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

Genomics of forest trees

Street, N. R. (2018) · Advances in botanical research · doi:10.1016/bs.abr.2018.11.001 · Cited by 4

Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments

Stefano, M. D., Castillo, D., Serra, F., Farabella, I., Goodstadt, M. N., & Martı́-Renom, M. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0664-3_4 · Cited by 3

Epigenetic regulation in stem cells

Zhang, J., Arisha, A. H., & Hua, J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819753-0.00004-0 · Cited by 3

Benchmarking experiments with polymer modeling

Martı́-Renom, M. A. (2021) · Nature Methods · doi:10.1038/s41592-021-01134-2 · Cited by 5

Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts

Paulsen, J., & Collas, P. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1390-0_18 · Cited by 3

Structural and developmental dynamics of Matrix associated regions in Drosophila melanogaster genome

Sureka, R., Avvaru, A. K., Sowpati, D. T., Pathak, R. U., & Mishra, R. K. (2022) · BMC Genomics · doi:10.1186/s12864-022-08944-4 · Cited by 3

Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin cagingPreprint

Stefano, M. D., Stadhouders, R., Farabella, I., Castillo, D., Serra, F., Graf, T., & Martı́-Renom, M. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/642009 · Cited by 3

Suv39h-catalysed H3K9me3 is critical for euchromatic genome organisation and the maintenance of gene transcriptionPreprint

Keenan, C. R., Coughlan, H. D., Iannarella, N., Johanson, T. M., Chan, W. F., Garnham, A. L., Smyth, G. K., & Allan, R. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.13.249078 · Cited by 3

Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenetic States in Single Mammalian CellsPreprint

Xu, J., Ma, H., Jin, J., Uttam, S., Fu, R., Huang, Y., & Liu, Y. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3155874 · Cited by 3

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin OrganizationPreprint

Lin, X., & Zhang, B. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.16.541030 · Cited by 3

Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion

Jeong, D., Shi, G., Li, X., & Thirumalai, D. (2023) · eLife · doi:10.7554/elife.88564 · Cited by 10

Image-based analysis of the genome’s fractality during the cell cycle

Lee, S., Liu, X., Ziabkin, I., & Zidovska, A. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.02.014 · Cited by 2

Deciphering the 3D structures of plant genomes: building blocks of hierarchically organized chromatin domains

Lee, H., & Seo, P. J. (2025) · Journal of Experimental Botany · doi:10.1093/jxb/eraf218 · Cited by 3

Chromosome‐level genome assembly of Ctenoplusia agnata and its potential application in Plusiinae pest management

Kim, J., Faruquee, H. M., & Khan, M. (2025) · Pest Management Science · doi:10.1002/ps.8949 · Cited by 2

A multifaceted journey into higher-order chromatin organization: Insights from experimental and computational approaches

Yadav, V. K., & Jalmi, S. K. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.146721 · Cited by 3

Molecular systems, human noncoding sequence variants, and blood pressure

Qiu, Q., & Liang, M. (2026) · Physiological Reviews · doi:10.1152/physrev.00029.2025 · Cited by 3

CRISPR–Cas-based live cell imaging of genome dynamics

Zhu, Y., Moerner, W. E., & Qi, L. S. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00949-z · Cited by 5

Computational Epigenomics and Its Application in Regulatory Genomics

Jhanwar, S. (2018) · Springer eBooks · doi:10.1007/978-981-13-1562-6_6 · Cited by 2

Chromatin dynamics in regeneration epithelia: Lessons from Drosophila imaginal discs

Vizcaya-Molina, E., Klein, C. C., Serras, F., & Corominas, M. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.04.017 · Cited by 2

Characterization of Gene Regulatory Elements in Human Fetal Cortical Development: Enhancing Our Understanding of Neurodevelopmental Disorders and Evolution

Guo, Q., Wu, S. J., & Geschwind, D. H. (2023) · Developmental Neuroscience · doi:10.1159/000530929 · Cited by 2

Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis

Yu, J., Leng, J., Hou, Z., Sun, D., & Wu, L. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae093 · Cited by 2

LoopNetica: Predicting Chromatin Loops Using Convolutional Neural Networks and Attention Mechanisms

Yang, L., Tang, L., Luo, H., Huang, W., & Li, M. (2024) · Lecture notes in computer science · doi:10.1007/978-981-97-5087-0_2 · Cited by 2

Loopy virus or controlled contortionist? 3D regulation of HCMV gene expression by CTCF-driven chromatin interactions

Groves, I. J., & O’Connor, C. M. (2024) · Journal of Virology · doi:10.1128/jvi.01148-24 · Cited by 2

Beyond the double helix: Unraveling the intricacies of DNA and RNA networks

Odah, M. (2024) · African Research Journal of Biosciences · doi:10.62587/afrjbs.1.2.2024.1-16 · Cited by 2

Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function

Tsukamoto, S., & Mofrad, M. R. K. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0232328 · Cited by 2

DNA loops after cell lysis resemble chromatin loops in an intact nucleus

Afanasieva, K. S., Olefirenko, V. V., & Sivolob, A. (2018) · The Ukrainian Biochemical Journal · doi:10.15407/ubj90.05.043 · Cited by 2

DNA loop organization in glioblastoma T98G cells at their different functional states

Afanasieva, K. S., Semenova, A., Лукаш, Л. Л., & Sivolob, A. (2018) · Biopolymers and Cell · doi:10.7124/bc.00098d · Cited by 2

DNA loop domain rearrangements in blast transformed human lymphocytes and lymphoid leukaemic Jurkat T cells

Afanasieva, K. S., Olefirenko, V., Martyniak, A., Лукаш, Л. Л., & Sivolob, A. (2020) · The Ukrainian Biochemical Journal · doi:10.15407/ubj92.05.062 · Cited by 2

Spatial Organization of Epigenomes

Dube, J., Wang, X. Q. D., & Dostie, J. (2016) · Current Molecular Biology Reports · doi:10.1007/s40610-016-0028-4 · Cited by 3

Regulation of Vertebrate Conduction System Development

van Weerd, J. H., & Christoffels, V. M. (2016) · Springer eBooks · doi:10.1007/978-4-431-54628-3_38 · Cited by 2

A Combination Approach Based on Live-Cell Imaging and Computational Modeling to Further Our Understanding of Chromatin, Epigenetics, and the Genome

Hibino, K., Kaizu, K., Takahashi, K., & Maeshima, K. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803075-2.00011-8 · Cited by 2

From Identification to Function: Current Strategies to Prioritise and Follow-Up GWAS Results

Berlanga‐Taylor, A. J. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7868-7_15 · Cited by 2

Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq

Chen, Y., Wang, Y., Liu, X., Xu, J., & Zhang, M. Q. (2020) · PLoS ONE · doi:10.1371/journal.pone.0236666 · Cited by 2

Evaluation and measurement of epigenetic modifications in population-based studies

Stirzaker, C., & Armstrong, N. J. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820951-6.00014-4 · Cited by 2

Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis

Santos, F. J. P.-D. L., Sotelo-Fonseca, J. E., Ramírez-Colmenero, A., Nützmann, H., Fernández-Valverde, S. L., & Oktaba, K. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2429-6_13 · Cited by 2

Distinct chromosomal “niches” in the genome of Saccharomyces cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates

Stavropoulou, A., Tassios, E., Kalyva, M., Georgoulopoulos, M., Vakirlis, N., Iliopoulos, I., & Nikolaou, C. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac086 · Cited by 2

HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets

Rosen, J. D., Lee, L., Abnousi, A., Chen, J.-W., Wen, J., Hu, M., & Li, Y. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.003 · Cited by 2

Chromatin looping links gene expression to the assembly of transcription factories (Review)

Perillo, B., Migliaccio, A., & Castoria, G. (2024) · Molecular Medicine Reports · doi:10.3892/mmr.2024.13221 · Cited by 2

Plasticity of Chromatin Organization in the Plant Interphase Nucleus

Santos, A. P., Abranches, R., Oliveira, M. M., & Shaw, P. (2015) · Springer eBooks · doi:10.1007/978-1-4939-2386-1_4 · Cited by 2

Expanding the Utility of FUCCI Reporters Using FACS-Based Omics Analysis

Chappell, J., Boward, B., & Dalton, S. (2015) · Methods in molecular biology · doi:10.1007/7651_2015_214 · Cited by 2

Chromosome Conformation Capture

McLaughlin, K. (2018) · Materials and Methods · doi:10.13070/mm.en.8.2662 · Cited by 2

Clustering of the structures by using “snakes-&-dragons” approach, or correlation matrix as a signal

Andreev, V. P., Liu, G., Zee, J., Henn, L. L., Flores, G. E., & Merion, R. M. (2019) · PLoS ONE · doi:10.1371/journal.pone.0223267 · Cited by 2

Polycomb Complexes: Chromatin Regulators Required for Cell Diversity and Tissue Homeostasis

Vidal, M. (2014) · Epigenetics and human health · doi:10.1007/978-3-642-45198-0_5 · Cited by 2

Locus architecture affects mRNA expression levels in Drosophila embryosPreprint

Lydiard‐Martin, T., Bragdon, M. D. J., Eckenrode, K. B., Wunderlich, Z., & DePace, A. H. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/005173 · Cited by 3

Stratification of TAD boundaries identified in reproducible Hi-C contact matrices reveals preferential insulation of super-enhancers by strong boundariesPreprint

Gong, Y., Lazaris, C., Sakellaropoulos, T., Lozano, A., Kambadur, P., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/141481 · Cited by 2

Pharmacogenomics in the Age of GWAS, Omics Atlases, and PheWASPreprint

Allyn-Feuer, A., Higgins, G. A., & Athey, B. D. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1808.09481 · Cited by 2

Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to modulate chromatin structure and gene expressionPreprint

Miyaji, M., Furuta, R., Hosoya, O., Sano, K., Hara, N., Kuwano, R., Kang, J., Tateno, M., Tsutsui, K., & Tsutsui, K. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/484956 · Cited by 2

cis ‐Regulatory Driver Mutations in Cancer Genomes

Poulos, R. C., & Wong, J. W. H. (2017) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0027236 · Cited by 2

Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C ParadoxPreprint

Shi, G., & Thirumalai, D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/615120 · Cited by 2

OpenNucleome for high resolution nuclear structural and dynamical modelingPreprint

Lao, Z., Kamat, K. D., Jiang, Z., & Zhang, B. (2024) · eLife · doi:10.7554/elife.93223.1 · Cited by 2

Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells.Preprint

Sanbonmatsu, K. Y., Singhal, A., Roth, C., Micheva‐Viteva, S., Venu, V., Lappala, A., Lee, J. T., Starkenburg, S. R., & Steadman, C. R. (2024) · Research Square · doi:10.21203/rs.3.rs-3979539/v1 · Cited by 3

Substructure and maturation of lamina-associated domains in neurons of the developing and adult human brainPreprint

Zhang, C., Gil, E., Ahanger, S. H., Li, L., Wang, L., Huang, E. J., Li, J., Kriegstein, A. R., & Lim, D. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.27.625786 · Cited by 2

Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications

Arshadi, A., Tolomeo, D., Venuto, S., & Storlazzi, C. T. (2023) · Genes · doi:10.3390/genes14061304 · Cited by 1

Toward single-cell epigenome analysis: A microfluidic device for isolating, stretching, and imaging individual chromosomes

Noda, K., & Oana, H. (2023) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2023.134462 · Cited by 1

An integrative 3D-genome database for plants

Yang, Q., Wu, T., Liu, M., Zhang, X., Sun, X., Feng, D., Lu, Y. Y., Chen, X., Hong, Y., Ma, W., et al. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101346 · Cited by 1

Tasks and Visual Abstractions for 3D Chromatin Representation

Rychlý, A., Byška, J., Kozlíková, B., & Furmanová, K. (2025) · Computer Graphics Forum · doi:10.1111/cgf.70142 · Cited by 1

Genome Editing of the NF-YA8 Gene Modifies Tomato Plant Architecture and Fruit Traits

Petrou, N., Tsigarida, N., & Hilioti, Z. (2025) · Plants · doi:10.3390/plants14121826 · Cited by 1

Can random walking on a Hi-C contact matrix lead to data quality improvement? An assessment

Liu, Y., & Lin, S. (2025) · PLoS ONE · doi:10.1371/journal.pone.0327100 · Cited by 1

Organisation and dynamics of individual DNA segments in topologically complex genomes

Ramakrishnan, S., Grillo, G., Patnaik, A. V., Tubiana, L., & Michieletto, D. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf925 · Cited by 1

A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells

Heath, N. G., Gomez, J. A., McGinty, S. P., O’Geen, H., & Segal, D. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1324 · Cited by 1

Three-dimensional chromatin architecture in crustaceans: Emerging evidence, structural principles, and future directions: A review

Wikumpriya, G. C. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152499 · Cited by 1

Decoding and engineering 3D chromatin interactions governing pluripotent and totipotent cell states

Jiang, S., Liu, X., Zhang, Z., & Ding, J. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2026.102501 · Cited by 1

Lighting Up Genes in Single Cells at Scale

Liu, Z. J. (2015) · Cell · doi:10.1016/j.cell.2015.07.052 · Cited by 1

The danger of epigenetics misconceptions (epigenetics and stuff…)

Georgel, P. T. (2015) · Biochemistry and Cell Biology · doi:10.1139/bcb-2015-0091 · Cited by 1

Twisting chromatin in stem cells

Ginno, P. A., & Schübeler, D. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.179 · Cited by 1

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Zepeda‐Mendoza, C. J., Mukhopadhyay, S., Wong, E. S. W., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-2137-5 · Cited by 1

Mechanisms of Recurrent Chromosomal Translocations

Frock, R. L., Hu, J., & Alt, F. W. (2015) · Springer eBooks · doi:10.1007/978-3-319-19983-2_3 · Cited by 1

Concepts of polymer statistical topology

Nechaev, S. (2017) · Texts and readings in physical sciences · doi:10.1007/978-981-10-6841-6_15 · Cited by 2

Long-Range Control of Renin Gene Expression in Tsukuba Hypertensive Mice

Ushiki, A., Matsuzaki, H., Ishida, J., Fukamizu, A., & Tanimoto, K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166974 · Cited by 1

A tetrad of chromatin interactions for chromosome pairing in X inactivation

Krivega, I. V., & Dean, A. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3447 · Cited by 1

Investigate Global Chromosomal Interaction by Hi-C in Human Naive CD4 T Cells

Meng, X., Riley, N., Thompson, R. C., & Sharma, S. M. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7514-3_15 · Cited by 1

Cell Division: Single-Cell Physiology Reveals Secrets of Chromosome Condensation

Bloom, K. (2018) · Current Biology · doi:10.1016/j.cub.2017.12.032 · Cited by 1

Adaptive Immunity of Airway Inflammation in Asthma

Flayer, C. H., Killingbeck, S. S., Larson, E., Allakhverdi, Z., & Haczku, A. (2018) · Springer eBooks · doi:10.1007/978-3-319-77658-3_3 · Cited by 1

The Role of RNA Polymerase II Contiguity and Long-Range Interactions in the Regulation of Gene Expression in Human Pluripotent Stem Cells

Eiselleová, L., Lukjanov, V., Farkaš, Š., Svoboda, D., Štěpka, K., & Koutná, I. (2019) · Stem Cells International · doi:10.1155/2019/1375807 · Cited by 1

Integrative Analysis of Epigenomics Data

Taslim, C., Lessnick, S. L., & Lin, S. M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814513-5.00007-6 · Cited by 1

Inner and Outer DNA Loops in Cell Nuclei: Evidence from Pulsed-Field Comet Assay

Chopei, M., Olefirenko, V., Afanasieva, K. S., & Sivolob, A. (2022) · Cytology and Genetics · doi:10.3103/s0095452722040028 · Cited by 1

Effects of aging on sperm chromatin

Fice, H. E., & Robaire, B. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-91380-5.00029-0 · Cited by 1

Epigenetics: Mechanisms, theory, and social implications

Meloni, M. (2023) · Principles of Gender-Specific Medicine · doi:10.1016/b978-0-323-88534-8.00048-1 · Cited by 1

Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics

Molins-Pitarch, C., Khao, J., Bonet, S., Justicia, Y., Altube, C., Goodstadt, M. N., Ribot, F., Aiden, E. L., Neretti, N., McGill, G. G., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03646-y · Cited by 1

Quantification of DNA cleavage specificity in Hi-C experiments

Meluzzi, D., & Arya, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv820 · Cited by 1

Chromosome Conformation Capture for Research on Innate Antiviral Immunity

Kim, Y. J., & Kim, T. H. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7237-1_13 · Cited by 1

Polycomb Mechanisms and Epigenetic Control of Gene Activity

Pirrotta, V. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00007-9 · Cited by 2

Chromatin modification and remodeling in schizophrenia

Duan, J. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813796-3.00014-6 · Cited by 1

Real-Time Observation of Localization and Expression (ROLEX) System for Live Imaging of the Transcriptional Activity and Nuclear Position of a Specific Endogenous Gene

Ochiai, H. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9674-2_3 · Cited by 1

Chromatin and transcriptome changes in human myoblasts show spatio-temporal correlations and demonstrate DPP4 inhibition in differentiated myotubes

Kolanowski, T. J., Rozwadowska, N., Zimna, A., Nowaczyk, M., Siatkowski, M., Łabędź, W., Wiland, E., Gapiński, J., Jurga, S., & Kurpisz, M. K. (2020) · Scientific Reports · doi:10.1038/s41598-020-70756-x · Cited by 2

Function through absence: Active RNA exclusion from chromosomes leads to proper cell division

Teves, S. S. (2020) · The Journal of Cell Biology · doi:10.1083/jcb.202009193 · Cited by 1

Joint Modeling of Histone Modifications in 3D Genome Shape Through Hi-C Interaction Graph

Sefer, E. (2021) · Studies in computational intelligence · doi:10.1007/978-3-030-65351-4_33 · Cited by 1

ATAC-seq and psychiatric disorders

Fullard, J. F., Bendl, J. M., & Roussos, P. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823577-5.00036-2 · Cited by 1

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-v · Cited by 1

Isolation of Boechera stricta Developing Embryos for Hi-C

Tiscareño-Andrade, M., Oktaba, K., & Vielle‐Calzada, J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2429-6_14 · Cited by 1

Higher-order Chromatin Organization in Diseases, from Chromosomal Position Effect to Phenotype Variegation

Magdinier, F., & Robin, J. D. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91909-8.00003-7 · Cited by 1

Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulationPreprint

Dily, F. L., Baù, D., Pohl, A., Vicent, G. P., Soronellas, D., Castellano, G., Serra, F., Wright, R. H. G., Ballaré, C., Filion, G. J. P., et al. (2014) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/003293 · Cited by 1

Targeted mutations on 3D hub loci alter spatial interaction environmentPreprint

Ding, B., Zheng, L., Medovoy, D., & Wang, W. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/030999 · Cited by 1

Transposon regulation upon dynamic loss of DNA methylation

Walter, M. (2015) · HAL · doi:10.13140/rg.2.2.18747.21286 · Cited by 1

The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartmentPreprint

Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E. E. M., & Becker, P. B. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/101634 · Cited by 1

The CTCF Anatomy of Topologically Associating DomainsPreprint

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