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Oncogenic Signaling Pathways in The Cancer Genome Atlas

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The Molecular Taxonomy of Primary Prostate Cancer

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The long-range interaction landscape of gene promoters

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Modification of Enhancer Chromatin: What, How, and Why?

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A high-resolution map of the three-dimensional chromatin interactome in human cells

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Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

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Targeting the cancer epigenome for therapy

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Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

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YY1 Is a Structural Regulator of Enhancer-Promoter Loops

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The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia

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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

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The Varied Roles of Notch in Cancer

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Chromatin organization by an interplay of loop extrusion and compartmental segregation

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The Energetics and Physiological Impact of Cohesin Extrusion

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Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

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EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

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Genetic dissection of the α-globin super-enhancer in vivo

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H1 histones control the epigenetic landscape by local chromatin compaction

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Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

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Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene ExpressionPreprint

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Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T CellsPreprint

Jay, A., Zhou, Y., Yoon, S., Abeje, B. N., Chandra, A., Wald, J., Raj, A., Faryabi, R. B., & Vahedi, G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.30.656885

Inference of multi-enhancer interactions in T lymphocytes using Hi-CocietyPreprint

Yoon, S., & Vahedi, G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.12.659372

Lineage-determining transcription factors EBF1 and TCF1 shape chromatin fibre folding

(2025) · Nature Cell Biology · doi:10.1038/s41556-025-01843-2

Connecting multiway enhancer-promoter interactions to changes in gene expression in cancerPreprint

Kumari, K., Shin, S., Shi, G., Reed, K. S. M., Misteli, T., & Thirumalai, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.25.720760

High-Risk Multiple Myeloma: Redefining Risk and Rethinking Therapy

Morgan, G. J., Lee, D. D., Joseph, N. S., Lonial, S., Rodríguez‐Otero, P., & San-Miguel, J. (2026) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk-26-517494

Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer

Cao, H., Wu, Z., Ji, B., Yang, S., Gonzalez-Smith, L., Vu, A. H., & Rhie, S. K. (2026) · Genome biology · doi:10.1186/s13059-026-04178-9

Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

Jung, N., Lopez-Pajares, V., Donohue, L., Guo, M., Srinivasan, S., Siprashvili, Z., & Khavari, P. (2026) · Science Advances · doi:10.1126/sciadv.adz9441

The epigenetic landscape of hepatocellular carcinoma: from molecular mechanisms to early detection biomarkers and precision therapy

Dubey, S., & Gupta, H. (2026) · Gene · doi:10.1016/j.gene.2026.150438

Advanced techniques to study interactions between transcription factors and target gene promoters

Kumar, P., & Singh, J. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-33748-2.00032-x

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

Perlman, B. S., Burget, N., Zhou, Y., Schwartz, G. W., Petrovic, J., Modrusan, Z., & Faryabi, R. (2024) · Nature Communications · doi:10.1038/s41467-024-52375-6 · Cited by 20 · see citing works

Genetic and Epigenetic Dysregulation of Transcriptional Enhancers in Cancer

Botten, G. A., & Xu, J. (2024) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-060324-114306 · Cited by 7 · see citing works

Landscape and perturbation of enhancer-driven core transcription regulatory circuits in cancer

Xu, J., Jiang, T., Guo, J., Pan, T., & Li, Y. (2023) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2023.05.011 · Cited by 2 · see citing works

Deregulated enhancer‐promoter communication in cancer through altered nuclear architecture

Seufert, I., Vargas, C., Wille, S. J., & Rippe, K. (2025) · International Journal of Cancer · doi:10.1002/ijc.35424 · Cited by 3 · see citing works

3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

Uyehara, C. M., & Apostolou, E. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112068 · Cited by 143 · see citing works