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, Immunobiology and Experimental Pathology

Itmat Expertise

Computational Biology
DNA damage
DNA replication

Research Expertise

Mammalian cells orchestrate thousands of replication events along their genome.
Maintenance of genome integrity at the sites of DNA replication is a fundamental feature of proliferating cells and is essential for their survival and tissue homeostasis. Wide array of endogenous factors and exogenous agents known as replication stress conditions disrupt normal progression of DNA replication; which in turn lead to damaged DNA. In response to replication-mediated DNA damage cascades of cellular responses known as DNA damage response (DDR) pathways are activated. For the most part, DDR pathways counteract replicative stress and enable faithful replication. However, unfaithful repair of the replication-induced DNA lesions can lead to structural abnormalities that are reminiscent of those observed in cancers. While the process of sensing and repair of replication-mediated breaks irrespective of their genomic location has been extensively studied, we know very little about the genome-wide footprints of various sources of replicative stress.

The focus of Faryabi Lab is to explore the genome-wide signatures of mechanistically distinct sources of replicative stress and their contributions to hematological malignancies. More specifically, we strive to understand how various sources of intrinsic and/or extrinsic replicative stress shape the landscape of assaults on the genome integrity of immune cells; and furthermore investigate how replication stress-induced lesions contributing to the genesis of neoplastic structural variations observed in hematologic tumors.

To better understand the role of DNA replication and repair mechanisms in shaping the genomic landscape of tumors, we benefit from high-throughput measurement technologies to gather systems-level genomics, epigenomics, and functional genomics data on normal and perturbed immune cells. Our lab uses combinations of big data analytics, mathematical modeling and machine learning algorithms, and develop methods for integration and interrogation of these high-dimensional data sets. To learn more about us refer to


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
Edward S. Rogers Sr. Scholarship, University of Toronto, Ontario, Canada, 2004
Texas Student Research Award Prize, 2007
Cancer Research Training Award, 2009-2014

Memberships and Professional Organizations

Institute of Electrical and Electronics Engineers, 2003 - Present
International Society for Computational Biology, 2006 - Present

Web Links

Selected Publications

DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier.

Santos Margarida A, Faryabi Robert B, Ergen Aysegul V, Day Amanda M, Malhowski Amy, Canela Andres, Onozawa Masahiro, Lee Ji-Eun, Callen Elsa, Gutierrez-Martinez Paula, Chen Hua-Tang, Wong Nancy, Finkel Nadia, Deshpande Aniruddha, Sharrow Susan, Rossi Derrick J, Ito Keisuke, Ge Kai, Aplan Peter D, Armstrong Scott A, Nussenzweig André, Nature 514(7520): 107-11, 2014, PMID:25079327

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Identification of early replicating fragile sites that contribute to genome instability.

Barlow Jacqueline H*, Faryabi Robert B*, Callén Elsa, Wong Nancy, Malhowski Amy, Chen Hua Tang, Gutierrez-Cruz Gustavo, Sun Hong-Wei, McKinnon Peter, Wright George, Casellas Rafael, Robbiani Davide F, Staudt Louis, Fernandez-Capetillo Oscar, Nussenzweig André, Cell 152(3): 620-32, 2013 *co-first author, PMID:23352430

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53BP1 mediates productive and mutagenic DNA repair through distinct phosphoprotein interactions.

Callen Elsa, Di Virgilio Michela, Kruhlak Michael J, Nieto-Soler Maria, Wong Nancy, Chen Hua-Tang, Faryabi Robert B, Polato Federica, Santos Margarida, Starnes Linda M, Wesemann Duane R, Lee Ji-Eun, Tubbs Anthony, Sleckman Barry P, Daniel Jeremy A, Ge Kai, Alt Frederick W, Fernandez-Capetillo Oscar, Nussenzweig Michel C, Nussenzweig André, Cell 153(6): 1266-80, 2013, PMID:23727112

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Identification of early replicating fragile sites that contribute to genome instability

Faryabi RB, Keystone Symposia, DNA Replication and Recombination, Banff, AL, Canada, 2013

The DNA damage- and transcription-associated protein paxip1 controls thymocyte development and emigration.

Callen Elsa, Faryabi Robert B, Luckey Megan, Hao Bingtao, Daniel Jeremy A, Yang Wenjing, Sun Hong-Wei, Dressler Greg, Peng Weiqun, Chi Hongbo, Ge Kai, Krangel Michael S, Park Jung-Hyun, Nussenzweig André, Immunity 37(6): 971-85, 2012, PMID:23159437

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PTIP controls thymocyte development and emigration by regulating DNA recombination, transcription and repair

Faryabi RB, RECOMB Conference on Regulatory and Systems Genomics, San Francisco, CA, 2012

BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair.

Bunting Samuel F, Callén Elsa, Kozak Marina L, Kim Jung Min, Wong Nancy, López-Contreras Andrés J, Ludwig Thomas, Baer Richard, Faryabi Robert B, Malhowski Amy, Chen Hua-Tang, Fernandez-Capetillo Oscar, D'Andrea Alan, Nussenzweig André, Molecular cell 46(2): 125-35, 2012, PMID:22445484

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Mll4-dependent regulation of Hematopoietic Stem Cell Aging

Faryabi RB, Keystone Symposia, Epigenomics and Chromatin Dynamics, Keystone, CO, 2012

Sampling-Rate-Dependent Probabilistic Boolean Networks

G. Vahedi, R.B. Faryabi, J.-F. Chamberland, A. Datta, E. R. Dougherty, Journal of Theoretical Biology 261(4): 463-477, 2009

Recent Advances in the Control of Markovian Gene Regulatory Networks

R.B. Faryabi G. Vahedi, A. Datta, J.-F. Chamberland, E. R. Dougherty, Current Genomics 10(7): 540-547, 2009

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