Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829

Polymer Physics

Rubinstein, M., & Colby, R. H. (2003) · doi:10.1093/oso/9780198520597.001.0001 · Cited by 5,686

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895

The accessible chromatin landscape of the human genome

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

Cremer, T. J., & Cremer, C. G. (2001) · Nature Reviews Genetics · doi:10.1038/35066075 · Cited by 2,423

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

Guelen, L., Pagie, L., Brasset, É., Meuleman, W. R. A., Faza, M. B., Talhout, W., Eussen, B. H. J., de Klein, A., Wessels, L. F. A., de Laat, W. L., et al. (2008) · Nature · doi:10.1038/nature06947 · Cited by 2,042

Three-dimensional folding and functional organization principles of the Drosophila genome

Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983

Cancer induction and suppression with transcriptional control and epigenome editing technologies

Nakade, S., Yamamoto, T., & Sakuma, T. (2017) · Journal of Human Genetics · doi:10.1038/s10038-017-0377-8 · Cited by 11

Genome-wide search for higher order epistasis as modifiers of treatment effects on bone mineral density in childhood cancer survivors

Im, C., Ness, K. K., Kaste, S. C., Chemaitilly, W., Moon, W., Sapkota, Y., Brooke, R. J., Hudson, M. M., Robison, L. L., Yasui, Y., et al. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-017-0050-x · Cited by 13

Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

Wang, R., Wang, Y., Zhang, X., Zhang, Y., Du, X., Fang, Y., & Li, G. (2019) · BMC Genomics · doi:10.1186/s12864-019-5535-2 · Cited by 13

Core–periphery organization of the cryptocurrency market inferred by the modularity operator

Polovnikov, K., Kazakov, V., & Syntulsky, S. (2019) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2019.123075 · Cited by 12

Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders

Pratt, B. M., & Won, H. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.08.013 · Cited by 13

Influence of nuclear structure on the formation of radiation-induced lethal lesions

Friedman, D., Tait, L. M., & Vaughan, A. T. (2016) · International Journal of Radiation Biology · doi:10.3109/09553002.2016.1144941 · Cited by 13

Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcriptionPreprint

Keenan, C. R., Coughlan, H. D., Iannarella, N., del Fierro, A. T., Keniry, A., Johanson, T. M., Chan, W. F., Garnham, A. L., Whitehead, L. W., Blewitt, M. E., et al. (2024) · Genome Research · doi:10.1101/gr.279119.124 · Cited by 13

De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.

Mao, Y., Cui, X., Wang, H., Qin, X., Liu, Y., Yin, Y., Su, X., Tang, J., Wang, F., Ma, F., et al. (2022) · Plant Methods · doi:10.1186/s13007-022-00915-w · Cited by 11

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

Walter, J., Walliser, N.-O., David, G., Dorignac, J., Geniet, F., Palmeri, J., Parmeggiani, A., Wingreen, N. S., & Broedersz, C. P. (2018) · New Journal of Physics · doi:10.1088/1367-2630/aaad39 · Cited by 11

Active Remodeling of Chromatin and Implications for In Vivo Folding

Natesan, R., Gowrishankar, K., Kuttippurathu, L., Kumar, P. B. S., & Rao, M. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c08655 · Cited by 11

Developing bioimaging and quantitative methods to study 3D genome

Gao, J. T., Yang, X., Djekidel, M. N., Wang, Y., Xi, P., & Zhang, M. Q. (2016) · Quantitative Biology · doi:10.1007/s40484-016-0065-2 · Cited by 11

Mouse Models of Human GWAS Hits for Obesity and Diabetes in the Post Genomic Era: Time for Reevaluation

Laber, S., & Cox, R. (2017) · Frontiers in Endocrinology · doi:10.3389/fendo.2017.00011 · Cited by 12

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches

Martin-Herranz, D. E., Ribeiro, A. J. M., Krueger, F., Thornton, J. M., Reik, W., & Stubbs, T. M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx814 · Cited by 12

Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers

Lander, J. M., Supp, D. M., He, H., Martin, L. J., Chen, X., Weirauch, M. T., Boyce, S. T., & Kopan, R. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184500 · Cited by 11

Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors

Vahedi, G. (2021) · Immunological Reviews · doi:10.1111/imr.12942 · Cited by 11

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

Diament, A., & Tuller, T. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004298 · Cited by 11

Principles for the organization of gene-sets

Li, W., Freudenberg, J., & Oswald, M. (2015) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2015.04.005 · Cited by 12

3D view of chromosomes, DNA damage, and translocations

Schwartz, M., & Hakim, O. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.12.008 · Cited by 10

Regulatory genomics: Combined experimental and computational approaches

Ignatieva, E. V., Podkolodnaya, O. A., Orlov, Y. L., Vasiliev, G. V., & Kolchanov, N. A. (2015) · Russian Journal of Genetics · doi:10.1134/s1022795415040067 · Cited by 10

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding

Cui, X., Yin, Q., Gao, Z., Li, Z., Chen, X., Lv, H., Chen, S., Liu, Q., Zeng, W., & Jiang, R. (2025) · Nature Communications · doi:10.1038/s41467-025-59780-5 · Cited by 10

Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathways

Higgins, G. A., Allyn-Feuer, A., Georgoff, P. E., Nikolian, V. C., Alam, H. B., & Athey, B. D. (2017) · Methods · doi:10.1016/j.ymeth.2017.03.012 · Cited by 10

Three-Dimensional Image of Cleavage Bodies in Nuclei Is Configured Using Gas Cluster Ion Beam with Time-of-Flight Secondary Ion Mass Spectrometry

Masaki, N., Ishizaki, I., Hayasaka, T., Fisher, G. L., Sanada, N., Yokota, H., & Setou, M. (2015) · Scientific Reports · doi:10.1038/srep10000 · Cited by 10

Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

Isami, S., Sakamoto, N., Nishimori, H., & Awazu, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0143760 · Cited by 10

Heterogeneous Spatial Distribution of Transcriptional Activity in Budding Yeast Nuclei

Tokuda, N., & Sasai, M. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.11.3201 · Cited by 10

An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer

Kubota, N., & Suyama, M. (2020) · BMC Medical Genomics · doi:10.1186/s12920-020-0662-9 · Cited by 11

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Sajid, A., Lalani, E., Chen, B., Hashimoto, T., Griffin, D. K., Bhartiya, A., Thompson, G. E., Robinson, I. K., & Yusuf, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115987 · Cited by 10

Loss of KMT2C reprograms the epigenomic landscape in hPSCs resulting in NODAL overexpression and a failure of hemogenic endothelium specification

Maurya, S. S., Yang, W., Tamai, M., Zhang, Q., Erdmann-Gilmore, P., Bystry, A., Rodrigues, F. M., Valentine, M. C., Wong, W., Townsend, R., et al. (2021) · Epigenetics · doi:10.1080/15592294.2021.1954780 · Cited by 10

Integrative epigenomics in chronic lymphocytic leukaemia: Biological insights and clinical applications

Kulis, M., & Martín-Subero, J. I. (2022) · British Journal of Haematology · doi:10.1111/bjh.18465 · Cited by 11

The Nuclear Physique

Pederson, T. (2014) · International review of cytology · doi:10.1016/b978-0-12-800046-5.00001-1 · Cited by 12

Characterisation of non-coding genetic variation in histamine receptors using AnNCR-SNP

Rojano, E., Ranea, J. A. G., & Perkins, J. R. (2016) · Amino Acids · doi:10.1007/s00726-016-2265-5 · Cited by 10

Three‐dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2‐regulated cancer gene signature

Gerrard, D. L., Wang, Y., Gaddis, M., Zhou, Y., Wang, J., Witt, H. N., Lin, S., Farnham, P., Jin, V. X., & Frietze, S. E. (2018) · Journal of Cellular Biochemistry · doi:10.1002/jcb.27449 · Cited by 10

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

Maffeo, C., Chou, H., & Aksimentiev, A. (2019) · Advanced Theory and Simulations · doi:10.1002/adts.201800191 · Cited by 10

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data

Meluzzi, D., & Arya, G. (2019) · Methods · doi:10.1016/j.ymeth.2019.08.008 · Cited by 10

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter InteractionsPreprint

Doyle, B., Fudenberg, G., Imakaev, M., & Mirny, L. A. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/003087 · Cited by 11

Shaping of genome by long noncoding RNAs

Ichikawa, Y., & Saitoh, N. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823579-9.00018-7 · Cited by 9

CTPredictor: A comprehensive and robust framework for predicting cell types by integrating multi-scale features from single-cell Hi-C data

Shi, Z., & Wu, H. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108336 · Cited by 9

Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets

Thakur, R., Xu, M., Sowards, H., Yon, J., Jessop, L., Myers, T., Zhang, T., Chari, R., Long, E., Rehling, T., et al. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.04.015 · Cited by 10

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Goodstadt, M. N., & Martı́-Renom, M. A. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.11.008 · Cited by 10

Into the chromatin world: Role of nuclear architecture in epigenome regulation

Bianchi, A., & Lanzuolo, C. (2015) · AIMS Biophysics · doi:10.3934/biophy.2015.4.585 · Cited by 9

Identifying functional noncoding variants from genome-wide association studies for cardiovascular disease and related traits

Smith, A. J. P., Humphries, S. E., & Talmud, P. J. (2015) · Current Opinion in Lipidology · doi:10.1097/mol.0000000000000158 · Cited by 9

FISH Is in the Limelight Again As More Than a Cytogenetical Technique for Metaphase Chromosomes

Matsunaga, S. (2016) · CYTOLOGIA · doi:10.1508/cytologia.81.3 · Cited by 9

Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique

Chechetkin, V. R., & Lobzin, V. V. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.05.033 · Cited by 9

Origin of spatial organization of DNA-polymer in bacterial chromosomes

Agarwal, T., Manjunath, G. P., Habib, F., & Chatterji, A. (2018) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/121/18004 · Cited by 9

TCR Signaling Circuits in αβ/γδ T Lineage Choice

Fahl, S. P., Kappes, D. J., & Wiest, D. L. (2017) · CRC Press eBooks · doi:10.1201/9781315371689-6 · Cited by 10

Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model

Zhang, C., & Huang, J. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.624679 · Cited by 8

Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach

Mourad, R., Li, L., & Cuvier, O. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005538 · Cited by 10

Chromosome territory relocation paradigm during DNA damage response: Some insights from molecular biology to physics

Fatakia, S. N., Kulashreshtha, M., Mehta, I. S., & Rao, B. J. (2017) · Nucleus · doi:10.1080/19491034.2017.1313938 · Cited by 9

Mapping the 3D genome architecture

Tavallaee, G., & Orouji, E. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.12.018 · Cited by 10

DNA Specimen Preservation Using DESS and DNA Extraction in Museum Collections

Ogiso‐Tanaka, E., Shimada, D., Ogawa, A., Ishiyama, G., Okumura, K.-I., Hosaka, K., Ishii, C., Nam, K.-O., Hoshino, M., Nomura, S., et al. (2025) · Biology · doi:10.3390/biology14060730 · Cited by 11

Universality and Identity Ordering in Heteropolymer Coil–Globule Transition

Singh, T. V., & Shagolsem, L. S. (2022) · Macromolecules · doi:10.1021/acs.macromol.2c01559 · Cited by 8

scHiCSC: A Novel Single-Cell Hi-C Clustering Framework by Contact-Weight-Based Smoothing and Feature Fusion

Zhou, X., Shi, Z., Wu, Y., Zhao, J., & Wu, H. (2022) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm55620.2022.9995134 · Cited by 8

Explicit ion modeling predicts physicochemical interactions for chromatin organization

Lin, X., & Zhang, B. (2024) · eLife · doi:10.7554/elife.90073.3 · Cited by 8

CD-Loop: a chromatin loop detection method based on the diffusion model

Shen, J., Wang, Y., & Luo, J. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1393406 · Cited by 8

Superresolution microscopy for bioimaging at the nanoscale: from concepts to applications in the nucleus

Nöllmann, M., & Georgieva, M. (2015) · Research and Reports in Biology · doi:10.2147/rrb.s60501 · Cited by 8

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line

Steininger, A., Ebert, G., Becker, B. V., Assaf, C., Möbs, M., Schmidt, C. A., Grabarczyk, P., Jensen, L. R., Przybylski, G. K., Port, M., et al. (2018) · Frontiers in Oncology · doi:10.3389/fonc.2018.00183 · Cited by 8

Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions

Nurick, I., Ron Shamir, A., & Elkon, R. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0220-2 · Cited by 9

Chromosome Genome Sequencing and Comparative Transcriptome-Based Analyses of Kloeckera apiculata 34-9 Unveil the Potential Biocontrol Mechanisms Against Citrus Green Mold

Tian, Z., Du, Y., Yang, F., Zhao, J., Liu, S., Zhang, D., & Long, C.-A. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.752529 · Cited by 8

TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction

Mourad, R. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04614-0 · Cited by 8

Modeling cell biological features of meiotic chromosome pairing to study interlock resolution

Navarro, E. J., Marshall, W. F., & Fung, J. C. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010252 · Cited by 8

Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation

García-Luis, J., Bordelet, H., Thierry, A., Koszul, R., & Aragón, L. (2022) · eLife · doi:10.7554/elife.80147 · Cited by 8

Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation

Luchsinger-Morcelle, S. J., Gribnau, J. H., & Mira-Bontenbal, H. (2024) · Epigenomes · doi:10.3390/epigenomes8010006 · Cited by 8

DNA content of a functioning chicken kinetochore

Ribeiro, S. A., Vagnarelli, P., & Earnshaw, W. C. (2014) · Chromosome Research · doi:10.1007/s10577-014-9410-3 · Cited by 8

ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures

Ye, T., & Ma, W. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa872 · Cited by 8

FIREcaller: Detecting Frequently Interacting Regions from Hi-C DataPreprint

Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/619288 · Cited by 8

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotesPreprint

Bista, B., González-Rodelas, L., Álvarez-González, L., Wu, Z., Montiel, E. E., Lee, L., Badenhorst, D., Radhakrishnan, S., Literman, R., Navarro-Domínguez, B. M., et al. (2024) · Genome Research · doi:10.1101/gr.279443.124 · Cited by 8

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Morgan, S. L., Chang, E. Y., Mariano, N. C., Bermudez, A., Arruda, N. L., Wu, F., Luo, Y., Shankar, G., Huynh, S. K., Huang, C.-C., et al. (2018) · Journal of Visualized Experiments · doi:10.3791/57457 · Cited by 7

Communities in C. elegans connectome through the prism of non-backtracking walks

Onuchin, A. A., Chernizova, A. V., Lebedev, M., & Polovnikov, K. (2023) · Scientific Reports · doi:10.1038/s41598-023-49503-5 · Cited by 7

Genome im Fokus: Entwicklung und Anwendungen von CRISPR‐Cas9‐Bildgebungstechnologien

Knight, S. C., Tjian, R., & Doudna, J. A. (2017) · Angewandte Chemie · doi:10.1002/ange.201709201 · Cited by 7

Disrupted chromatin architecture in olfactory sensory neurons: looking for the link from COVID-19 infection to anosmia

Tan, Z. W., Toong, P. J., Guarnera, E., & Berezovsky, I. N. (2023) · Scientific Reports · doi:10.1038/s41598-023-32896-8 · Cited by 7

When Dad’s Stress Gets under Kid’s Skin—Impacts of Stress on Germline Cargo and Embryonic Development

Kretschmer, M., Fischer, V., & Gapp, K. (2023) · Biomolecules · doi:10.3390/biom13121750 · Cited by 7

Regulation of 3 D genome organization during T cell activation

Wang, B., & Bian, Q. (2024) · FEBS Journal · doi:10.1111/febs.17211 · Cited by 7

Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis

Sutthibutpong, T., Noy, A., & Harris, S. A. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3631-1_15 · Cited by 7

Applications of integrative OMICs approaches to gene regulation studies

Qin, J., Yan, B., Hu, Y., Wang, P., & Wang, J. (2016) · Quantitative Biology · doi:10.1007/s40484-016-0085-y · Cited by 10

A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation

Marti-Marimon, M., Vialaneix, N., Voillet, V., Martine Yerle, B., Lahbib-Mansais, Y., & Liaubet, L. (2018) · Scientific Reports · doi:10.1038/s41598-018-28173-8 · Cited by 7

Genomic 3D compartments emerge from unfolding mitotic chromosomes

Kumar, R., Lizana, L., & Stenberg, P. (2018) · Chromosoma · doi:10.1007/s00412-018-0684-7 · Cited by 7

Single-cell diploid Hi-C reveals the role of spatial aggregations in complex rearrangements and KMT2A fusions in leukemia

Xing, Z., Mai, H., Liu, X., Fu, X., Zhang, X., Xie, L., Chen, Y., Shlien, A., & Wen, F. (2022) · Genome biology · doi:10.1186/s13059-022-02740-9 · Cited by 7

SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks

Pan, J.-H., & Du, P.-F. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad494 · Cited by 7

Analysis of a transgenic Oct4 enhancer reveals high fidelity long-range chromosomal interactions

Cai, M., Gao, F., Zhang, P., An, W., Shi, J., Wang, K., & Lu, W. (2015) · Scientific Reports · doi:10.1038/srep14558 · Cited by 7

Insight into the machinery that oils chromatin dynamics

Wright, R. H. G., Fernández‐Fuentes, N., Oliva, B., & Beato, M. (2016) · Nucleus · doi:10.1080/19491034.2016.1255392 · Cited by 7

R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi‐C Datasets

Stansfield, J. C., Tran, D., Nguyen, T., & Dozmorov, M. G. (2019) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.76 · Cited by 7

Genome Topology Control of Antigen Receptor Gene Assembly

Allyn, B. M., Lee, K. D., & Bassing, C. H. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1901356 · Cited by 6

Higher-Order Chromatin Organization in Diseases: From Chromosomal Position Effect to Phenotype Variegation

Robin, J. D., & Magdinier, F. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00006-7 · Cited by 7

Chromatin plates in the interphase nucleus

Chicano, A., & Daban, J. (2019) · FEBS Letters · doi:10.1002/1873-3468.13370 · Cited by 8

From Schizophrenia Genetics to Disease Biology: Harnessing New Concepts and Technologies

Duan, J., Sanders, A. R., & Gejman, P. V. (2019) · Journal of Psychiatry and Brain Science · doi:10.20900/jpbs.20190014 · Cited by 8

Rearranging the chromatin for pluripotency

Ferrari, F., Apostolou, E., Park, P. J., & Hochedlinger, K. (2013) · Cell Cycle · doi:10.4161/cc.27028 · Cited by 7

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisationPreprint

Dillinger, S., Straub, T., & Németh, A. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/054908 · Cited by 7

Genome Architecture Leads a Bifurcation in Cell IdentityPreprint

Liu, S., Chen, H., Ronquist, S., Seaman, L., Ceglia, N., Muir, L. A., Meixner, W., Chen, P., Higgins, G. A., Baldi, P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/151555 · Cited by 7

L1 and B1 repeats blueprint the spatial organization of chromatinPreprint

Lu, J. Y., Chang, L., Li, T., Wang, T., Yin, Y., Zhan, G., Zhang, K., Percharde, M., Wang, L., Peng, Q., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/802173 · Cited by 7

Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C

Rudan, M. V., Hadjur, S., & Sexton, T. (2016) · Methods in molecular biology · doi:10.1007/7651_2015_261 · Cited by 6

Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges

Zhou, W., Sherwood, B., & Ji, H. (2016) · Human Heredity · doi:10.1159/000450827 · Cited by 7

Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers

Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00533-x · Cited by 6

Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Navrátilová, P., Pavlu, S., Zhu, Z., Tulpová, Z., Kopecky, O., Novák, P., Stein, N., & Šimková, H. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101037 · Cited by 6

Framework for efficient synthesis of spatially embedded morphologies

Vanherpe, L., Kanari, L., Atenekeng, G., Palacios, J. C., & Shillcock, J. C. (2016) · Physical review. E · doi:10.1103/physreve.94.023315 · Cited by 6

In silico analysis of human renin gene–gene interactions and neighborhood topologically associated domains suggests breakdown of insulators contribute to ageing-associated diseases

Donlon, T. A., & Morris, B. J. (2019) · Biogerontology · doi:10.1007/s10522-019-09834-1 · Cited by 6

Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere

Eshghi, I., Zidovska, A., & Grosberg, A. Y. (2023) · The European Physical Journal E · doi:10.1140/epje/s10189-023-00327-1 · Cited by 9

A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1

Xiang, J., Fan, C., Dong, H., Ma, Y., & Xu, P. (2023) · eLife · doi:10.7554/elife.85412 · Cited by 5

CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction

Rapakoulia, T., Vargas, S. L. R. D., Omgba, P. A., Laupert, V., Ulitsky, I., & Vingron, M. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad687 · Cited by 6

Gene Regulation at a Distance: Higher-Order Chromatin Folding and the Coordinated Control of Gene Transcription at the Epidermal Differentiation Complex Locus

Fessing, M. Y. (2014) · Journal of Investigative Dermatology · doi:10.1038/jid.2014.247 · Cited by 6

Le génome intime… et en trois dimensions

Umlauf, D. (2015) · médecine/sciences · doi:10.1051/medsci/20153103016 · Cited by 12

Filling the gap: Micro-C accesses the nucleosomal fiber at 100–1000 bp resolution

Mozziconacci, J., & Koszul, R. (2015) · Genome biology · doi:10.1186/s13059-015-0744-8 · Cited by 6

Modeling and Analysis of Spatial Chromatin Interactions

Lin, S., Scholtens, D. M., & Datta, S. (2022) · Chapman & Hall/CRC eBooks · doi:10.1201/9781315153728-7

Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C

Rudan, M. V., Hadjur, S., & Sexton, T. (2016) · Methods in molecular biology · doi:10.1007/7651_2015_261 · Cited by 6

A (3D-Nuclear) Space Odyssey: Making Sense of Hi-C Maps

Mota-Gómez, I., & Lupiáñez, D. G. (2019) · Genes · doi:10.3390/genes10060415 · Cited by 16

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data

Meluzzi, D., & Arya, G. (2019) · Methods · doi:10.1016/j.ymeth.2019.08.008 · Cited by 10

Inferential analysis of genomic 3D organization

Paulsen, J. (2014) · NORA - Norwegian Open Research Archives · Cited by 1