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 organization and regulation. Our expertise in chromatin, cancer, and computational biology enables us to deploy multidisciplinary and multimodal approaches to rigorously define cause-and-effect relationships among transcriptional regulators, chromatin folding, and gene expression in cancer.
Current projects focus on lymphoma and breast cancer and explore: (i) how epigenetic control of gene expression is disrupted, (ii) how transcriptional dependencies arise and are maintained, and (iii) how the heterogeneity and plasticity of these dependencies enable drug resistance.
More details are available 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, Andre Nussenzweig Lab, 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) Study Section, National Institutes of Health, 2025-Present
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*, Nature Cell Biology 28(1): 149–165, 2025, PMID:41331087
OLIVE provides rapid visualization and analysis of chromatin tracing experiments
Zhou Y, Sheng Y, Hu D, Jay A, Vahedi G, Faryabi RB., Cell Reports Methods 5(): 101209, 2025
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*, Science Immunology 10(113): eadz0472, 2025, PMID:41270190
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, PMID:39110799
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, PMID:9277592
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
Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes.
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*, Nature Metabolism 4(2): 284-299, 2022, PMID:35228745
EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells.
Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB, Molecular Cell 82(5): 1003-1020, 2022, PMID:35182476
Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques.
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*, Molecular Cell 73(6): 1174-1190.e12, 2019, PMID:30745086
