Robert Babak Faryabi, Ph.D.
Associate Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations
Contact information
Room 14-114, 3600 Civic Center Boulevard
Philadelphia, PA 19104
Philadelphia, PA 19104
Office: (215)573-8220
Publications
Education:
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.
Permanent linkBSc (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.
Description of Research Expertise
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.More details on the Faryabi Lab website https://faryabilab.com/
Selected Publications
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.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 review at Cell Metabolism 2026.
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.
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.
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.
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.
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.
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: In revision for Genomic Medicine.
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.
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.