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 refolding of cancer genome drives tumor pathogenicity, and to leverage this mechanistic understanding for improved treatments.

To learn about our research interests and specifics of our projects check the lab's website. Briefly, our lab studies breast, B, and T Notch-mutated malignancies to elucidate how oncogenic subversion of transcription factors instruct genome mis-folding. We use established genome-wide chromatin assays and combine them with novel technologies such as chromatin conformation capture and single-cell genomics and imaging. We complement the readouts of these data-rich assays with novel computational methods to elucidate precise epigenetic drivers of transcription mis-regulation in Notch-addicted 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.


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
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
Institute for Biomedical Informatics, 2015 - present
Abramson Family Cancer Research Institute, 2015 - present
Institute for Immunology, 2015 - present
Abramson Cancer Center, 2015 - present
Penn Epigenetic Institute, Cancer and Metabolic Epigenetics Interest Group, 2016 - Present
American Association for Cancer Research, 2017 - present

Web Links

Selected Publications

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, 2020, PMID:32123397

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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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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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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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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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