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


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


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

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

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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

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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

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TooManyCells Identifies and Visualizes Relationships of Single-cell Clades.

Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Pear WS, Vahedi G, Faryabi RB, Nature Methods 17(): 405-413, 2020, PMID:32123397

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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

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Genetic Variation in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells.

Fasolino M, Goldman N, Wang W, Cattau B, Zhou Y, Petrovic J, Link, VM, Cote A, Chandra A, Silverman, M, Joyce EF, Little SC, the HPAP Consortium, Kaestner KH, Naji A, Raj A, Henao-Mejia J, Faryabi RB, Vahedi G, Immunity 52(2): 257-274, 2020, PMID:32049053

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A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas

Ryan RJH^, Petrovic J^, Rausch DM, Zhou Y, Lareau C, Kluk MJ, Christie AL, Lee W, Guo B, Donohue LKH, Gillespie S, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE*, Aster JC*, Pear WS*, Cell Reports 21(3): 784-797, 2017, PMID:29045844

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The Vascular Landscape of Human Cancer.

Kahn BM^, Lacus A^, Alur RG, Wengyn MD, Schwartz GW, Li J, Sun K, Maurer HC, Olive KP, Faryabi RB*, Stanger BZ*, Journal of Clinical Investigation 1311(2): 10.1172/JCI136655, 2021, PMID:33258803

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Classes of ITD predict outcomes in AML patients treated with FLT3 inhibitors

Schwartz GW, Manning BS, Zhou Y, Velu PD, Bigdeli A, Astles R, Lehman AW, Morrissette JJ, Perl AE, Li M, Carroll M, Faryabi RB., Clinical Cancer Research 25(2): 573-583, 2019, PMID:30181385

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Differential Integration of Transcriptome and Proteome Identifies Pan-cancer Prognostic Biomarkers

Schwartz G, Petrovic J, Zhou Y, Faryabi RB, Frontiers in Genetics 9(): 205, 2018, PMID:29971090

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