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Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory

Michelatti, D., Beyes, S., Bernardis, C., Negri, M. L., Morelli, L., Bediaga, N. G., Poli, V., Fagnocchi, L., Lago, S., D’Annunzio, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46524-0 · Cited by 19

Physical mechanisms of chromatin spatial organization

Chiariello, A. M., Bianco, S., Esposito, A., Fiorillo, L., Conte, M., Irani, E., Musella, F., Abraham, A., Prisco, A., & Nicodemi, M. (2021) · FEBS Journal · doi:10.1111/febs.15762 · Cited by 20

Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges

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Genome-wide profiling of DNA repair proteins in single cells

de Luca, K. L., Rullens, P. M. J., Karpińska, M. A., de Vries, S., Gacek‐Matthews, A., Pongor, L. S., Legube, G., Jachowicz, J. W., Oudelaar, A. M., & Kind, J. (2024) · Nature Communications · doi:10.1038/s41467-024-54159-4 · Cited by 21

Erythrocytes 3D genome organization in vertebrates

Ryzhkova, A. S., Taskina, A., Khabarova, A. A., Fishman, V., & Баттулин, Н. Р. (2021) · Scientific Reports · doi:10.1038/s41598-021-83903-9 · Cited by 18

Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units

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Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome

Papantonis, A., & Oudelaar, A. M. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-012301 · Cited by 19

The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

Agelopoulos, M., Foutadakis, S., & Thanos, D. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.682397 · Cited by 19

Chromatin Hubs: A biological and computational outlook

Mora, A., Huang, X., Jauhari, S., Jiang, Q. L., & Li, X. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.002 · Cited by 18

Three‐dimensional genome structure and function

Liu, H., Tsai, H., Yang, M., Li, G., Bian, Q., Ding, G., Wu, D., & Dai, J. (2023) · MedComm · doi:10.1002/mco2.326 · Cited by 25

Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells

Zhao, J.-R., Zhou, Y., Tzelepis, I., Burget, N., Shi, J.-W., & Faryabi, R. (2024) · Science Advances · doi:10.1126/sciadv.adl4043 · Cited by 14

90 YEARS OF PROGESTERONE: Molecular mechanisms of progesterone receptor action on the breast cancer genome

Beato, M., Wright, R. H. G., & Dily, F. L. (2020) · Journal of Molecular Endocrinology · doi:10.1530/jme-19-0266 · Cited by 17

Many-body contacts in fractal polymer chains and fractional Brownian trajectories

Polovnikov, K., Nechaev, S., & Владимирович, Т. М. (2019) · Physical review. E · doi:10.1103/physreve.99.032501 · Cited by 15

Three-dimensional regulatory hubs support oncogenic programs in glioblastoma

Breves, S. L., Giammartino, D. C. D., Nicholson, J., Cirigliano, S. M., Mahmood, S. R., Lee, U. J., Martinez‐Fundichely, A., Jungverdorben, J., Singhania, R., Rajkumar, S., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2025.03.007 · Cited by 15

Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C

Liu, N., Low, W. Y., Alinejad‐Rokny, H., Pederson, S., Sadlon, T. J., Barry, S. C., & Breen, J. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00417-4 · Cited by 16

An enhancer RNA recruits KMT2A to regulate transcription of Myb

Kim, J., Diaz, L. F., Miller, M. J., Leadem, B. R., Krivega, I. V., & Dean, A. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114378 · Cited by 16

Using functional genomics to advance the understanding of psoriatic arthritis

Shi, C., Rattray, M., Barton, A. C., Bowes, J., & Orozco, G. (2020) · Rheumatology · doi:10.1093/rheumatology/keaa283 · Cited by 15

Polymer models are a versatile tool to study chromatin 3D organization

Esposito, A., Bianco, S., Fiorillo, L., Conte, M., Abraham, A., Musella, F., Nicodemi, M., Prisco, A., & Chiariello, A. M. (2021) · Biochemical Society Transactions · doi:10.1042/bst20201004 · Cited by 14

Technologies to study spatial genome organization: beyond 3C

Übelmesser, N., & Papantonis, A. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz019 · Cited by 13

Higher-order Chromosome Structures Investigated by Polymer Physics in Cellular Morphogenesis and Differentiation

Esposito, A., Chiariello, A. M., Conte, M., Fiorillo, L., Musella, F., Sciarretta, R., & Bianco, S. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.12.017 · Cited by 16

Robust and efficient gene regulation through localized nuclear microenvironments

Tsai, A., Galupa, R., & Crocker, J. (2020) · Development · doi:10.1242/dev.161430 · Cited by 12

Making connections: enhancers in cellular differentiation

Herrmann, J. C., Beagrie, R. A., & Hughes, J. R. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.10.008 · Cited by 14

Super-enhancer interactomes from single cells link clustering and transcriptionPreprint

Le, D. J., Hafner, A., Gaddam, S., Wang, K., & Boettiger, A. N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.08.593251 · Cited by 13

The three-dimensional regulatory landscapes of the globin genes

Oudelaar, A. M. (2018) · Oxford University Research Archive (ORA) (University of Oxford) · doi:10.5287/ora-eyqagexnb

Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture

Zhu, Y., Rosenfeld, M. G., & Suh, Y. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313285120 · Cited by 8

Capturing Complex Enhancer Regulatory Hubs? Try Tri-C

Varsally, W., & Hadjur, S. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.11.021

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation

Karpińska, M. A., Zhu, Y., Ghazvini, Z. F., Ramasamy, S., Barbieri, M., Cao, T. B. N., Varahram, N., Aljahani, A., Lidschreiber, M., Papantonis, A., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01555-z · Cited by 35

Identification of cis-regulatory elements from chromosome conformation capture data.

Schöpflin, R., & Vingron, M. (2015) · Max Planck Digital Library