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

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Polymer Physics

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Capturing Chromosome Conformation

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

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The accessible chromatin landscape of the human genome

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Chromosome territories, nuclear architecture and gene regulation in mammalian cells

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

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

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Epigenetic characteristics of the mitotic chromosome in 1D and 3D

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Comparison of Normalization Methods for Hi-C Data

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Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding

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Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

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Gene regulation during development in the light of topologically associating domains

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ProbC: joint modeling of epigenome and transcriptome effects in 3D genome

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Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein–DNA binding site

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Chromatin barcodes as biomarkers for melanoma

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Pioneer Factors in Animals and Plants—Colonizing Chromatin for Gene Regulation

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High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection

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CHO Cell Line Development and Engineering via Site-specific Integration: Challenges and Opportunities

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Topological isolation of developmental regulators in mammalian genomes

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The (unusual) heuristic value of Hox gene clusters; a matter of time?

Duboule, D. (2022) · Developmental Biology · doi:10.1016/j.ydbio.2022.02.007 · Cited by 36

Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes

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Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements

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Interplay Between Genetic and Epigenetic Mechanisms in Rheumatoid Arthritis

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Motion blur filtering: A statistical approach for extracting confinement forces and diffusivity from a single blurred trajectory

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Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals

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Local loop opening in untangled ring polymer melts: a detailed “Feynman test” of models for the large scale structure

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Hi–C interaction graph analysis reveals the impact of histone modifications in chromatin shape

Sefer, E. (2021) · Applied Network Science · doi:10.1007/s41109-021-00396-1 · Cited by 28

A Liquid State Perspective on Dynamics of Chromatin Compartments

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Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters

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Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

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Regulatory variants of FOXG1 in the context of its topological domain organisation

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scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information

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Establishing epigenetic domains via chromatin‐bound histone modifiers

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A statistical model of intra-chromosome contact maps

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Real-time visualization of chromatin modification in isolated nuclei

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Ribosomal RNA genes shape chromatin domains associating with the nucleolus

Picart-Picolo, A., Picault, N., & Pontvianne, F. (2019) · Nucleus · doi:10.1080/19491034.2019.1591106 · Cited by 29

On the relations of phase separation and Hi-C maps to epigenetics

Singh, P. B., & Newman, A. G. (2020) · Royal Society Open Science · doi:10.1098/rsos.191976 · Cited by 27

GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

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Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

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Understanding epigenomics based on the rice model

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Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation

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Computational schemes for the prediction and annotation of enhancers from epigenomic assays

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Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies

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Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations

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Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

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Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer’s Disease

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Distinct IL‐1α‐responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner

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Understanding the genetic liability to schizophrenia through the neuroepigenome

Fullard, J. F., Halene, T. B., Giambartolomei, C., Haroutunian, V. H., Akbarian, S., & Roussos, P. (2016) · Schizophrenia Research · doi:10.1016/j.schres.2016.01.039 · Cited by 26

3D Genome Reconstruction with ShRec3D+ and Hi-C Data

Li, J., Zhang, W., & Li, X. (2016) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2016.2535372 · Cited by 25

Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei

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History and evolution of cytogenetic techniques: Current and future applications in basic and clinical research

Balajee, A. S., & Hande, M. P. (2018) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2018.08.008 · Cited by 25

Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic Domains

Collas, P., Ali, T. M. L., Brunet, A., & Germier, T. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00602 · Cited by 24

Characterizing chromatin folding coordinate and landscape with deep learning

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Roadmap to a plasma cell: Epigenetic and transcriptional cues that guide B cell differentiation

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Noncoding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability

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Chromatin associations in Arabidopsis interphase nuclei

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A novel method to identify topological domains using Hi‐C data

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Mechanical Pulling of Linked Ring Polymers: Elastic Response and Link Localisation

Caraglio, M., Micheletti, C., & Orlandini, E. (2017) · Polymers · doi:10.3390/polym9080327 · Cited by 25

The transcriptional factor ZEB1 represses Syndecan 1 expression in prostate cancer

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Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA

Liu, L., & Hyeon, C. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.04.020 · Cited by 25

Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease

Brown, C. Y., Sadlon, T. J., Hope, C. M., Wong, Y. Y., Wong, S. W., Liu, N., Withers, H., Brown, K. A., Bandara, V., Gundsambuu, B., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01269 · Cited by 25

HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test

Lagler, T. M., Abnousi, A., Hu, M., Yang, Y., & Li, Y. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.01.009 · Cited by 24

Spatial features for Escherichia coli genome organization

Xie, T., Fu, L.-Y., Yang, Q., Xiong, H., Xu, H., Ma, B., & Zhang, H. (2015) · BMC Genomics · doi:10.1186/s12864-015-1258-1 · Cited by 24

The Molecular Revolution in Cutaneous Biology: Chromosomal Territories, Higher-Order Chromatin Remodeling, and the Control of Gene Expression in Keratinocytes

Botchkarev, V. A. (2017) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2016.04.040 · Cited by 24

Viruses in the NucleusPreprint

Lucic, B., de Castro, I. J., & Lušić, M. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039446 · Cited by 26

SARS-CoV-2 Restructures the Host Chromatin ArchitecturePreprint

Wang, R.-Y., Lee, J.-H., Xiong, F., Kim, J., Hasani, L. A., Yuan, X.-Y., Shivshankar, P., Krakowiak, J., Qi, C.-Y., Wang, Y.-Y., et al. (2021) · bioRxiv · doi:10.1101/2021.07.20.453146 · Cited by 40

RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop ExtrusionPreprint

Lawrimore, J., Friedman, B., Doshi, A., & Bloom, K. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.033696 · Cited by 26

Dynamic enhancer function in the chromatin context

Goldstein, I., & Hager, G. L. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1390 · Cited by 25

A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation

Li, L., Li, X., & Wu, H. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf289 · Cited by 25

The Future of Neuroepigenetics in the Human Brain

Mitchell, A., Roussos, P., Peter, C. J., Tsankova, N. M., & Akbarian, S. (2014) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-800977-2.00008-5 · Cited by 24

Genome Editing in Neurosciences

Jaenisch, R., Gage, F. H., & Zhang, F. (2017) · Research and perspectives in neurosciences · doi:10.1007/978-3-319-60192-2 · Cited by 23

p -Adic mathematics and theoretical biology

Dragovich, B. G., Khrennikov, A. Y., Kozyrev, S. V., & Mišić, N. Ž. (2020) · Biosystems · doi:10.1016/j.biosystems.2020.104288 · Cited by 23

Understanding the function of regulatory DNA interactions in the interpretation of non-coding GWAS variants

Zhong, W., Liu, W., Chen, J. C., Sun, Q., Hu, M., & Li, Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.957292 · Cited by 24

Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization

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Exploring the genetic basis of coronary artery disease using functional genomics

Rodríguez, M. L., Arasu, U. T., & Kaikkonen, M. U. (2023) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2023.01.019 · Cited by 25

Coming to terms with chromatin structure

Even‐Faitelson, L., Hassan‐Zadeh, V., Baghestani, Z., & Bazett‐Jones, D. P. (2015) · Chromosoma · doi:10.1007/s00412-015-0534-9 · Cited by 24

The “lnc” between 3D chromatin structure and X chromosome inactivation

Pandya‐Jones, A., & Plath, K. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.04.002 · Cited by 22

Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells

Sun, M., & Zhang, J. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008389 · Cited by 25

Structures and functions in the crowded nucleus: new biophysical insights

Hancock, R. (2014) · Frontiers in Physics · doi:10.3389/fphy.2014.00053 · Cited by 23

Challenges for visualizing three‐dimensional data in genomic browsers

Goodstadt, M. N., & Martı́-Renom, M. A. (2017) · FEBS Letters · doi:10.1002/1873-3468.12778 · Cited by 23

TADs as modular and dynamic units for gene regulation by hormones

Dily, F. L., & Beato, M. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.026 · Cited by 22

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of Arabidopsis thaliana

Prete, S., Arpòn, J., Sakai, K., Andrey, P., & Gaudin, V. (2014) · Cytogenetic and Genome Research · doi:10.1159/000363724 · Cited by 22

DNA loop domain organization as revealed by single-cell gel electrophoresis

Afanasieva, K. S., Chopei, M., Zazhytska, M., Vikhreva, M., & Sivolob, A. (2013) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2013.09.021 · Cited by 24

Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure

Florescu, A., Therizols, P., & Rosa, A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004987 · Cited by 23

Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization

Nikumbh, S., & Pfeifer, N. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1624-x · Cited by 22

TAD-free analysis of architectural proteins and insulators

Mourad, R., & Cuvier, O. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1246 · Cited by 21

“Looping In” Mechanics: Mechanobiologic Regulation of the Nucleus and the Epigenome

Dai, E. N., Heo, S., & Mauck, R. L. (2020) · Advanced Healthcare Materials · doi:10.1002/adhm.202000030 · Cited by 22

Protein/DNA interactions in complex DNA topologies: expect the unexpected

Noy, A., Sutthibutpong, T., & Harris, S. A. (2016) · Biophysical Reviews · doi:10.1007/s12551-016-0241-7 · Cited by 21

Hematopoietic transcriptional mechanisms: From locus-specific to genome-wide vantage points

DeVilbiss, A., Sanalkumar, R., Johnson, K. D., Keleş, S., & Bresnick, E. H. (2014) · Experimental Hematology · doi:10.1016/j.exphem.2014.05.004 · Cited by 21

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Wang, M., Hancock, T., Chamberlain, A. J., Jagt, C. J. V., Pryce, J. E., Cocks, B. G., Goddard, M. E., & Hayes, B. J. (2018) · BMC Genomics · doi:10.1186/s12864-018-4800-0 · Cited by 20

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data

Stavrovskaya, E. D., Niranjan, T., Fertig, E. J., Wheelan, S. J., Favorov, A. V., & Mironov, A. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx379 · Cited by 21

Supramolecular multilayer organization of chromosomes: possible functional roles of planar chromatin in gene expression and DNA replication and repair

Daban, J. (2019) · FEBS Letters · doi:10.1002/1873-3468.13724 · Cited by 21

Understanding three-dimensional chromatin organization in diploid genomes

Li, J., Lin, Y., Tang, Q., & Li, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.06.018 · Cited by 20

Regulation of 3D Organization and Its Role in Cancer Biology

Peng, A., Peng, W., Wang, R., Zhao, H., Yu, X., & Sun, Y. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.879465 · Cited by 22

DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis

Simmonds, P., Loomis, E. W., & Curry, E. W. (2017) · Genome Medicine · doi:10.1186/s13073-017-0443-z · Cited by 21

Temporal autoregulation during human PU.1 locus SubTAD formation

Schuetzmann, D., Walter, C., van Riel, B., Kruse, S., König, T., Erdmann, T., Tönges, A., Bindels, E. M., Weilemann, A., Gebhard, C., et al. (2018) · Blood · doi:10.1182/blood-2018-02-834721 · Cited by 19

A principled strategy for mapping enhancers to genes

Kim, D., An, H., Shearer, R. S., Sharif, M. A., Fan, C., Choi, J., Ryu, S., & Park, Y. (2019) · Scientific Reports · doi:10.1038/s41598-019-47521-w · Cited by 20

MomicPred: A Cell Cycle Prediction Framework Based on Dual-Branch Multi-Modal Feature Fusion for Single-Cell Multi-Omics Data

Shi, Z., Cong, L., & Wu, H. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3595904 · Cited by 22

A matter of scale: how emerging technologies are redefining our view of chromosome architecture

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Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets

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