PEOPLE

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

Cancer Epigenetics
Computational Biology
Genomics
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

Education

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, 2009-2013
Cancer Research Training Award, 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
Cancer and Metabolic Epigenetics Interest Group, 2016 - Present
Association for Molecular Pathology, 2016 - Present

Web Links


Selected Publications

Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas

Delphine Rolland, Venkatesha Basrur, Yoon Kyung Jeon, Carla McNeil-Schwalm, Damian Fermin, Kevin Conlon, Yeqiao Zhou, Samuel Ng, Chih-Chiang Tsou, Noah Brown, Dafydd Thomas, Nathanael Bailey, Gilbert Omenn, Alexey Nesvizhskii, David Root, David Weinstock, Robert B. Faryabi, and Megan Lim, Kojo Elenitoba-Johnson, Proceedings of the National Academy of Sciences, 2017

Notch-Regulated Enhancers in B-Cell Lymphoma Activate MYC and Potentiate B-Cell Receptor Signaling

Russell JH Ryan, Jelena Petrovic, Dylan Rausch, Caleb Lareau, Winston Lee, Laura Donohue, Amanda L Christie, Shawn Gillespie, Michael J Kluk, Valentina Nardi, Robert B Faryabi, Ephraim P Hochberg, David M Weinstock, Bradley E Bernstein, Jon C Aster, Warren S Pear, Blood, 2016

ITDprofiler web-service for accurate characterization of internal tandem duplication (ITD) mutations

Gregory W. Schwartz, Yeqiao Zhou, Anne W. Lehman, Jennifer J. D. Morrissette, Martin Carroll, Robert B. Faryabi, Mid-Atlantic Bioinformatics Conference, 2016

Leveraging Unique Molecular Barcode Sequencing to Reduce False Positives in Somatic Mutation Calling Absent a Matched-Normal

Ashkan Bigdeli, Karthik Ganapathy, Robert B. Faryabi, Mid-Atlantic Bioinformatics Conference, 2016

ITDprofiler: Computational Framework for Accurate Characterization of Structural Variants of Fms-like Tyrosine Kinase (FLT3) Internal Tandem Duplication (ITD) in Acute Myeloid Leukemia

G.W. Schwartz, Y. Zhou, A.W. Lehman, J.J. Morrissette, M. Carroll, R.B. Faryabi, Association of Molecular Pathology Annual Meeting, 2016

Lowering the Bar to Raise the Stakes: Using Unique Molecular Barcoding Identifiers to Lower Reporting Frequencies in Tumors and to Improve Variant Detection

K. Ganapathy, A. Fox, A. Bigdeli, S. Sukhadia, R.B. Faryabi, J.J. Morrissette, Association of Molecular Pathology Annual Meeting, 2016

Classification of B-cell lymphoma using enhancers

Y. Zhou, J. Petrovic, W.S. Pear, R.B. Faryabi, Mid-Atlantic Bioinformatics Conference, 2016

Modular domains within a super enhancer determine drug resistance in T-cell acute lymphoblastic leukemia

W.S. Pear, Y. Yashiro-Ohtani, J. Petrovic, S. Yu, V. Mercado, L. Xu, R.B. Faryabi , X. S. Liu, J. Aster, G. Zan, Experimental Hematology, 2016

Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL

Sarah J Stein, Ethan A Mack, Kelly S Rome, Kostandin V Pajcini, Takuya Ohtani, Lanwei Xu, Yunlei Li, Jules PP Meijerink, Robert B Faryabi, Warren S Pear, PLoS ONE, 2016

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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