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 Folding
Chromatin Biology
Computational Biology
Clinical Expertise
Cancer Genomics
Research Expertise
Cancer is typically considered a genetic disease. However, recent progress in our understanding of epigenetic aberrations in cancer has challenged this view. Overarching goal of Faryabi lab is to understand epigenetic mechanisms of transcriptional addiction in cancer and exploit this information to advance cancer therapeutics.
To pursue this objective, we use cutting-edge chromatin conformation capture, high-content imaging, single-cell epigenomics, functional genomics, and combine these technologies with our expertise in computational sciences to systematically explore: i) how epigenetic control of gene expression is disrupted in cancer, ii) why transcriptional addiction can develop, and iii) how heterogeneity and plasticity of transcriptional dependencies enable drug resistance.
More details on the Faryabi Lab website faryabiLab.com
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
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
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
Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity
Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, John Wherry E, Sidoli S, Maillard I, Vahedi G, Nature Immunology 24(10): , 2023, PMID:37592014
The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR+ CD8+ effector state, and its deletion improves checkpoint blockade
McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS, Cell Reports 42(8): , 2023, PMID:36824931
Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program
Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G, Nature Metabolism 5(5): 713-715, 2023, PMID:37188822
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
TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes.
Schwartz WG, Zhou Y, Petrovic J, Pear WS, Faryabi RB, Cell Reports 38(8): , 2021, PMID:34433064
