Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works

FLASH: fast length adjustment of short reads to improve genome assemblies

Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366 · see citing works

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C.-J., Vert, J.-P., Heard, E., Dekker, J., & Barillot, E. (2015) · Genome Biology · doi:10.1186/s13059-015-0831-x · Cited by 2,565 · see citing works

Formation of chromosomal domains by loop extrusion

Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003 · see citing works

Mediator and cohesin connect gene expression and chromatin architecture

Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939 · see citing works

Cohesin Loss Eliminates All Loop Domains

Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883 · see citing works

A Phase Separation Model for Transcriptional Control

Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K., & Sharp, P. A. (2017) · Cell · doi:10.1016/j.cell.2017.02.007 · Cited by 1,753 · see citing works

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730 · see citing works

The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works

Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus

Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344 · see citing works

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196 · see citing works

Condensin-driven remodelling of X chromosome topology during dosage compensation

Crane, E. E., Bian, Q., McCord, R. P., Lajoie, B. R., Wheeler, B. S., Ralston, E. J., Uzawa, S., Dekker, J., & Meyer, B. J. (2015) · Nature · doi:10.1038/nature14450 · Cited by 972 · see citing works

The 3D Genome as Moderator of Chromosomal Communication

Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937 · see citing works

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

Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892 · see citing works

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

Wutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201798004 · Cited by 864 · see citing works

3D structures of individual mammalian genomes studied by single-cell Hi-C

Stevens, T. J., Lando, D., Basu, S., Atkinson, L. P., Cao, Y., Lee, S. F., Leeb, M., Wohlfahrt, K. J., Boucher, W., O’Shaughnessy-Kirwan, A., et al. (2017) · Nature · doi:10.1038/nature21429 · Cited by 832 · see citing works

Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis

Nasmyth, K. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.091334 · Cited by 805 · see citing works

Cell-cycle dynamics of chromosomal organization at single-cell resolution

Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794 · see citing works

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Flyamer, I. M., Gassler, J., Imakaev, M., Brandão, H. B., Ulianov, S. V., Abdennur, N., Razin, S. V., Mirny, L. A., & Tachibana-Konwalski, K. (2017) · Nature · doi:10.1038/nature21711 · Cited by 753 · see citing works

Complex multi-enhancer contacts captured by genome architecture mapping

Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C. A., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L.-M., Branco, M. R., et al. (2017) · Nature · doi:10.1038/nature21411 · Cited by 715 · see citing works

Enhancer redundancy provides phenotypic robustness in mammalian development

Osterwalder, M., Barozzi, I., Tissières, V., Fukuda-Yuzawa, Y., Mannion, B. J., Afzal, S. Y., Lee, E. A., Zhu, Y., Plajzer-Frick, I., Pickle, C. S., et al. (2018) · Nature · doi:10.1038/nature25461 · Cited by 642 · see citing works

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613 · see citing works

The Energetics and Physiological Impact of Cohesin Extrusion

Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581 · see citing works

Complexity of chromatin folding is captured by the strings and binders switch model

Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.-M., Dostie, J., Pombo, A., & Nicodemi, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204799109 · Cited by 570 · see citing works

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

Frankel, N., Davis, G. K., Vargas, D., Wang, S., Payre, F., & Stern, D. L. (2010) · Nature · doi:10.1038/nature09158 · Cited by 510 · see citing works

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · see citing works

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

Giorgetti, L., Galupa, R., Nora, E. P., Piolot, T., Lam, F., Dekker, J., Tiana, G., & Heard, E. (2014) · Cell · doi:10.1016/j.cell.2014.03.025 · Cited by 460 · see citing works

Structural organization of the inactive X chromosome in the mouse

Giorgetti, L., Lajoie, B. R., Carter, A. C., Attia, M., Zhan, Y., Xu, J., Chen, C. J., Kaplan, N., Chang, H. Y., Heard, É., et al. (2016) · Nature · doi:10.1038/nature18589 · Cited by 410 · see citing works

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

Perry, M. W., Boettiger, A. N., Bothma, J. P., & Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.07.043 · Cited by 396 · see citing works

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

Hay, D., Hughes, J. R., Babbs, C., Davies, J. O. J., Graham, B. J., Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Sharpe, J. A., Suciu, M. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3605 · Cited by 385 · see citing works

Poretools: a toolkit for analyzing nanopore sequence data

Loman, N. J., & Quinlan, A. R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu555 · Cited by 376 · see citing works

Deletion of <i>DXZ4</i> on the human inactive X chromosome alters higher-order genome architecture

Darrow, E. M., Huntley, M. H., Dudchenko, O., Stamenova, E. K., Durand, N. C., Sun, Z., Huang, S.-C., Sanborn, A. L., Machol, I., Shamim, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1609643113 · Cited by 276 · see citing works

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Davies, J. O. J., Telenius, J. M., McGowan, S. J., Roberts, N. A., Taylor, S., Higgs, D. R., & Hughes, J. R. (2016) · Nature Methods · doi:10.1038/nmeth.3664 · Cited by 268 · see citing works

Enhancer hubs and loop collisions identified from single-allele topologies

Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J. H. I., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0161-5 · Cited by 227 · see citing works

Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Biggs, D., Preece, C., Downes, D. J., Gosden, M., Sharpe, J. A., Sloane-Stanley, J. A., Hughes, J. R., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3573 · Cited by 219 · see citing works

Polymer physics of chromosome large-scale 3D organisation

Chiariello, A. M., Annunziatella, C., Bianco, S., Esposito, A., & Nicodemi, M. (2016) · Scientific Reports · doi:10.1038/srep29775 · Cited by 194 · see citing works

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Cattoni, D. I., Gizzi, A. M. C., Georgieva, M., Stefano, M. D., Valeri, A., Chamousset, D., Houbron, C., Déjardin, S., Fiche, J.-B., González, I., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01962-x · Cited by 165 · see citing works

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

Olivares‐Chauvet, P., Mukamel, Z., Lifshitz, A., Schwartzman, O., Elkayam, N. O., Lubling, Y., Deikus, G. Y., Sebra, R., & Tanay, A. (2016) · Nature · doi:10.1038/nature20158 · Cited by 141 · see citing works

How best to identify chromosomal interactions: a comparison of approaches

Davies, J., Oudelaar, A. M., Higgs, D., & Hughes, J. R. (2017) · Nature Methods · doi:10.1038/nmeth.4146 · Cited by 133 · see citing works

Scc2/Nipbl hops between chromosomal cohesin rings after loading

Rhodes, J., Mazza, D., Nasmyth, K., & Uphoff, S. (2017) · eLife · doi:10.7554/elife.30000 · Cited by 99 · see citing works

UMI-4C for quantitative and targeted chromosomal contact profiling

Schwartzman, O., Mukamel, Z., Elkayam, N. O., Olivares‐Chauvet, P., Lubling, Y., Landan, G., Izraeli, S., & Tanay, A. (2016) · Nature Methods · doi:10.1038/nmeth.3922 · Cited by 94 · see citing works

TADtool: visual parameter identification for TAD-calling algorithms

Kruse, K., Hug, C. B., Hernández-Rodríguez, B., & Vaquerizas, J. M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw368 · Cited by 91 · see citing works

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Barbieri, M., Xie, S. Q., Triglia, E. T., Chiariello, A. M., Bianco, S., de Santiago, I., Branco, M. R., Rueda, D., Nicodemi, M., & Pombo, A. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3402 · Cited by 89 · see citing works

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

Brown, J. M., Roberts, N. A., Graham, B., Waithe, D., Lagerholm, C., Telenius, J. M., De Ornellas, S., Oudelaar, A. M., Scott, C., Szczerbal, I., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06248-4 · Cited by 72 · see citing works

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

Ay, F., Vu, T. H., Zeitz, M. J., Varoquaux, N., Carette, J. E., Vert, J., Hoffman, A. R., & Noble, W. S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1236-7 · Cited by 54 · see citing works

Bladder cancer: 4 big questions

Berdik, C. (2017) · Nature · doi:10.1038/551s51a · Cited by 54 · see citing works

The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation

Bender, M. A., Ragoczy, T., Lee, J., Byron, R., Telling, A., Dean, A., & Groudine, M. (2012) · Blood · doi:10.1182/blood-2011-09-380485 · Cited by 53 · see citing works

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

Jiang, T., Raviram, R., Snetkova, V., Rocha, P. P., Proudhon, C., Badri, S., Bonneau, R., Skok, J. A., & Kluger, Y. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw568 · Cited by 48 · see citing works

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

Oudelaar, A. M., Davies, J. O. J., Downes, D. J., Higgs, D. R., & Hughes, J. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1194 · Cited by 30 · see citing works

Quantitative analysis of genomic element interactions by molecular colony technique

Gavrilov, A. A., Chetverina, H. V., Chermnykh, E. S., Razin, S. V., & Chetverin, A. B. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1322 · Cited by 25 · see citing works

Between form and function: the complexity of genome folding

Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R., & Higgs, D. R. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx306 · Cited by 16 · see citing works

Tri-C

Oudelaar, A. M., Oudelaar, A. M., Downes, D. J., & Hughes, J. R. (2018) · Protocol Exchange · doi:10.1038/protex.2018.113 · Cited by 4 · see citing works

Transcription factors and 3D genome conformation in cell-fate decisions

Stadhouders, R., Filion, G. J. P., & Graf, T. (2019) · Nature · doi:10.1038/s41586-019-1182-7 · Cited by 519 · see citing works

Methods for mapping 3D chromosome architecture

Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 502 · see citing works

The AP-1 transcriptional complex: Local switch or remote command?

Bejjani, F., Evanno, E., Zibara, K., Piechaczyk, M., & Jariel‐Encontre, I. (2019) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2019.04.003 · Cited by 355 · see citing works

The relationship between genome structure and function

Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304 · see citing works

Pairtools: From sequencing data to chromosome contacts

Abdennur, N. A., Fudenberg, G., Flyamer, I. M., Galitsyna, A., Goloborodko, A., Imakaev, M., & Venev, S. V. (2024) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1012164 · Cited by 73 · see citing works

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

McCord, R. P., Kaplan, N., & Giorgetti, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.021 · Cited by 204 · see citing works

Super-enhancers include classical enhancers and facilitators to fully activate gene expression

Blayney, J. W., Francis, H., Rampasekova, A., Camellato, B., Mitchell, L., Stolper, R., Cornell, L., Babbs, C., Boeke, J. D., Higgs, D. R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.11.030 · Cited by 196 · see citing works

Defining genome architecture at base-pair resolution

Peng, H., Badat, M., Hanssen, L. L. P., Hentges, L. D., Crump, N. T., Downes, D. J., Jeziorska, D. M., Oudelaar, A. M., Schweßinger, R., Taylor, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03639-4 · Cited by 176 · see citing works

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

Giammartino, D. C. D., Kloetgen, A., Polyzos, A., Liu, Y., Kim, D., Murphy, D., Abuhashem, A., Cavaliere, P., Aronson, B. E., Shah, V., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0390-6 · Cited by 174 · see citing works

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Espinola, S. M., Götz, M., Bellec, M., Messina, O., Fiche, J.-B., Houbron, C., Dejean, M., Reim, I., Cardozo Gizzi, A. M., Lagha, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00816-z · Cited by 174 · see citing works

Unraveling Hematopoiesis through the Lens of Genomics

Liggett, L. A., & Sankaran, V. G. (2020) · Cell · doi:10.1016/j.cell.2020.08.030 · Cited by 163 · see citing works

How subtle changes in 3D structure can create large changes in transcription

Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162 · see citing works

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

Deshpande, A. S., Ulahannan, N., Pendleton, M., Dai, X., Ly, L., Behr, J. M., Schwenk, S., Liao, W., Augello, M. A., Tyer, C., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01289-z · Cited by 155 · see citing works

The spatial organization of transcriptional control

Hafner, A., & Boettiger, A. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00526-0 · Cited by 150 · 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

Loop stacking organizes genome folding from TADs to chromosomes

Hafner, A., Park, M., Berger, S. E., Murphy, S. E., Nora, E. P., & Boettiger, A. N. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.008 · Cited by 120 · see citing works

BET inhibition disrupts transcription but retains enhancer-promoter contact

Crump, N. T., Ballabio, E., Godfrey, L., Thorne, R., Repapi, E., Kerry, J., Tapia, M., Hua, P., Lagerholm, C., Filippakopoulos, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20400-z · Cited by 123 · see citing works

Dynamics of the 4D Genome during in Vivo Lineage Specification and Differentiation

Oudelaar, A. M., Beagrie, R. A., Gosden, M., de Ornellas, S., Georgiades, E., Kerry, J., Hidalgo, D., Carrelha, J., Shivalingam, A., El-Sagheer, A. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16598-7 · Cited by 119 · see citing works

Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

Chakraborty, S., Kopitchinski, N., Zuo, Z., Eraso, A., Awasthi, P., Chari, R., Mitra, A., Tobias, I. C., Moorthy, S. D., Dale, R. K., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01295-6 · Cited by 120 · see citing works

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

Choi, J., Lysakovskaia, K., Stik, G., Demel, C., Söding, J., Tian, T. V., Graf, T., & Cramer, P. (2021) · eLife · doi:10.7554/elife.65381 · Cited by 117 · see citing works

Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms

Grosveld, F., van Staalduinen, J., & Stadhouders, R. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-122220-093818 · Cited by 115 · see citing works

To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

Cavalheiro, G. R., Pollex, T., & Furlong, E. E. M. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.015 · Cited by 101 · see citing works

Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

Madsen, J. G. S., Madsen, M. S., Rauch, A., Traynor, S., Hauwaert, E. L. V., Haakonsson, A. K., Javierre, B. M., Hyldahl, M., Fraser, P., & Mandrup, S. (2020) · Nature Genetics · doi:10.1038/s41588-020-0709-z · Cited by 94 · see citing works

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

An, L., Yang, T., Yang, J., Nuebler, J., Xiang, G., Hardison, R. C., Li, Q., & Zhang, Y. (2019) · Genome biology · doi:10.1186/s13059-019-1893-y · Cited by 91 · see citing works

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

Oudelaar, A. M., Harrold, C. L., Hanssen, L. L. P., Telenius, J. M., Higgs, D. R., & Hughes, J. R. (2019) · Nature Communications · doi:10.1038/s41467-019-13404-x · Cited by 80 · see citing works

TADs and their borders: free movement or building a wall?

Chang, L.-H., Ghosh, S., & Noordermeer, D. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.025 · Cited by 81 · see citing works

Transcriptional enhancers and their communication with gene promoters

Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works

Transcription factors: building hubs in the 3D space

Giammartino, D. C. D., Polyzos, A., & Apostolou, E. (2020) · Cell Cycle · doi:10.1080/15384101.2020.1805238 · Cited by 66 · see citing works

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcárate, I., Esposito, A., Abraham, A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01135-1 · Cited by 68 · see citing works

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

Chang, L.-H., Ghosh, S., Papale, A., Luppino, J. M., Miranda, M., Piras, V., Degrouard, J., Edouard, J., Poncelet, M., Lecouvreur, N., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41265-y · Cited by 38 · see citing works

Capture-C: A modular and flexible approach for high-resolution chromosome conformation capture

Downes, D., Smith, A. L., Karpińska, M. A., Velychko, T., Rue-Albrecht, K., Sims, D., Milne, T., Davies, J., Oudelaar, A. M., & Hughes, J. (2022) · Nature Protocols · doi:10.1038/s41596-021-00651-w · Cited by 52 · see citing works

Determining chromatin architecture with Micro Capture-C

Hamley, J. C., Li, H.-P., Denny, N., Downes, D., & Davies, J. O. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00817-8 · Cited by 49 · see citing works

LDB1 establishes multi-enhancer networks to regulate gene expression

Aboreden, N. G., Lam, J. C., Goel, V. Y., Wang, S., Wang, X., Midla, S. C., Quijano, A., Keller, C. A., Giardine, B. M., Hardison, R. C., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.11.037 · Cited by 61 · see citing works

Higher-Order Chromosomal Structures Mediate Genome Function

Jerković, I., Szabo, Q., Bantignies, F., & Cavalli, G. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.10.014 · Cited by 55 · see citing works

scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order chromatin structures within individual cells

Li, W., Lu, J., Lü, P., Gao, Y., Bai, Y., Chen, K., Su, X., Li, M., Liu, J., Chen, Y., et al. (2023) · Nature Methods · doi:10.1038/s41592-023-01978-w · Cited by 59 · see citing works

3D genome organization: a role for phase separation and loop extrusion?

Stam, M. E., Tark‐Dame, M., & Fransz, P. F. (2019) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2019.03.008 · Cited by 54 · see citing works

Reactivation of a developmentally silenced embryonic globin gene

King, A. J., Songdej, D., Downes, D. J., Beagrie, R. A., Liu, S., Buckley, M., Peng, H., Suciu, M., Oudelaar, A. M., Hanssen, L. L. P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24402-3 · Cited by 53 · see citing works

Genetics and Genomics Approaches for Diagnosis and Research Into Hereditary Anemias

Russo, R., Marra, R., Rosato, B. E., Iolascon, A., & Andolfo, I. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.613559 · Cited by 54 · see citing works

High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding

Zhong, J., Niu, L., Lin, Z., Bai, X., Chen, Y., Luo, F., Hou, C., & Xiao, C. (2023) · Nature Communications · doi:10.1038/s41467-023-36899-x · Cited by 58 · see citing works

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structurePreprint

Ulahannan, N., Pendleton, M., Deshpande, A. S., Schwenk, S., Behr, J. M., Dai, X., Tyer, C., Rughani, P., Kudman, S., Adney, E. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/833590 · Cited by 48 · see citing works

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Xu, H., Zhang, S., Yi, X., Plewczyński, D., & Li, M. J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.02.013 · Cited by 48 · see citing works

Deciphering multi-way interactions in the human genome

Dotson, G. A., Chen, C., Lindsly, S., Cicalo, A., Dilworth, S., Ryan, C. W., Jeyarajan, S., Meixner, W., Stansbury, C. M., Pickard, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32980-z · Cited by 48 · see citing works

The macro and micro of chromosome conformation capture

Goel, V. Y., & Hansen, A. S. (2020) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.395 · Cited by 46 · see citing works

Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the <i>Sox2</i> locus

Taylor, T., Sikorska, N., Shchuka, V. M., Chahar, S., Ji, C., Macpherson, N. N., Moorthy, S. D., de Kort, M. A. C., Mullany, S., Khader, N., et al. (2022) · Genes &amp; Development · doi:10.1101/gad.349489.122 · Cited by 45 · see citing works

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

Scholes, C., Biette, K. M., Harden, T. T., & DePace, A. H. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.115 · Cited by 44 · see citing works

A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells

Chiariello, A. M., Bianco, S., Oudelaar, A. M., Esposito, A., Annunziatella, C., Fiorillo, L., Conte, M., Corrado, A., Prisco, A., Larke, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.044 · Cited by 41 · see citing works

Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

Bejjani, F., Tolza, C., Boulanger, M., Downes, D. J., Romero, R., Maqbool, M. A., Aabidine, A. Z. E., Andrau, J., Lèbre, S., Bréhélin, L., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab053 · Cited by 42 · see citing works

Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs

Wu, H., Zhang, J., Tan, L., & Xie, X. S. (2025) · Nature Genetics · doi:10.1038/s41588-025-02247-6 · Cited by 41 · see citing works

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells

Perez-Rathke, A., Sun, Q., Wang, B., Boeva, V., Shao, Z., & Liang, J. (2020) · Genome biology · doi:10.1186/s13059-019-1904-z · Cited by 35 · see citing works

Hierarchical chromatin organization detected by TADpole

Soler-Vila, P., Cuscó, P., Farabella, I., Stefano, M. D., & Martı́-Renom, M. A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa087 · Cited by 39 · see citing works

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

Downes, D. J., Beagrie, R. A., Gosden, M. E., Telenius, J. M., Carpenter, S. J., Nußbaum, L., Ornellas, S. D., Sergeant, M. J., Eijsbouts, C. Q., Schweßinger, R., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20809-6 · Cited by 43 · see citing works

CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.

Liu, Y., Wan, X., Li, H., Chen, Y.-X., Hu, X.-D., Chen, H., Zhu, D.-H., Li, C., & Zhang, Y. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113259 · Cited by 31 · see citing works

Computational approaches from polymer physics to investigate chromatin folding

Bianco, S., Chiariello, A. M., Conte, M., Esposito, A., Fiorillo, L., Musella, F., & Nicodemi, M. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.01.002 · Cited by 37 · see citing works

Chromatin modules and their implication in genomic organization and gene regulation

van Mierlo, G., Pushkarev, O., Kribelbauer, J. F., & Deplancke, B. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.11.003 · Cited by 32 · see citing works

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

Vermeulen, C., Allahyar, A., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., Valdes‐Quezada, C., Renkens, I., Straver, R., Kloosterman, W. P., et al. (2020) · Nature Protocols · doi:10.1038/s41596-019-0242-7 · Cited by 35 · see citing works

Blood disease–causing and –suppressing transcriptional enhancers: general principles and GATA2 mechanisms

Bresnick, E. H., & Johnson, K. D. (2019) · Blood Advances · doi:10.1182/bloodadvances.2019000378 · Cited by 32 · see citing works

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 34 · see citing works

Differential 3D chromatin organization and gene activity in genomic imprinting.

Noordermeer, D., & Feil, R. (2020) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2020.03.004 · Cited by 25 · see citing works

Spatial promoter–enhancer hubs in cancer: organization, regulation, and function

Zhao, J., & Faryabi, R. B. (2023) · Trends in Cancer · doi:10.1016/j.trecan.2023.07.017 · Cited by 28 · see citing works

The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization

Oudelaar, A. M., Beagrie, R. A., Kassouf, M. T., & Higgs, D. R. (2021) · Current Opinion in Genetics &amp; Development · doi:10.1016/j.gde.2020.10.003 · Cited by 27 · see citing works

Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction

Wang, J., Zhang, S., Lu, H., & Xu, H. (2022) · Nature Communications · doi:10.1038/s41467-022-30315-6 · Cited by 25 · see citing works

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution

Neguembor, M. V., Arcon, J. P., Buitrago, D., Lema, R., Walther, J., Garate, X., Martin, L., Romero-Marimon, P., Abed, J. A., Gut, M. O., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00839-y · Cited by 27 · see citing works

Pancreatic Islet Transcriptional Enhancers and Diabetes

Cebola, I. (2019) · Current Diabetes Reports · doi:10.1007/s11892-019-1230-6 · Cited by 25 · see citing works

Contributions of 3D chromatin structure to cell-type-specific gene regulation

Schaeffer, M., & Nöllmann, M. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102032 · Cited by 26 · see citing works

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., Fontana, A., Vercellone, F., Conte, M., & Nicodemi, M. (2024) · Nature Communications · doi:10.1038/s41467-024-48370-6 · Cited by 26 · see citing works

Competition Between Transcription and Loop Extrusion Modulates Promoter and Enhancer DynamicsPreprint

Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., Kocanova, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.25.538222 · Cited by 26 · see citing works

Extracting multi-way chromatin contacts from Hi-C data

Liu, L., Zhang, B., & Hyeon, C. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009669 · Cited by 26 · see citing works

Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia

Song, H., Liu, Y., Tan, Y., Zhang, Y., Jin, W. Y., Chen, L., Wu, S., Yan, J., Li, J., Chen, Z., et al. (2022) · Blood · doi:10.1182/blood.2021014945 · Cited by 23 · see citing works

CSynth: an interactive modelling and visualization tool for 3D chromatin structure

Todd, S. J. P., Todd, P., McGowan, S. J., Hughes, J. R., Kakui, Y., Leymarie, F. F., Latham, W., & Taylor, S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa757 · Cited by 23 · see citing works

Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells

Bianco, S., Annunziatella, C., Andrey, G., Chiariello, A. M., Esposito, A., Fiorillo, L., Prisco, A., Conte, M., Campanile, R., & Nicodemi, M. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.07.013 · Cited by 22 · see citing works

CaptureCompendium: a comprehensive toolkit for 3C analysisPreprint

Telenius, J., Downes, D., Sergeant, M., Oudelaar, A. M., McGowan, S., Kerry, J., Hanssen, L., Schwessinger, R., Eijsbouts, C., Davies, J. O. J., et al. (2020) · bioRxiv · doi:10.1101/2020.02.17.952572 · Cited by 21 · see citing works

Super-enhancers require a combination of classical enhancers and novel facilitator elements to drive high levels of gene expressionPreprint

Blayney, J., Francis, H. S., Camellato, B. R., MITCHELL, L. A., Stolper, R. J., Boeke, J. D., Higgs, D. R., & Kassouf, M. T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.20.496856 · Cited by 21 · see citing works

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 20 · see citing works

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data

Kos, P., Galitsyna, A., Ulianov, S., Gelfand, M., Razin, S., & Chertovich, A. (2021) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1009546 · Cited by 17 · see citing works

A functional overlap between actively transcribed genes and chromatin boundary elementsPreprint

Harrold, C. L., Gosden, M. E., Hanssen, L. L. P., Stolper, R. J., Downes, D. J., Telenius, J. M., Biggs, D., Preece, C., Alghadban, S., Sharpe, J. A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.01.182089 · Cited by 18 · see citing works

The Impact of Space and Time on the Functional Output of the GenomePreprint

Nollmann, M., Bennabi, I., Götz, M., & Gregor, T. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040378 · Cited by 20 · see citing works

capC-MAP: software for analysis of Capture-C data

Buckle, A., Gilbert, N., Marenduzzo, D., & Brackley, C. (2019) · Bioinform. · doi:10.1093/bioinformatics/btz480 · Cited by 16 · see citing works

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., Poli, V., Fagnocchi, L., Lago, S., D'Annunzio, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46524-0 · Cited by 16 · see citing works

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 17 · see citing works

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

Kravchuk, E. V., Ashniev, G. A., Gladkova, M. G., Орлов, А. В., Vasileva, A. V., Boldyreva, A., Burenin, A. G., Skirda, A. M., Nikitin, P. I., & Orlova, N. N. (2023) · Cells · doi:10.3390/cells12081191 · Cited by 19 · see citing works

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 · see citing works

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 · see citing works

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

Liang, J., & Perez-Rathke, A. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.017 · Cited by 16 · see citing works

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 18 · see citing works

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 17 · see citing works

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 17 · see citing works

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 18 · see citing works

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 · see citing works

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 16 · see citing works

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 · see citing works

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 · see citing works

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 14 · see citing works

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 15 · see citing works

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 · see citing works

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 13 · see citing works

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 · see citing works

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 13 · see citing works

Robust and efficient gene regulation through localized nuclear microenvironments

Tsai, A., Galupa, R., & Crocker, J. (2020) · Development · doi:10.1242/dev.161430 · Cited by 11 · see citing works

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 13 · see citing works

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 · see citing works

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 · see citing works

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 34 · see citing works

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

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