Faculty

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Robert Babak Faryabi, Ph.D.

Associate Professor of Pathology and Laboratory Medicine

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Department: Pathology and Laboratory Medicine

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1f Graduate Group Affiliations 8

46 Contact information
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Room 553 BRB II/III, 421 Curie Boulevard
Philadelphia, PA 19104

30 Office: (215)573-8220
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Email:
faryabi@pennmedicine.upenn.edu

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18 Publications
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26 Search PubMed for articles c

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13 Education:
21 8 BSc 30 (Electrical and Computer Engineering) c
46 Sharif University of Technology, Tehran, Iran, 1995.
21 8 MSc 30 (Electrical and Computer Engineering) c
46 Sharif University of Technology, Tehran, Iran, 1997.
21 8 PhD 22 (Computational Biology) c
42 Texas A&M University, College Station, TX, 2009.
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Links
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4e Lab Website
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b6 > Perelman School of Medicine > Faculty > Details a

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Description of Clinical Expertise

1f Cancer Genomics
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Description of Research Expertise

2c4 The overarching goal of our lab is to advance the mechanistic understanding of human cancer genome architecture and regulation. The lab expertise in chromatin, cancer, and computational biology allows us to deploy multidisciplinary approaches to rigorously define the cause-and-effect relationship between transcriptional regulators, chromatin organization, and gene expression in cancer. Current projects in the lab focuses on lymphoma and breast cancer and explore: i) how epigenetic control of gene expression is disrupted, ii) how transcriptional dependencies can develop, and iii) how heterogeneity and plasticity of transcriptional dependencies enable drug resistance in these cancers.
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46 More details on the Faryabi Lab website https://faryabilab.com/
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Selected Publications

12d Zhou Y, Jay A, Burget N, Friedrich T, Yoon S, Alsing J, Nir G, Grosschedl R, Vahedi G, Faryabi RB.: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation. Nat Cell Biol Dec 2025.

19a Abedi M, Rai P, Zhou Y, Liu C, Johnson I, Chandra A, Fasolino M, Rostami S, Wang W, Min Z, Li Y, Yu M, Jay A, Lian V, Silverman M, Kaestner KH, Naji A, Faryabi RB, Vahedi G.: Joint profiling of gene expression and chromatin accessibility in pancreatic lymph nodes and spleens in human type 1 diabetes. Sci Immunol 10: eadz0472, Nov 2025.

f5 Zhou Y, Sheng Y, Hu D, Jay A, Vahedi G, Faryabi RB.: OLIVE provides rapid visualization and analysis of chromatin tracing experiments. Cell Rep Methods 5: 101209, Nov 2025.

22c Jafari H, Brown-Burke F, Pray B, Sloan S, Helmig-Mason J, Hout I, Leon S, Long M, Chan WK, Hanel W, Corps K, Leshchenko VV, Edwards D, Prakash Shukla R, Reci S, Vaddi K, Scherle P, Collier P, La Ferlita A, Singh S, Distefano R, Lapalombella R, Sehgal L, Faryabi RB, Meydan C, Mason CE, Baiocchi RA, Parekh S, Alinari L.: The Novel Immunocompetent Eµ-SOX11CCND1 Mouse Model Phenotypically and Molecularly Resembles Human Mantle Cell Lymphoma. Clin Cancer Res 31: 4571-4585, Nov 2025.

147 Jay A*, Zhou Y*, Yoon S, Abeje BN, Chandra A, Wald J, Raj A, Faryabi RB#, Vahedi G#: Single-allele chromatin tracing reveals genomic clustering of paralogous transcription factors as a mechanism for developmental robustness in T Cells. bioRxiv June 2025.

13a Bigdeli A, Chandrashekar DS, Chitturi A, Rushton C, Mackinnon AC, Segal J, Harada S, Sacan A, Faryabi RB: Azurify integrates cancer genomics with machine learning to classify the clinical significance of somatic variants. bioRxiv April 2025.

129 Perlman BS, Burget NG, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nature Communications 15(1), September 2024.

11b Zhao J, Zhou Y, Tzelepis I, Burget NG, Shi J, Faryabi RB: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells. Science Advances 10(22), August 2024.

158 Mongia A, Zohora FT, Burget NG, Zhou Y, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW, Faryabi RB: AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics. Nature Communications 15(1), May 2024.

168 Patil AR, Schug J, Liu C, Lahori D, Descamps HC; Human Pancreas Analysis Consortium; Naji A, Kaestner KH, Faryabi RB, Vahedi G.: Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Cell Reports Medicine 5(5), May 2024.

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