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Robert Babak Faryabi, Ph.D.

Robert Babak Faryabi, Ph.D.

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Assistant Professor of Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania
Department: Pathology and Laboratory Medicine

Contact information
Room 553 BRB II/III, 421 Curie Boulevard
Philadelphia, PA 19104-6160
Philadelphia, PA 19104
Office: (215)573-8220
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.
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Description of Clinical Expertise

Cancer Genomics

Description of 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

Selected Publications

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: Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. Proceedings of the National Academy of Sciences May 2017.

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: Notch-Regulated Enhancers in B-Cell Lymphoma Activate MYC and Potentiate B-Cell Receptor Signaling. Blood Dec 2016.

Gregory W. Schwartz, Yeqiao Zhou, Anne W. Lehman, Jennifer J. D. Morrissette, Martin Carroll, Robert B. Faryabi: ITDprofiler web-service for accurate characterization of internal tandem duplication (ITD) mutations. Mid-Atlantic Bioinformatics Conference Oct 2016.

Ashkan Bigdeli, Karthik Ganapathy, Robert B. Faryabi: Leveraging Unique Molecular Barcode Sequencing to Reduce False Positives in Somatic Mutation Calling Absent a Matched-Normal. Mid-Atlantic Bioinformatics Conference Oct 2016.

G.W. Schwartz, Y. Zhou, A.W. Lehman, J.J. Morrissette, M. Carroll, R.B. Faryabi: ITDprofiler: Computational Framework for Accurate Characterization of Structural Variants of Fms-like Tyrosine Kinase (FLT3) Internal Tandem Duplication (ITD) in Acute Myeloid Leukemia. Association of Molecular Pathology Annual Meeting Oct 2016.

K. Ganapathy, A. Fox, A. Bigdeli, S. Sukhadia, R.B. Faryabi, J.J. Morrissette: Lowering the Bar to Raise the Stakes: Using Unique Molecular Barcoding Identifiers to Lower Reporting Frequencies in Tumors and to Improve Variant Detection. Association of Molecular Pathology Annual Meeting Oct 2016.

Y. Zhou, J. Petrovic, W.S. Pear, R.B. Faryabi: Classification of B-cell lymphoma using enhancers. Mid-Atlantic Bioinformatics Conference Oct 2016.

W.S. Pear, Y. Yashiro-Ohtani, J. Petrovic, S. Yu, V. Mercado, L. Xu, R.B. Faryabi , X. S. Liu, J. Aster, G. Zan: Modular domains within a super enhancer determine drug resistance in T-cell acute lymphoblastic leukemia. Experimental Hematology Sep 2016.

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: Trib2 Suppresses Tumor Initiation in Notch-Driven T-ALL. PLoS ONE Aug 2016.

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: DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier. Nature 514(7520): 107-11, Oct 2014.

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Last updated: 05/16/2017
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