Robert Babak Faryabi, Ph.D.
Associate Professor of Pathology and Laboratory Medicine
Associate Investigator, Abramson Family Cancer Research Institute
Bioinformatics Faculty Lead, Penn Center for Personalized Diagnostics
Faculty Member, Institute for Immunology
Member, Abramson Cancer Center
Senior Fellow, Institute for Biomedical Informatics
Core Faculty Member, Penn Epigenetics Institute
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations
Contact information
Room 553 BRB II/III, 421 Curie Boulevard
Philadelphia, PA 19104
Philadelphia, PA 19104
Office: (215)573-8220
Publications
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.
Permanent linkBSc (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.
Description of Clinical Expertise
Cancer GenomicsDescription of 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
Selected Publications
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), September 2024.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), August 2024.
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.
Patil AR, Schug J, Liu C, Lahori D, Descamps HC; Human Pancreas Analysis Consortium; Naji A, Kaestner KH, Faryabi RB, Vahedi G.: Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Cell Reports Medicine 5(5), May 2024.
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: Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nature Immunology 24(10), October 2023.
McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS: The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR+ CD8+ effector state, and its deletion improves checkpoint blockade. Cell Reports 42(8), August 2023.
Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G: Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. Nature Metabolism 5(5): 713-715, May 2023.
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, February 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, February 2022 Notes: Preview, Bayer M and Grosschedl R, Mol Cell: 82(5), 884-886, February 2022.
Schwartz WG, Zhou Y, Petrovic J, Pear WS, Faryabi RB: TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes. Cell Reports 38(8), August 2021.