Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

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

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

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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,752

A map of the cis-regulatory sequences in the mouse genome

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HiChIP: efficient and sensitive analysis of protein-directed genome architecture

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

Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982

Topology of mammalian developmental enhancers and their regulatory landscapes

de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression

Mortenson, K. L., Dawes, C., Wilson, E. R., Patchen, N. E., Johnson, H. E., Gertz, J., Bailey, S. D., Yang, J., Varley, K. E., & Zhang, X. (2024) · Nature Communications · doi:10.1038/s41467-024-50387-w · Cited by 35

PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids

Jourdon, A., Scuderi, S., Capauto, D., Abyzov, A. S., & Vaccarino, F. M. (2020) · Neuropsychopharmacology · doi:10.1038/s41386-020-0763-3 · Cited by 29

HiCuT: An efficient and low input method to identify protein-directed chromatin interactions

Sati, S., Jones, P., Kim, H. S., Zhou, L., Rapp-Reyes, E., & Leung, T. H. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010121 · Cited by 22

Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease

Nott, A., & Holtman, I. R. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1168539 · Cited by 33

Annotating genetic variants to target genes using H-MAGMA

Sey, N. Y. A., Pratt, B. M., & Won, H. (2022) · Nature Protocols · doi:10.1038/s41596-022-00745-z · Cited by 27

Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath

Ren, X., Wang, M., Li, B., Jamieson, K., Zheng, L., Jones, I. R., Li, B., Takagi, M. A., Lee, J., Maliskova, L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abi4360 · Cited by 28

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

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

Ma, W., Ay, F., Lee, C., Gülsoy, G., Deng, X., Cook, S. M., Hesson, J., Cavanaugh, C., Ware, C. B., Krumm, A., et al. (2018) · Methods · doi:10.1016/j.ymeth.2018.01.014 · Cited by 28

Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

Lange, M., Begolli, R., & Giakountis, A. (2021) · Non-Coding RNA · doi:10.3390/ncrna7030047 · Cited by 26

Predicting 3D chromatin interactions from DNA sequence using Deep Learning

Piecyk, R. S., Schlegel, L., & Johannes, F. M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.06.047 · Cited by 27

3D genome organization links non-coding disease-associated variants to genes

Orozco, G., Schoenfelder, S., Walker, N. J., Eyre, S., & Fraser, P. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.995388 · Cited by 30

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

DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD‐Like Domains in the Single Cells

Li, A., Zeng, G., Wang, H., Li, X., & Zhang, Z. (2023) · Advanced Science · doi:10.1002/advs.202300366 · Cited by 25

Tissue-specific enhancer functional networks for associating distal regulatory regions to disease

Chen, X. X., Zhou, J., Zhang, R., Wong, A. K., Park, C. Y., Theesfeld, C. L., & Troyanskaya, O. G. (2021) · Cell Systems · doi:10.1016/j.cels.2021.02.002 · Cited by 25

In situ Chromatin Interaction Analysis Using Paired‐End Tag Sequencing

Wang, P., Feng, Y., Zhu, K., Chai, H., Chang, Y., Yang, X., Liu, X., Shen, C., Gega, E., Lee, B., et al. (2021) · Current Protocols · doi:10.1002/cpz1.174 · Cited by 26

Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures

Nair, S. J., Suter, T., Wang, S. S., Lu, Y., Yang, F., & Rosenfeld, M. G. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.05.015 · Cited by 27

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells

Wu, D., Poddar, A., Ninou, E., Hwang, E. E., Cole, M. A., Liu, S. J., Horlbeck, M. A., Chen, J., Replogle, J. M., Carosso, G. A., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100177 · Cited by 27

ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

Chai, H.-X., Tjong, H., Li, P., Liao, W., Wang, P., Wong, C.-H., Ngan, C., Leonard, W., Wei, C.-L., & Ruan, Y. (2023) · Nature Communications · doi:10.1038/s41467-023-35879-5 · Cited by 23

Structural aspects of the inactive X chromosome

Bonora, G., & Distèche, C. M. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0357 · Cited by 26

NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolutionPreprint

Luo, Z.-Y., Zhang, R., Hu, T.-F., Zhu, Y.-T., Wu, Y.-M., Li, W.-F., Zhang, Z., Yao, X.-B., Liang, H.-Y., & Song, X.-Y. (2022) · Genome Research · doi:10.1101/gr.275986.121 · Cited by 20

Advances in the multimodal analysis of the 3D chromatin structure and gene regulation

Han, M.-H., Park, J., & Park, M. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01246-7 · Cited by 30

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

Measuring significant changes in chromatin conformation with ACCOST

Cook, K. B., Hristov, B. H., Roch, K. G. L., Vert, J., & Noble, W. S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa069 · Cited by 22

3D Chromosomal Landscapes in Hematopoiesis and Immunity

Kloetgen, A., Thandapani, P., Tsirigos, A., & Aifantis, I. (2019) · Trends in Immunology · doi:10.1016/j.it.2019.07.003 · Cited by 25

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

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

Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation

Torre, D., Fstkchyan, Y. S., Ho, J., Cheon, Y., Patel, R. S., DeGrace, E. J., Mzoughi, S., Schwarz, M. C., Mohammed, K., Seo, J.-S., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.036 · Cited by 26

Mitochondrial nucleoid in cardiac homeostasis: bidirectional signaling of mitochondria and nucleus in cardiac diseases

Feng, Y., Huang, W. C., Paul, C., Liu, X., Sadayappan, S., Wang, Y., & Pauklin, S. (2021) · Basic Research in Cardiology · doi:10.1007/s00395-021-00889-1 · Cited by 22

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

Zhu, X., Qi, C.-Y., Wang, R.-Y., Lee, J.-H., Shao, J., Bei, L.-X., Xiong, F., Nguyen, P. T., Li, G., Krakowiak, J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111576 · Cited by 20

The 3D genome and its impacts on human health and disease

Wang, S., Luo, Z., Liu, W., Hu, T., Zhao, Z., Rosenfeld, M. G., & Song, X. (2023) · Life Medicine · doi:10.1093/lifemedi/lnad012 · Cited by 22

Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy

Liu, C., Abnousi, A., Bazeley, P. S., Ni, Y., Morley, M. P., Moravec, C. S., Hu, M., & Tang, W. H. W. (2020) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2020.06.001 · Cited by 23

Diverse gene regulatory mechanisms mediated by Polycomb group proteins during neural development

Tsuboi, M., Hirabayashi, Y., & Gotoh, Y. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.07.003 · Cited by 23

Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers

Fath, M. K., Karimfar, N., Naghibi, A. F., Shafa, S., Shiran, M. G., Ataei, M., Dehghanzadeh, H., Nabi‐Afjadi, M., Ghadiri, T., Payandeh, Z., et al. (2022) · Cancer Cell International · doi:10.1186/s12935-022-02617-8 · Cited by 21

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

Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis

Catta-Preta, R., Lindtner, S., Ypsilanti, A. R., Seban, N., Price, J. D., Abnousi, A., Su-Feher, L., Wang, Y., Cichewicz, K., Boerma, S. A., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.10.004 · 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

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 25

Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits

Chawla, A., Nagy, C., & Turecki, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147612 · Cited by 22

MSL2 ensures biallelic gene expression in mammals

Sun, Y., Wiese, M., Hmadi, R., Karayol, R., Seyfferth, J., Greene, J. A. M., Erdogdu, N. U., Deboutte, W., Arrigoni, L., Holz, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06781-3 · Cited by 22

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

Alterations in Chromatin Structure and Function in the Microglia

Fujita, Y., & Yamashita, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.626541 · Cited by 22

Dynamics of Viral and Host 3D Genome Structure upon Infection

Friedman, M. J., Lee, H., Kwon, Y., & Oh, S. (2022) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2208.08020 · Cited by 20

Machine and Deep Learning Methods for Predicting 3D Genome Organization

Wall, B. P. G., Nguyen, M., Harrell, J. C., & Dozmorov, M. G. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4136-1_22 · Cited by 20

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia

Gambi, G., Boccalatte, F. E., Rodriguez-Hernaez, J., Lin, Z., Nadorp, B., Polyzos, A., Tan, J., Avrampou, K., Inghirami, G., Kentsis, A., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.040 · Cited by 18

Comparison of computational methods for 3D genome analysis at single-cell Hi-C level

Li, X., An, Z., & Zhang, Z. (2019) · Methods · doi:10.1016/j.ymeth.2019.08.005 · Cited by 18

When function follows form: Nuclear compartment structure and the epigenetic landscape of the aging neuron

Schlachetzki, J. C. M., Toda, T., & Mertens, J. (2020) · Experimental Gerontology · doi:10.1016/j.exger.2020.110876 · Cited by 18

Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis

Wang, D., Xiao, S., Shu, J., Luo, L., Yang, M., Calonje, M., He, H., Song, B., & Zhou, Y. (2024) · Genome biology · doi:10.1186/s13059-024-03465-7 · Cited by 19

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

Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies

Xu, Z., & Dixon, J. R. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz026 · Cited by 18

Genomic convergence in hibernating mammals elucidates the genetics of metabolic regulation in the hypothalamus

Ferris, E., Murcia, J. D. G., Rodriguez, A. C., Steinwand, S., Hörndli, C. S., Tränkner, D., Maldonado-Catala, P. J., & Gregg, C. J. (2025) · Science · doi:10.1126/science.adp4025 · Cited by 16

BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data

Wang, Z., Zhang, Y., & Zang, C. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab173 · Cited by 16

BAT Hi-C maps global chromatin interactions in an efficient and economical way

Huang, J. S., Jiang, Y., Zheng, H., & Ji, X. (2019) · Methods · doi:10.1016/j.ymeth.2019.08.004 · Cited by 16

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms

Kim, M., Zheng, M., Tian, S. Z., Capurso, D., Lee, B., Chuang, J. H., & Ruan, Y. (2019) · Genome biology · doi:10.1186/s13059-019-1868-z · Cited by 15

Enhancers navigate the three-dimensional genome to direct cell fate decisions

Kim, J., & Dean, A. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.005 · Cited by 15

Core regulatory circuitries in defining cancer cell identity across the malignant spectrum

Jahangiri, L., Tsaprouni, L., Trigg, R. M., Williams, J. A., Gkoutos, G. V., Turner, S. D., & Pereira, J. D. (2020) · Open Biology · doi:10.1098/rsob.200121 · Cited by 14

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

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

A comprehensive review of bioinformatics tools for chromatin loop calling

Liu, L., Han, K., Sun, H., Han, L., Gao, D., Xi, Q., Zhang, L., & Lin, H. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad072 · Cited by 14

Perspective on recent developments and challenges in regulatory and systems genomics

Zeitlinger, J., Roy, S., Ay, F., Mathelier, A., Medina-Rivera, A., Mahony, S., Sinha, S. K., & Ernst, J. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf106 · Cited by 18

Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies

Lopes, K. P., Snijders, G. J. L., Humphrey, J., de Witte, L. D., & Raj, T. (2021) · Alzheimer s & Dementia · doi:10.1002/alz.050942 · Cited by 18

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Yu, M., Juric, I., Abnousi, A., Hu, M., & Ren, B. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1597-3_10 · Cited by 12

Locus-specific chromatin profiling of evolutionarily young transposable elements

Taylor, D., Lowe, R., Philippe, C., Cheng, K. C. L., Grant, O. A., Zabet, N. R., Cristofari, G., & Branco, M. R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1232 · Cited by 15

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian CellsPreprint

Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D. U., Yu, M., et al. (2020) · bioRxiv · doi:10.1101/2020.03.21.001693 · Cited by 10

Trimodal single-cell profiling of transcriptome, epigenome, and 3D genome in complex tissues with scHiCAR

Wei, X., Xu, Y.-Y., Yang, D.-C., Kim, K., Yi, L., Luo, W.-Z., Lin, X., Xiang, Y., Williams, A. B., Wang, X.-T., et al. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03013-7 · Cited by 16

Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription

Kim, M., Wang, P., Clow, P. A., Chien, E., Wang, X., Peng, J., Chai, H., Liu, X., Lee, B., Ngan, C. Y., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01708-0 · Cited by 13

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

Architectural proteins for the formation and maintenance of the 3D genome

Li, M., Gan, J., Sun, Y., Xu, Z., Yang, J., Sun, Y., & Li, C. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1613-3 · Cited by 15

Intraoperative neuromonitoring (IONM) for recurrent laryngeal nerve protection: comparison of intermittent and continuous nerve stimulation.

Jonas, J., & Boskovic, A. (2014) · PubMed · Cited by 13

Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization

Liu, W., Zhong, W., Chen, J. C., Huang, B., Hu, M., & Li, Y. (2022) · Genes · doi:10.3390/genes13040586 · Cited by 11

CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin DomainsPreprint

Huang, H., Zhu, Q.-S., Jussila, A. P., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y.-X., Bianco, S., Chiariello, A., et al. (2020) · bioRxiv · doi:10.1101/2020.07.07.192526 · Cited by 14

A meta-analysis of single-nucleus expression quantitative trait loci linking genetic risk to brain disorders

Jang, B., Kailash, B. P., Tokolyi, A., Dredge, W. H., Ravi, A., Jung, S., Naito, T., Kim, B., Kim, M. S., Cho, M., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02541-x · Cited by 29

Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression

Li-Bao, L., Díaz-Díaz, C., Raiola, M., Sierra, R., Temiño, S., Moya, F., Rodríguez, S., Santos, E., Giovinazzo, G., Bleckwehl, T., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48258-5 · Cited by 12

Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR

Flynn, S. M., Dhir, S., Herka, K., Doyle, C., Melidis, L., Simeone, A., Hui, W. W. I., Tavares, R. D. C. A., Schoenfelder, S., Tannahill, D., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03377-6 · Cited by 11

RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture

Bertero, A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.645863 · Cited by 12

Advances in higher-order chromatin architecture: the move towards 4D genome

Jung, N., & Kim, T.-K. (2021) · BMB Reports · doi:10.5483/bmbrep.2021.54.5.035 · Cited by 14

Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective

Wang, X., Dong, Y., Zheng, Y., & Chen, Y. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.05.008 · Cited by 13

Building a Mammalian Retina: An Eye on Chromatin Structure

Daghsni, M., & Aldiri, I. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.775205 · Cited by 11

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

Lohia, R., Fox, N., & Gillis, J. (2022) · Genome biology · doi:10.1186/s13059-022-02790-z · Cited by 11

3D genomics and its applications in precision medicine

Chen, M.-J., Liu, X., Liu, Q.-Y., Shi, D., & Li, H. (2023) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-023-00428-x · 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

Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency

Hörnblad, A., & Remeseiro, S. (2022) · Cells · doi:10.3390/cells11091404 · Cited by 14

When 3D genome technology meets viral infection, including SARS‐CoV‐2

Liang, W., Wang, S., Wang, H., Li, X., Meng, Q., Zhao, Y., & Zheng, C. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28040 · Cited by 10

Modeling three-dimensional genomic organization in evolution and pathogenesis

Diament, A., & Tuller, T. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.008 · Cited by 11

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

Jang, B., Kailash, B., Tokolyi, A., Cuddleston, W. H., Ravi, A., Jung, S.-H., Naito, T., Kim, B., Kim, M. S., Cho, M., et al. (2025) · doi:10.1101/2025.03.06.25323424 · Cited by 11

Chromatin insulators in gene regulation and 3D genome organization

Sultana, H., Kunar, R., & Matera, A. G. (2025) · Biochemical Society Transactions · doi:10.1042/bst20253036 · Cited by 11

Epigenome rewiring in human pluripotent stem cells

Yan, J., & Huangfu, D. (2021) · Trends in Cell Biology · doi:10.1016/j.tcb.2021.12.001 · Cited by 11

Spatial genome architecture and the emergence of malignancy

Danieli‐Mackay, A., & Papantonis, A. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa128 · 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

THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data

Rowland, B., Huh, R., Hou, Z., Crowley, C., Wen, J., Shen, Y., Hu, M., Giusti‐Rodríguez, P., Sullivan, P. F., & Li, Y. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010102 · Cited by 11

3D genome organization in the central nervous system, implications for neuropsychological disorders

Sun, D., Weng, J., Dong, Y., & Jiang, Y. (2021) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.06.017 · Cited by 10

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

Reyna, J., Fetter, K., Ignacio, R., Marandi, C. C. A., Ma, A., Rao, N., Jiang, Z., Figueroa, D. S., Bhattacharyya, S., & Ay, F. (2025) · Genome biology · doi:10.1186/s13059-025-03615-5 · Cited by 9

Functional analysis of PCSK2 coding variants: A founder effect in the Old Order Amish population

Winters, A. H., Ramos‐Molina, B., Jarvela, T. S., Yerges‐Armstrong, L. M., Pollin, T. I., & Lindberg, I. (2017) · Diabetes Research and Clinical Practice · doi:10.1016/j.diabres.2017.06.023 · Cited by 10

HiCAR: a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility, and cis-regulatory chromatin contactsPreprint

Wei, X., Xiang, Y., Abnousi, A., Sun, T., Lin, X., Li, W., Hu, M., & Diao, Y.-R. (2020) · bioRxiv · doi:10.1101/2020.11.02.366062

Chromatin accessibility provides a window into the genetic etiology of human brain disease

Bendl, J. M., Fullard, J. F., Girdhar, K., Dong, P., Kosoy, R., Zeng, B., Hoffman, G. E., & Roussos, P. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.01.001 · Cited by 9

Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP

Metelova, M., Vigh, M. L., & Krietenstein, N. (2025) · Nature Communications · doi:10.1038/s41467-025-64350-w · Cited by 11

Functional genomic assays to annotate enhancer–promoter interactions genome wide

Leung, A. K.-Y., Li, Y., & Yu, H. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac204 · Cited by 9

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

Yu, M., Zemke, N. R., Chen, Z., Jurić, I., Hu, R., Raviram, R., Abnousi, A., Fang, R., Zhang, Y., Gorkin, D. U., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01431-2 · Cited by 9

Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture

Tjalsma, S. J. D., & de Laat, W. L. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.10.002 · Cited by 9

HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets

Rosen, J. D., Yang, Y.-C., Abnousi, A., Chen, J.-W., Song, M., Jones, I. R., Shen, Y., Hu, M., & Li, Y. (2020) · bioRxiv · doi:10.3390/cimb43020082 · Cited by 8

Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

Qi, X., Zhang, L., Zhao, Q., Zhou, P., Zhang, S., Li, J., Zheng, Z., Xiang, Y., Dai, X., Jin, Z., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-023-2441-0 · Cited by 3

ChromE-seq: Chromatin and Expression Co-assay with Sequencing v1Preprint

Liao, Z., & Ma, S. (2025) · doi:10.17504/protocols.io.e6nvwbq4wvmk/v1

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121

Deciphering the effects of proximity ligation in chromatin contact maps to understand single molecule interactions data

Kim, M., Zheng, M., Tian, S. Z., Lee, B., Capurso, D., Chuang, J. H., & Ruan, Y. (2018) · Research in Computational Molecular Biology

ChIP‐based methods for the identification of long‐range chromatin interactions

Fullwood, M. J., & Ruan, Y. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22116 · Cited by 251