R. Babak Faryabi Lab – Penn Epigenetics

Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4+ T cells

Atishay Jay, Yeqiao Zhou, Sora Yoon, Bereketab N Abeje, Aditi Chandra, Michael F Michieletto, Julia Wald, Jorge Henao-Mejia, Arjun Raj, Robert B Faryabi, Golnaz Vahedi. Single-allele chromatin tracing reveals cytokine-dependent […]

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Yeqiao Zhou, Atishay Jay, Noah Burget, Tobias Friedrich, Sora Yoon, Jessica Alsing, Guy Nir, Rudolf Grosschedl, Golnaz Vahedi, Robert B. Faryabi. Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene [...]

OLIVE provides rapid visualization and analysis of chromatin tracing experiments

Yeqiao Zhou, Yimin Sheng, Dongbo Hu, Atishay Jay, Golnaz Vahedi, Robert B. Faryabi. OLIVE provides rapid visualization and analysis of chromatin tracing experiments. Cell Rep Methods. 2025 Nov 17;5(11):101209. doi: [...]

Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes

Maryam Abedi, Priyadarshini Rai, Yeqiao Zhou, Chengyang Liu, Isabelle Johnson, Aditi Chandra, Maria Fasolino, Susan Rostami, Wei Wang, Zaw Min, Yanjing Li, Ming Yu, Atishay Jay, Vung Lian, Michael Silverman, [...]

Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells

Jingru Zhao, Yeqiao Zhou, Illias Tzelepi, Noah G. Burget, Junwei Shi, & Robert B. Faryabi. Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells. 7 Aug […]

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

Brent S. Perlman, Noah Burget, Yeqiao Zhou, Gregory W. Schwartz, Jelena Petrovic, Zora Modrusan & Robert B. Faryabi. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nat Commun 15, 8070 (2024). […]

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Aanchal Mongia, Fatema Tuz Zohora, Noah G. Burget, Yeqiao Zhou, Diane C. Saunders, Yue J. Wang, Marcela Brissova, Alvin C. Powers, Klaus H. Kaestner, Golnaz Vahedi, Ali Naji, Gregory W. […]

Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets

Abhijeet R. Patil, Jonathan Schug, Chengyang Liu, Deeksha Lahori, Hélène C. Descamps, the Human Pancreas Analysis Consortium, Ali Naji, Klaus H. Kaestner, Robert B. Faryabi, Golnaz Vahedi. Modeling type 1 […]

Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity

Naomi Goldman, Aditi Candra, Isabelle Johnson, Matthew A. Sullivan, Abhijeet R. Patil, Ashley Vanderbeck, Atishay Jay, Yeqiao Zhou, Emily K. Ferrari, Leland Mayne, Jennifer Aguilan, Hai-Hui Xue, Robert B. Faryabi, […]

TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes

Schwartz GW, Zhou Y, Petrovic J, Pear WS, Faryabi RB. Cell Rep. 2021;36(8):109575. doi: 10.1016/j.celrep.2021.109575. PMID: 34433064.

Publication Lab: R. Babak Faryabi Lab