Robert Babak Faryabi, PhD
Associate Professor of Pathology and Laboratory Medicine
Assistant Professor of Cancer Biology
Perelman School of Medicine at the University of Pennsylvania
Contact InformationBiomedical Research Building (BRB) II/III, Room 553
421 Curie Boulevard
Philadelphia, PA 19104
Office: 215-573-8220
Email: faryabi@pennmedicine.upenn.edu
Specialty Division
Precision and Computational Diagnostics, Cancer and Immunobiology
Itmat Expertise
Cancer Epigenetics
Genome Architecture
Chromatin Biology
Computational Biology
Clinical Expertise
Cancer Genomics
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/
Graduate Groups
Cell and Molecular Biology
Genomics and Computational Biology
Immunology
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
Specialty Certification
Postgraduate Training
Postdoctoral Research Fellow, Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, 2009-2015
Awards and Honors
Edward S. Rogers Sr. Scholarship, University of Toronto, Ontario, Canada, 2003-2004
Texas Student Research Award Prize, 2007
Cancer Research Training Award, National Cancer Institute, 2009-2014
Institute of Biomedical Informatics Travel Award, University of Pennsylvania, 2016
Cooper Scholar Award, Abramson Cancer Center, 2017
Conquer Cancer Now Award, Concern Foundation, 2018
Career Catalyst Research Award, Susan G. Komen Foundation, 2018
Standing Member, Gene Regulation In Cancer (GRIC), National Institutes of Health, 2025
Memberships and Professional Organizations
Institute of Electrical and Electronics Engineers, 2003-present
International Society for Computational Biology, 2006-present
American Association for Cancer Research, 2017-present
PA Breast Cancer Coalition, 2017-2018
Netherlands Organization for Scientific Research, 2020
Department of Defense, 2020
National Institute of Health, 2020-Present
Molecular and Organismic Biology, German Research Foundation, 2022-2022
Web Links
Selected Publications
Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation
Zhou Y, Jay A, Burget N, Friedrich T, Yoon S, Alsing J, Nir G, Grosschedl R, Vahedi G, Faryabi RB., Nat Cell Biol, 2025, PMID:41331087
Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes
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., Sci Immunol 10(): eadz0472, 2025, PMID:41270190
OLIVE provides rapid visualization and analysis of chromatin tracing experiments
Zhou Y, Sheng Y, Hu D, Jay A, Vahedi G, Faryabi RB., Cell Rep Methods 5(): 101209, 2025, PMID:41118766
The Novel Immunocompetent Eµ-SOX11CCND1 Mouse Model Phenotypically and Molecularly Resembles Human Mantle Cell Lymphoma
Jafari H, Brown-Burke F, Pray B, Sloan S, Helmig-Mason J, Hout I, Leon S, Long M, Chan WK, Hanel W, Corps K, Leshchenko VV, Edwards D, Prakash Shukla R, Reci S, Vaddi K, Scherle P, Collier P, La Ferlita A, Singh S, Distefano R, Lapalombella R, Sehgal L, Faryabi RB, Meydan C, Mason CE, Baiocchi RA, Parekh S, Alinari L., Clin Cancer Res 31(): 4571-4585, 2025, PMID:40857109
Single-allele chromatin tracing reveals genomic clustering of paralogous transcription factors as a mechanism for developmental robustness in T Cells
Jay A*, Zhou Y*, Yoon S, Abeje BN, Chandra A, Wald J, Raj A, Faryabi RB#, Vahedi G#, bioRxiv, 2025
Azurify integrates cancer genomics with machine learning to classify the clinical significance of somatic variants
Bigdeli A, Chandrashekar DS, Chitturi A, Rushton C, Mackinnon AC, Segal J, Harada S, Sacan A, Faryabi RB, bioRxiv, 2025
Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance
Perlman BS, Burget NG, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB, Nature Communications 15(1): , 2024
Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells
Zhao J, Zhou Y, Tzelepis I, Burget NG, Shi J, Faryabi RB, Science Advances 10(22): , 2024
AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics
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, Nature Communications 15(1): , 2024, PMID:38702321
Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets
Patil AR, Schug J, Liu C, Lahori D, Descamps HC; Human Pancreas Analysis Consortium; Naji A, Kaestner KH, Faryabi RB, Vahedi G., Cell Reports Medicine 5(5): , 2024, PMID:38677282
