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

We are a computational biology lab with focus on cancer epigenomics. Our research spans the areas of cancer biology, computational biology and machine learning. The overarching goal of our lab is to explore how oncogenic cell signaling pathways dysregulate enhancers' landscape of a tumor and understand their function in cancer.

The lab is specifically interested in lymphoma and leukemia which are the cancers of hematopoietic system. In addition to genetic alterations, abnormalities at epigenetic levels may give rise to these malignancies. We use genomics to identify the genetic variations in these tumor types and further elucidate how these genetic events alter a tumor's epigenome using population and single-cell epigenomics techniques.

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 a tumor genome 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

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

Web Links

Selected Publications

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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