develops and validates a STARR-Seq-based method, Lenti-STARR-Seq, to identify functional cis-regulatory elements in primary human CD4+ T cells, revealing differences between enhancers and negative regulatory elements.

maxATAC provides deep learning models for predicting transcription factor binding sites from ATAC-seq data, improving prediction in primary and single-cell contexts.

The paper identifies Polycomb's role in suppressing a female gene regulatory network in Sertoli cells to maintain testicular differentiation.

This study identifies endogenous retroviruses as drivers of species-specific germline transcriptomes in mammals, particularly through their role in gene activation and enhancer function in spermatogenesis.

The paper shows that super-enhancer switching drives bursts in germline gene expression during the mitosis-to-meiosis transition in testis.

CWL-Airflow extends Apache Airflow to support Common Workflow Language, enabling portable and reproducible computational workflows across various environments.

The paper investigates how genetic, inflammatory, and epithelial cell differentiation factors regulate CAPN14 expression in eosinophilic esophagitis.

BioWardrobe provides a web-based platform for analyzing epigenomics and transcriptomics data with automated pipelines and visualization tools.