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 14-114, 3600 Civic Center 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

178 Zhou W^, Tzelepis I^, Zhou Y, Iglesias S, Friedrich T, Marmorstein R, Faryabi RB: Mastermind-Like 1 intrinsic disorder regions differentially regulate enhancer activation and positioning to set oncogenic Notch transcriptional programs. In Preparation for submission by Jun 2026 Notes: ^ co-first author.

125 Samanta N, Hu D, Sheng Y, Burget N, Roman J, Kaestner KH, Naji A, HPAP, Vahedi G, Faryabi RB: PANC-DB: A multi-modal resource for studying pancreatic and immune organs in diabetes. Under revision at Cell Metabolism 2026.

17c 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. Nature Cell Biology 28(1): 149–165, Dec 2025 Notes: ^ co-first author, * co-corresponding author.

1de 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. Science Immunology 10(113): eadz0472, Nov 2025 Notes: ^ co-first author, * co-corresponding author.

f9 Zhou Y, Sheng Y, Hu D, Jay A, Vahedi G, Faryabi RB.: OLIVE provides rapid visualization and analysis of chromatin tracing experiments. Cell Reports Methods 5: 101209, Nov 2025.

27a 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. Clinical Cancer Research 31(21): 4571-4585, Nov 2025 Notes: Contributed to bulk and single-cell transcriptomic studies.

193 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 Jun 2025 Notes: ^ co-first author, * co-corresponding author. Resubmitted to Immunity.

162 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 Apr 2025 Notes: Under revision at Genomic Medicine.

2a2 Allman A, Gaudette BT, Kelly S, Alouche N, Carrington LJ, Perkey E, Brandstadter JD, Outen R, Vanderbeck A, Lederer K, Zhou Y, Faryabi RB, Robertson TF, Burkhardt JK, Tikhonova A, Aifantis I, Scarpellino L, Koch U, Radtke F, Lütge M, De Martin A, Ludewig B, Tveriakhina L, Gossler A, Mosteiro L, Siebel CW, Gómez Atria D, Luther SA, Allman D, Maillard I: Splenic fibroblasts control marginal zone B cell movement and function via two distinct Notch2-dependent regulatory programs. Immunity 58(1): 143-161, Jan 2025 Notes: Performed and analyzed chromatin conformation capture, ChIP-seq, and RNA-seq.

16a Friedrich T, Chandra A, Zhou Y, Abedi M, Rai P, Rostami S, Naji A, Vahedi G, Faryabi RB: Single-cell-based Hi-C Deconvolution Reveals Chromatin Topology Reorganization in CD4+ T Cell Subpopulations of Type 1 Diabetes. The Human Islet Research Network Symposium, Washington DC, DC Jan 2025.

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