The 4D nucleome project

An integrated encyclopedia of DNA elements in the human genome

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

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

Imaging Intracellular Fluorescent Proteins at Nanometer Resolution

Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S. G., Bonifacino, J. S., Davidson, M. W., Lippincott‐Schwartz, J., & Hess, H. F. (2006) · Science · doi:10.1126/science.1127344 · Cited by 8,941

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

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

Rust, M., Bates, M., & Zhuang, X. (2006) · Nature Methods · doi:10.1038/nmeth929 · Cited by 7,823

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

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy

Hess, S. T., Girirajan, T. P. K., & Mason, M. D. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.091116 · Cited by 3,684

Capturing Chromosome Conformation

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

HDAC inhibitors rescue multiple disease-causing CFTR variants

Anglès, F., Hutt, D. M., & Balch, W. E. (2019) · Human Molecular Genetics · doi:10.1093/hmg/ddz026 · Cited by 28

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

Calandrelli, R., Wu, Q., Guan, J., & Zhong, S. (2018) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2018.06.006 · Cited by 28

Epigenetic and metabolic regulation of epidermal homeostasis

Wagner, R. N., Hofbauer, J. P., Wally, V., Kofler, B., Schmuth, M., Rosa, L. D., Luca, M. D., & Bauer, J. W. (2021) · Experimental Dermatology · doi:10.1111/exd.14305 · Cited by 33

Gaining insight into metabolic diseases from human genetic discoveries

Claussnitzer, M., & Suszták, K. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.07.005 · Cited by 28

Nuclear dynamics and stress responses in Alzheimer’s disease

Iatrou, A., Clark, E. M., & Wang, Y. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00489-6 · Cited by 31

A Liquid State Perspective on Dynamics of Chromatin Compartments

Laghmach, R., Pierro, M. D., & Potoyan, D. A. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.781981 · Cited by 25

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

Richer, S., Tian, Y., Schoenfelder, S., Hurst, L., Murrell, A., & Pisignano, G. (2022) · bioRxiv · doi:10.1186/s13059-023-02876-2 · Cited by 25

The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting

Dunlevy, K. L., Medvedeva, V., Wilson, J. E., Hoque, M., Pellegrin, T., Maynard, A. G., Kremp, M. M., Wasserman, J. S., Poleshko, A. S., & Katz, R. A. (2020) · Journal of Cell Science · doi:10.1242/jcs.240416 · Cited by 29

Autopolyploidy: an epigenetic macromutation

Doyle, J. J., & Coate, J. E. (2020) · American Journal of Botany · doi:10.1002/ajb2.1513 · Cited by 27

Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics

Chu, X., & Wang, J. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009596 · Cited by 23

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Bourget, M.-H., Kamentsky, L. D., Ghosh, S., Mazzamuto, G., Lazari, A., Markiewicz, C. J., Oostenveld, R., Niso, G., Halchenko, Y. O., Lipp, I., et al. (2022) · Frontiers in Neuroscience · doi:10.3389/fnins.2022.871228 · Cited by 27

Evaluating the role of the nuclear microenvironment in gene function by population-based modeling

Yıldırım, A., Hua, N., Boninsegna, L., Zhan, Y., Polles, G., Gong, K. Q., Hao, S., Li, W., Zhou, X. J., & Alber, F. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01036-1 · Cited by 28

Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains

Oldach, P., & Nieduszynski, C. A. (2019) · Genes · doi:10.3390/genes10030196 · Cited by 27

The multi‐faceted regulation of nuclear tRNA gene transcription

Hummel, G., Warren, J. M., & Maréchal‐Drouard, L. (2019) · IUBMB Life · doi:10.1002/iub.2097 · Cited by 26

Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development

Geusz, R. J., Wang, A., Chiou, J., Lancman, J. J., Wetton, N., Kefalopoulou, S., Wang, J., Qiu, Y., Yan, J., Aylward, A., et al. (2021) · eLife · doi:10.7554/elife.59067 · Cited by 25

Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO

Wang, H., Yang, J., Zhang, Y., Qian, J., & Wang, J. (2022) · Nature Communications · doi:10.1038/s41467-022-30270-2 · Cited by 28

Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization

Yang, M., & Ma, J. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167666 · Cited by 27

Three‐dimensional chromosome re‐modelling: The integral mechanism of transcription regulation in bacteria

Rashid, F. M., & Dame, R. T. (2023) · Molecular Microbiology · doi:10.1111/mmi.15062 · Cited by 26

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

Widespread chromatin context-dependencies of DNA double-strand break repair proteins

Vergara, X., Manjón, A. G., de Haas, M., Morris, B., Schep, R., Leemans, C., Friskes, A., Beijersbergen, R. L., Sanders, M. A., Medema, R. H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49232-x · Cited by 26

A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains

Xu, J., Xu, X., Huang, D., Luo, Y., Lin, L., Bai, X., Zheng, Y., Yang, Q., Cheng, Y., Huang, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48593-7 · Cited by 25

Exploring the roles of RNAs in chromatin architecture using deep learning

Kuang, S., & Pollard, K. S. (2024) · Nature Communications · doi:10.1038/s41467-024-50573-w · Cited by 26

ChromoGen: Diffusion model predicts single-cell chromatin conformations

Schuette, G., Lao, Z., & Zhang, B. (2025) · Science Advances · doi:10.1126/sciadv.adr8265 · Cited by 27

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

Rodríguez-Carballo, E., Lopez‐Delisle, L., Yakushiji‐Kaminatsui, N., Ullate‐Agote, A., & Duboule, D. (2019) · BMC Biology · doi:10.1186/s12915-019-0677-x · Cited by 22

Methods for comparative ChIA-PET and Hi-C data analysis

Capurso, D., Tang, Z., & Ruan, Y. (2019) · Methods · doi:10.1016/j.ymeth.2019.09.019 · Cited by 25

Advances in technologies for 3D genomics research

Zhang, Y., & Li, G. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1704-2 · Cited by 27

Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome

Zhu, X., Zhang, Y., Wang, Y., Tian, D., Belmont, A. S., Swedlow, J. R., & Ma, J. (2022) · Nature Methods · doi:10.1038/s41592-022-01559-3 · Cited by 29

BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes

Weng, Z., Ruan, F., Chen, W., Chen, Z., Xie, Y., Luo, M., Xie, Z., Zhang, C., Wang, J., Sun, Y., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02896-y · Cited by 24

Power-law behavior of transcriptional bursting regulated by enhancer–promoter communicationPreprint

Wang, Z., Zhang, Z., Luo, S., Zhou, T., & Zhang, J. (2024) · Genome Research · doi:10.1101/gr.278631.123 · Cited by 27

Three-dimensional genome: developmental technologies and applications in precision medicine

Li, Y., Tao, T., Du, L., & Zhu, X. M. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-0737-7 · Cited by 24

3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells

Papadogkonas, G., Papamatheakis, D.-A., & Spilianakis, C. G. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.921375 · Cited by 25

Viral remodeling of the 4D nucleome

Kim, K.-D., & Lieberman, P. M. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01207-0 · Cited by 25

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols

Lando, D., Stevens, T. J., Basu, S., & Laue, E. D. (2018) · Nucleus · doi:10.1080/19491034.2018.1438799 · Cited by 25

Advances in the computational and molecular understanding of the prostate cancer cell nucleus

Carleton, N. M., Lee, G., Madabhushi, A., & Veltri, R. W. (2018) · Journal of Cellular Biochemistry · doi:10.1002/jcb.27156 · Cited by 24

Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

Tjalsma, S. J. D., Rinzema, N. J., Verstegen, M. J. A. M., Robers, M. J., Nieto-Aliseda, A., Gremmen, R., Allahyar, A., Muraro, M. J., Krijger, P. H. L., & de Laat, W. L. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100778 · Cited by 30

TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells

Xu, H., Wang, J., Liang, Y., Fu, Y., Li, S., Huang, J., Xu, H., Zou, W., & Chen, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1170 · Cited by 23

The Role of Epigenomic Regulatory Pathways in the Gut-Brain Axis and Visceral Hyperalgesia

Higgins, G. A., Hong, S., & Wiley, J. W. (2021) · Cellular and Molecular Neurobiology · doi:10.1007/s10571-021-01108-0 · 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

Super-Resolution Microscopy of Chromatin

Birk, U. J. (2019) · Genes · doi:10.3390/genes10070493 · Cited by 23

In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators

Franks, J. L., Martinez‐Chacin, R. C., Wang, X., Tiedemann, R. L., Bonacci, T., Choudhury, R., Bolhuis, D. L., Enrico, T. P., Mouery, R. D., Damrauer, J. S., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000975 · Cited by 22

What Do We Know About the Genetic Architecture of Psychopathology?

Giangrande, E. J., Weber, R. S., & Turkheimer, E. (2022) · Annual Review of Clinical Psychology · doi:10.1146/annurev-clinpsy-081219-091234 · Cited by 22

Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser

Li, D., Harrison, J. K., Purushotham, D., & Wang, T. (2022) · Nature Methods · doi:10.1038/s41592-022-01550-y · Cited by 22

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Ghaemi, Z., Peterson, J. R., Gruebele, M., & Luthey-Schulten, Z. A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007717 · Cited by 24

Uncovering the Principles of Genome Folding by 3D Chromatin ModelingPreprint

Yıldırım, A., Boninsegna, L., Zhan, Y., & Alber, F. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039693 · Cited by 25

Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

Schep, R., Trauernicht, M., Vergara, X., Friskes, A., Morris, B., Gregoricchio, S., Manzo, S. G., Zwart, W. T., Beijersbergen, R. L., Medema, R. H., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae570 · Cited by 21

Chromophore‐Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells

Ding, T., Zhu, L., Fang, Y., Liu, Y., Tang, W., & Zou, P. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202005486 · Cited by 21

Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence

Chen, L., Wang, Y., & Zhao, F. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac214 · Cited by 21

Network models of chromatin structure

Pancaldi, V. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102051 · Cited by 21

4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction

Wang, Z., Luo, S., Zhang, Z., Zhou, T., & Zhang, J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011722 · Cited by 23

From association to mechanism in complex disease genetics: the role of the 3D genome

Fu, Y., Tessneer, K. L., Li, C., & Gaffney, P. M. (2018) · Arthritis Research & Therapy · doi:10.1186/s13075-018-1721-x · Cited by 21

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions

Dong, X., Sun, S., Zhang, L., Kim, S., Tu, Z., Montagna, C., Maslov, A. Y., Suh, Y., Wang, T., Campisi, J., et al. (2021) · Aging Cell · doi:10.1111/acel.13357 · Cited by 22

A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure

Fiorillo, L., Bianco, S., Esposito, A., Conte, M., Sciarretta, R., Musella, F., & Chiariello, A. M. (2019) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1454 · Cited by 24

Radionuclide partitioning coefficients in soils and plants and their correlation.

Sheppard, M. I. (1985) · PubMed · Cited by 21

Functional Assays to Screen and Dissect Genomic Hits

Musunuru, K., Bernstein, D., Cole, F. S., Khokha, M. K., Lee, F. S., Lin, S., McDonald, T. V., Moskowitz, I. P. G., Quertermous, T., Sankaran, V. G., et al. (2018) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.118.002178 · Cited by 20

scGHOST: identifying single-cell 3D genome subcompartments

Xiong, K., Zhang, R., & Ma, J. (2024) · Nature Methods · doi:10.1038/s41592-024-02230-9 · Cited by 21

An Introduction to Epigenetic Mechanisms

Radford, E. J. (2018) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2018.04.002 · Cited by 24

UV-induced reorganization of 3D genome mediates DNA damage response

Kaya, V. O., & Adebalı, O. (2025) · Nature Communications · doi:10.1038/s41467-024-55724-7 · Cited by 19

Physics of biomolecular recognition and conformational dynamics

Chu, W., Yan, Z., Chu, X., Zheng, X., Liu, Z., Xu, L., Zhang, K., & Wang, J. (2021) · Reports on Progress in Physics · doi:10.1088/1361-6633/ac3800 · Cited by 22

Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes

Ma, S., Dalgleish, J. L. T., Lee, J., Wang, C., Liu, L., Gill, R. J., Buxbaum, J. D., Chung, W. K., Aschard, H., Silverman, E. K., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2105191118 · Cited by 17

Nuclear architecture

Liehr, T. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823579-9.00011-4 · Cited by 19

Quantifying Chromosome Structural Reorganizations during Differentiation, Reprogramming, and Transdifferentiation

Chu, X., & Wang, J. (2022) · Physical Review Letters · doi:10.1103/physrevlett.129.068102 · Cited by 17

Germline intergenic duplications at Xq26.1 underlie Bazex–Dupré–Christol basal cell carcinoma susceptibility syndrome *

Liu, Y.-S., Banka, S., Huang, Y., Hardman-Smart, J., Pye, D., Torrelo, A., Beaman, G., Kazanietz, M., Baker, M. J., Ferrazzano, C., et al. (2022) · British Journal of Dermatology · doi:10.1111/bjd.21842 · Cited by 18

NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors

Meroni, A., Grosser, J., Agashe, S., Ramakrishnan, N., Jackson, J., Verma, P., Baranello, L., & Vindigni, A. (2022) · Science Advances · doi:10.1126/sciadv.abq0648 · Cited by 20

Decoding the plant genome: From epigenome to 3D organization

Ouyang, W., Cao, Z., Xiong, D., Li, G., & Li, X. (2020) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2020.06.007 · Cited by 19

Integrative studies of 3D genome organization and chromatin structure

Stefano, M. D., & Cavalli, G. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102493 · Cited by 23

Observing DNA in live cells

Weiss, L. E., Naor, T., & Shechtman, Y. (2018) · Biochemical Society Transactions · doi:10.1042/bst20170301 · Cited by 19

Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

Spracklin, G., & Pradhan, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1150 · Cited by 20

Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements

Rosenberg, T., Marco, A., Kisliouk, T., Haron, A., Shinder, D., Druyan, S., & Meiri, N. (2022) · The FASEB Journal · doi:10.1096/fj.202101948r · Cited by 17

Acute multi-level response to defective de novo chromatin assembly in S-phase

Dreyer, J., Ricci, G., van den Berg, J., Bhardwaj, V., Funk, J., Armstrong, C., van Batenburg, V., Sine, C. C., VanInsberghe, M. A., Tjeerdsma, R. B., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.10.023 · Cited by 18

DNA Replication Timing Enters the Single-Cell Era

Hiratani, I., & Takahashi, S. (2019) · Genes · doi:10.3390/genes10030221 · Cited by 21

Nucleosome Positioning

Teif, V. B., & Clarkson, C. T. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20242-2 · Cited by 17

Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data

Stear, B. J., Ahooyi, T. M., Simmons, J. A., Kollar, C., Hartman, L., Beigel, K., Lahiri, A., Vasisht, S., Callahan, T. J., Nemarich, C., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-04070-w · Cited by 28

Plant 3D Chromatin Organization: Important Insights from Chromosome Conformation Capture Analyses of the Last 10 Years

Zhang, X., & Wang, T. (2021) · Plant and Cell Physiology · doi:10.1093/pcp/pcab134 · Cited by 18

Deep learning identifies and quantifies recombination hotspot determinants

Li, Y., Chen, S., Rapakoulia, T., Kuwahara, H., Yip, K. Y.-L., & Gao, X. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac234 · Cited by 15

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

Martin, R. S., Das, P., Sanders, J. T., Hill, A. M., & McCord, R. P. (2022) · eLife · doi:10.7554/elife.81290 · Cited by 17

3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data

Fernandez, L. R., Gilgenast, T. G., & Phillips‐Cremins, J. E. (2020) · Genome biology · doi:10.1186/s13059-020-02061-9 · Cited by 17

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics

Pancaldi, V. (2021) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2021.742216 · Cited by 17

Functional organization of the maternal and paternal human 4D Nucleome

Lindsly, S., Jia, W., Chen, H., Liu, S., Ronquist, S., Chen, C., Wen, X., Stansbury, C. M., Dotson, G. A., Ryan, C., et al. (2021) · iScience · doi:10.1016/j.isci.2021.103452 · Cited by 17

3DGenBench: a web-server to benchmark computational models for 3D Genomics

Belokopytova, P. S., Viesná, E., Chiliński, M., Qi, Y., Salari, H., Stefano, M. D., Esposito, A., Conte, M., Chiariello, A. M., Teif, V. B., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac396 · Cited by 17

Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data

Gilgenast, T. G., & Phillips‐Cremins, J. E. (2019) · Cell Systems · doi:10.1016/j.cels.2019.02.006 · Cited by 17

Cis-regulatory elements: systematic identification and horticultural applications

Li, T., Zeng, W., Zhu, F., & Lü, P. (2025) · aBIOTECH · doi:10.1007/s42994-025-00237-0 · Cited by 17

Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Lee, B. H., & Rhie, S. K. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00390-y · Cited by 17

Machine learning for profile prediction in genomics

Schreiber, J. M., & Singh, R. (2021) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2021.04.008 · Cited by 15

Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach

Yu, H., Li, Y., Han, W., Bao, L., Liu, F., Ma, Y., Pu, Z., Zeng, Q., Zhang, L., Bao, Z., et al. (2024) · Nature Protocols · doi:10.1038/s41596-024-00966-4 · Cited by 18

Inter-chromosomal contacts demarcate genome topology along a spatial gradient

Mokhtaridoost, M., Chalmers, J. J., Soleimanpoor, M., McMurray, B. J., Lato, D. F., Nguyen, S. C., Musienko, V., Nash, J. O., Espeso‐Gil, S., Ahmed, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53983-y · Cited by 18

Engineering three-dimensional genome folding

Zhang, D., Lam, J. C., & Blobel, G. A. (2021) · Nature Genetics · doi:10.1038/s41588-021-00860-9 · Cited by 17

Recruitment of TRIM33 to cell‐context specific PML nuclear bodies regulates nodal signaling in mESCs

Sun, H., Chen, Y., Yan, K. H., Shao, Y., Zhang, Q. C., Lin, Y., & Xi, Q. (2022) · The EMBO Journal · doi:10.15252/embj.2022112058 · Cited by 18

Transient crosslinking kinetics optimize gene cluster interactions

Walker, B. L., Taylor, D., Lawrimore, J., Hult, C., Adalsteinsson, D., Bloom, K., & Forest, M. G. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007124 · Cited by 19

An Integrated Platform for High-Throughput NanoscopyPreprint

Barentine, A. E. S., Lin, Y., Courvan, E. M. C., Kidd, P., Liu, M., Balduf, L., Phan, T., Rivera-Molina, F. E., Grace, M. R., Marin, Z., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/606954 · Cited by 16

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

Fukai, Y. T., Kujirai, T., Wakamori, M., Kanamura, S., Yamauchi, L., Zeraati, S., Morita, S., Tanegashima, C., Kadota, M., Shirouzu, M., et al. (2025) · Science Advances · doi:10.1126/sciadv.adx9282 · Cited by 14

TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells

Xu, H., Wang, J., Liang, Y., Fu, Y., Li, S., Huang, J., Xu, H., Zou, W., & Chen, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa906 · Cited by 15

Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities

Narumi, S., Nagasaki, K., Kiriya, M., Uehara, E., Akiba, K., Tanase‐Nakao, K., Shimura, K., Abe, K., Sugisawa, C., Ishii, T., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01735-5 · Cited by 15

C3D: a tool to predict 3D genomic interactions between cis-regulatory elements

Mehdi, T., Bailey, S. D., Guilhamon, P., & Lupien, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty717 · Cited by 15

Integrating transposable elements in the 3D genome

Bousios, A., Nützmann, H., Buck, D., & Michieletto, D. (2020) · Mobile DNA · doi:10.1186/s13100-020-0202-3 · Cited by 16

Controlling gene activation by enhancers through a drug-inducible topological insulator

Tsujimura, T., Takase, O., Yoshikawa, M., Sano, E., Hayashi, M., Hoshi, K., Takato, T., Toyoda, A., Okano, H., & Hishikawa, K. (2020) · eLife · doi:10.7554/elife.47980 · Cited by 16

MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text

Ryan, J., Pengo, T., Rigano, A., Llopis, P. D. L. M. M., Itano, M. S., Cameron, L., Marqués, G., Strambio‐De‐Castillia, C., Sanders, M. A., & Brown, C. M. (2021) · Nature Methods · doi:10.1038/s41592-021-01290-5 · Cited by 15

Parkinson’s disease risk enhancers in microglia

Booms, A., Pierce, S. E., der Schans, E. J. C. V., & Coetzee, G. A. (2024) · iScience · doi:10.1016/j.isci.2024.108921 · Cited by 14

MorPhiC Consortium: towards functional characterization of all human genes

Adli, M., Przybyla, L., Burdett, T., Burridge, P. W., Cacheiro, P., Chang, H. Y., Engreitz, J., Gilbert, L. A., Greenleaf, W. J., Hsu, L.-I., et al. (2025) · Nature · doi:10.1038/s41586-024-08243-w · Cited by 21

UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C

Ramos-Rodríguez, M., Subirana-Granés, M., & Pasquali, L. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab392 · Cited by 14

GILoop: Robust chromatin loop calling across multiple sequencing depths on Hi-C data

Wang, F., Gao, T., Lin, J., Zheng, Z., Huang, L., Toseef, M., Li, X., & Wong, K. (2022) · iScience · doi:10.1016/j.isci.2022.105535 · Cited by 14

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B. J., Bruneau, B. G., Belmont, A. S., Bintu, L., Boettiger, A. N., Calandrelli, R., Distèche, C. M., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.018 · Cited by 98

Dynamic Network Analysis of the 4D NucleomePreprint

Liu, S., Chen, P., Hero, A. O., & Rajapakse, I. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/268318 · Cited by 5

Elucidating the structure and function of the nucleus—The NIH Common Fund 4D Nucleome program

Roy, A. L., Conroy, R., Taylor, V. G., Mietz, J. A., Fingerman, I. M., Pazin, M. J., Smith, P., Hutter, C. M., Singer, D. S., & Wilder, E. L. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.025 · Cited by 9

Evolving methodologies and concepts in 4D nucleome research

Sparks, T. M., Harabula, I., & Pombo, A. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.04.005 · Cited by 10

4D nucleome: dynamic three-dimensional genome organization over time

Kim, H. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01248-5