Robert Babak Faryabi, Ph.D.

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Associate Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine

Contact information
Room 553 BRB II/III, 421 Curie Boulevard
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

Cancer is typically considered a genetic disease. However, recent progress in our understanding of epigenetic aberrations in cancer has challenged this view. Overarching goal of Faryabi lab is to understand epigenetic mechanisms of transcriptional addiction in cancer and exploit this information to advance cancer therapeutics.

To pursue this objective, we use cutting-edge chromatin conformation capture, high-content imaging, single-cell epigenomics, functional genomics, and combine these technologies with our expertise in computational sciences to systematically explore: i) how epigenetic control of gene expression is disrupted in cancer, ii) why transcriptional addiction can develop, and iii) how heterogeneity and plasticity of transcriptional dependencies enable drug resistance.

More details on the Faryabi Lab website faryabiLab.com

Selected Publications

Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB: EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Molecular Cell 82(5): 1003-1020, February 2022 Notes: Preview, Bayer M and Grosschedl R, Mol Cell: 82(5), 884-886, February 2022.

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 Notes: ^ co-first author, * co-corresponding author.

Fasolino M^, Schwartz GW^, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, the HPAP Consortium, Feldman M, Moore JH, Japp AS, Betts MR, Faryabi RB*, Naji A*, Kaestner KH*, Vahedi G*: Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. Nature Metabolism 4(2): 284-299, February 2022 Notes: ^ co-first author, * co-corresponding author.

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 17: 405-413, March 2020.

Schwartz WG, Zhou Y, Petrovic J, Pear WS, Faryabi RB: TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes. Cell Reports 38(8), August 2021.

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: ^ co-first author, * co-corresponding author.

Kahn BM^, Lacus A^, Alur RG, Wengyn MD, Schwartz GW, Li J, Sun K, Maurer HC, Olive KP, Faryabi RB*, Stanger BZ*: The Vascular Landscape of Human Cancer. Journal of Clinical Investigation 1311(2): 10.1172/JCI136655, January 2021 Notes: ^ co-first author, * co-corresponding author.

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: Commentary, Gallipoli P and Huntly BJP, Clin Cancer Res 2019 Jan 15;25(2):460-462.

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.

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Last updated: 05/28/2024
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