Faculty

Robert Babak Faryabi, Ph.D.

Associate Professor of Pathology and Laboratory Medicine

Department: Pathology and Laboratory Medicine

Graduate Group Affiliations

Contact information

Room 14-114, 3600 Civic Center Boulevard
Philadelphia, PA 19104

Office: (215)573-8220

Email:
faryabi@pennmedicine.upenn.edu

Publications

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Education:
BSc (Electrical and Computer Engineering)
Sharif University of Technology, Tehran, Iran, 1995.
MSc (Electrical and Computer Engineering)
Sharif University of Technology, Tehran, Iran, 1997.
PhD (Computational Biology)
Texas A&M University, College Station, TX, 2009.

Links
Search PubMed for articles
Lab Website

Permanent link

> Perelman School of Medicine > Faculty > Details

Description of Clinical Expertise

Cancer Genomics

Description of Research Expertise

The overarching goal of our lab is to advance the mechanistic understanding of human cancer genome architecture and regulation. The lab expertise in chromatin, cancer, and computational biology allows us to deploy multidisciplinary approaches to rigorously define the cause-and-effect relationship between transcriptional regulators, chromatin organization, and gene expression in cancer. Current projects in the lab focuses on lymphoma and breast cancer and explore: i) how epigenetic control of gene expression is disrupted, ii) how transcriptional dependencies can develop, and iii) how heterogeneity and plasticity of transcriptional dependencies enable drug resistance in these cancers.

More details on the Faryabi Lab website https://faryabilab.com/

Selected Publications

Zhou Y^, Jay A^, Burget N, Friedrich T, Yoon S, Alsing J, Nir G, Grosschedl R, Vahedi G*, Faryabi RB*: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation. Nature Cell Biology 28(1): 149–165, Dec 2025 Notes: ^ co-first author, * co-corresponding author.

Zhou Y, Sheng Y, Hu D, Jay A, Vahedi G, Faryabi RB.: OLIVE provides rapid visualization and analysis of chromatin tracing experiments. Cell Reports Methods 5: 101209, Nov 2025.

Abedi M^, Rai P^, Zhou Y^, Liu C, Johnson I, Chandra A, Fasolino M, Rostami S, Wang W, Min Z, Li Y, Yu M, Jay A, Lian V, Silverman M, Kaestner KH, Naji A, Faryabi RB*, Vahedi G*: Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes. Science Immunology 10(113): eadz0472, Nov 2025 Notes: ^ co-first author, * co-corresponding author.

Zhao J, Zhou Y, Tzelepis I, Burget NG, Shi J, Faryabi RB: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells. Science Advances 10(22), Aug 2024.

Perlman BS^, Burget NG^, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nature Communications 15(1), Sep 2024 Notes: ^ co-first author.

Mongia A, Zohora FT, Burget NG, Zhou Y, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW*, Faryabi RB*: AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics. Nature Communications 15(1), May 2024 Notes: * co-corresponding author.

Fasolino M^, Schwartz GW^, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, the HPAP Consortium, Feldman M, Moore JH, Japp AS, Betts MR, Faryabi RB*, Naji A*, Kaestner KH*, Vahedi G*: Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. Nature Metabolism 4(2): 284-299, Feb 2022 Notes: ^ co-first author, * co-corresponding author.

Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Molecular Cell 82(5): 1003-1020, Feb 2022 Notes: Preview, Bayer M and Grosschedl R, Mol Cell: 82(5), 884-886, February 2022.

Petrovic J^, Zhou Y^, Fasolino M, Goldman N, Schwartz GW, Mumbach MR, Nguyen SC, Rome KS, Sela Y, Zapataro Z, Blacklow SC, Kruhlak MJ, Shi J, Aster JC, Joyce EF, Little SC, Vahedi G, Pear WS*, Faryabi RB*: Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques. Molecular Cell 73(6): 1174-1190.e12, Mar 2019 Notes: ^ co-first author, * co-corresponding author.