Robert Babak Faryabi, PhD

Assistant Professor of Cancer Biology
Assistant Professor of Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania
University of Pennsylvania Perelman School of Medicine

Contact InformationRoom 553 BRB II/III, 421 Curie Boulevard
Philadelphia, PA 19104
Office: (215) 573-8220


Specialty Division

Precision and Computational Diagnostics

Itmat Expertise

Cancer Epigenetics
Computational Biology
Machine Learning

Clinical Expertise

Cancer Genomics

Research Expertise

Our lab focuses on understanding the mechanism of epigenetic dysregulation in cancer. We are particularly interested in elucidating how oncogenic signals contribute to tumor pathogenicity through epigenetic misregulation, and to leverage this mechanistic understanding for improved treatments.

The lab mainly studies cancers with frequent mutations in Notch receptor families. We use combination of wet and dry techniques to understand how oncogenic Notch drives regulatory program in these tumors. Our lab benefits from various established data-rich assays and combine them with novel technologies such as chromatin conformation and single cell genomics to elucidate the mechanisms of epigenetic dysregulation in Notch-driven tumors at both population and single cell levels.

As a member of Center for Personalized Diagnostics, we are also developing computational oncology frameworks to enrich clinical significance of diagnostic tumor genomics. Our goal is to advance the paradigm of personalized medicine by leveraging big data analytics to drive correlation between the tumor genomes and clinical covariates.

To learn more about our research interests and specifics of our projects check our lab's website


BSc (Electrical Engineering), Sharif University of Technology, Tehran, Iran, 1995
MSc (Electrical 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
Career Catalyst Research Award, Susan G. Komen Foundation, 2018
Conquer Cancer Now Award, Concern Foundation, 2018

Memberships and Professional Organizations

Institute of Electrical and Electronics Engineers, 2003 - Present
International Society for Computational Biology, 2006 - Present
Abramson Family Cancer Research Institute, 2015 - present
Institute for Biomedical Informatics, 2015 - present
Abramson Cancer Center, 2015 - present
Institute for Immunology, 2015 - present
Penn Epigenetic Institute, Cancer and Metabolic Epigenetics Interest Group, 2016 - Present
American Association for Cancer Research, 2017 - present

Web Links

Selected Publications

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, 2019, PMID:30745086

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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, 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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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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Functional Proteogenomics Reveals Biomarkers and Therapeutic Targets in Lymphomas

Rolland DC, Basrur V, Jeon Y-K, McNeil-Schwalm C, Fermin D, Conlon K, Zhou Y, Ng SY, Tsou C-C, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ, Proceedings of the National Academy of Sciences 11(24): 6581-6586, 2017, PMID:28607076

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Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.

Barlow JH*, Faryabi RB*, Callen E, Wong N, Malhowski A, Chen H-T, Gutierrez-Cruz G, Sun H-W, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A, Cell 152(3): 620-32, 2013, PMID:23352430

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DNA-damage-induced Differentiation of Leukaemic Cells as an Anti-cancer Barrier.

Santos MA, Faryabi RB, Ergen AV, Day AM, Malhowski A, Canela A, Onozawa M, Lee J-E, Callen E, Gutierrez-Martinez P, Chen H-T, Wong N, Finkel N, Deshpande A, Sharrow S, Rossi DJ, Ito K, Ge K, Aplan PD, Armstrong SA, Nussenzweig A, Nature 514(7520): 107-11, 2014, PMID:25079327

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The DNA Damage- and Transcription-associated Protein Paxip1 Controls Thymocyte Development and Emigration.

Callen E, Faryabi RB, Luckey M, Hao B, Daniel JA, Yang W, Sun H-W, Dressler G, Peng W, Chi H, Ge K, Krangel MS, Park J-H, Nussenzweig A, Immunity 37(6): 971-85, 2012, PMID:23159437

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Recent Advances in the Control of Markovian Gene Regulatory Networks

Faryabi RB, Vahedi G, Datta A, Chamberland J-F, Dougherty ER, Current Genomics 10(7): 540-547, 2009, PMID:20436874

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