Robert Babak Faryabi, Ph.D.

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Assistant Professor of Pathology and Laboratory Medicine
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 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.
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Description of Clinical Expertise

Cancer Genomics

Description of 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.

Selected Publications

Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Pear WS, Vahedi G, Faryabi RB: TooManyCells Identifies and Visualizes Relationships of Single-cell Clades. Nature Methods March 2020 Notes: doi: 10.1038/s41592-020-0748-5.

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: Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques. Molecular cell 73(6): 1174-1190.e12, Mar 2019.

Schwartz GW, Manning BS, Zhou Y, Velu PD, Bigdeli A, Astles R, Lehman AW, Morrissette JJ, Perl AE, Li M, Carroll M, Faryabi RB. : Classes of ITD predict outcomes in AML patients treated with FLT3 inhibitors. Clinical Cancer Research 25(2): 573-583, Jan 2019 Notes: doi: 10.1158/1078-0432.CCR-18-0655.

Schwartz G, Petrovic J, Zhou Y, Faryabi RB: Differential Integration of Transcriptome and Proteome Identifies Pan-cancer Prognostic Biomarkers. Frontiers in Genetics 9: 205, June 2018 Notes: No issue number. doi: 10.3389/fgene.2018.00205. eCollection 2018.

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: Genetic Variation in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells. Immunity 52(2): 257-274, February 2020.

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+: A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Reports 21(3): 784-797, October 2017 Notes: doi: 10.1016/j.celrep.2017.09.066.

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: Functional Proteogenomics Reveals Biomarkers and Therapeutic Targets in Lymphomas. Proceedings of the National Academy of Sciences 11(24): 6581-6586, May 2017.

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 : Identification of Early Replicating Fragile Sites that Contribute to Genome Instability. Cell 152(3): 620-32, January 2013 Notes: *co-first author.

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: DNA-damage-induced Differentiation of Leukaemic Cells as an Anti-cancer Barrier. Nature 514(7520): 107-11, October 2014.

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: The DNA Damage- and Transcription-associated Protein Paxip1 Controls Thymocyte Development and Emigration. Immunity 37(6): 971-85, December 2012.

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Last updated: 02/16/2021
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