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

New insights into molecular mechanisms of epigenetic regulation in kidney disease

Mimura, I., Tanaka, T., & Nangaku, M. (2016) · Clinical and Experimental Pharmacology and Physiology · doi:10.1111/1440-1681.12663 · Cited by 20

Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes

Mahadevan, I. A., Kumar, S., & Rao, M. R. S. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-00335-x · Cited by 19

Gene regulation by non-coding RNAs in the 3D genome architecture

Tachiwana, H., Yamamoto, T., & Saitoh, N. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.03.002 · Cited by 19

Thinking embodiment with genetics: epigenetics and postgenomic biology in embodied cognition and enactivism

Meloni, M., & Reynolds, J. (2020) · Synthese · doi:10.1007/s11229-020-02748-3 · Cited by 19

Elementary Estimators for Sparse Covariance Matrices and other Structured Moments

Yang, E., Lozano, A. C., & Ravikumar, P. (2014) · Cited by 19

The organization of bacterial genomes: Towards understanding the interplay between structure and function

Brocken, D. J. W., Tark‐Dame, M., & Dame, R. T. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2018.02.007 · Cited by 19

A deep dive into genome assemblies of non-vertebrate animals

Guiglielmoni, N., Rivera‐Vicéns, R. E., Koszul, R., & Flot, J. (2022) · Peer Community Journal · doi:10.24072/pcjournal.128 · Cited by 16

Epigenetic Memories in Hematopoietic Stem and Progenitor Cells

Aoyama, K., Itokawa, N., Oshima, M., & Iwama, A. (2022) · Cells · doi:10.3390/cells11142187 · Cited by 21

Recent Advances in Ciliate Biology

Howard-Till, R. A., Kar, U. P., Fabritius, A. S., & Winey, M. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-020656 · Cited by 17

Studying Chromatin Epigenetics with Fluorescence Microscopy

Stepanov, A. I., Беседовская, З. В., Moshareva, M. A., Lukyanov, K. A., & Putlyaeva, L. V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23168988 · Cited by 19

Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization

Thuma, J. L., Chung, Y.-C., & Tu, L. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1173545 · Cited by 21

Roles of long noncoding RNAs in chromosome domains

Tomita, S., Abdalla, M. O. A., Fujiwara, S., Yamamoto, T., Iwase, H., Nakao, M., & Saitoh, N. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1384 · Cited by 18

Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics

Burby, P. E., Nye, T. M., Schroeder, J. W., & Simmons, L. A. (2016) · Journal of Bacteriology · doi:10.1128/jb.00560-16 · Cited by 20

3D Genome Organization Influences the Chromosome Translocation Pattern

McCord, R. P., & Balajee, A. S. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-0593-1_8 · Cited by 18

HiCeekR: A Novel Shiny App for Hi-C Data Analysis

Filippo, L. D., Righelli, D., Gagliardi, M., Matarazzo, M. R., & Angelini, C. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.01079 · Cited by 18

BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome

García‐Gutiérrez, P., & García‐Domínguez, M. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.709232 · Cited by 18

Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR -amplified glioblastoma

Yang, Q., Jiang, N., Zou, H., Fan, X., Liu, T., Huang, X., Wanggou, S., & Li, X. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.04.007 · Cited by 18

TADBD: A Sensitive and Fast Method for Detection of Typologically Associated Domain Boundaries

Lyu, H., Li, L., Wu, Z., Wang, T., Zheng, J., & Wang, H. (2020) · BioTechniques · doi:10.2144/btn-2019-0165 · Cited by 17

Chromatin Hubs: A biological and computational outlook

Mora, A., Huang, X., Jauhari, S., Jiang, Q. L., & Li, X. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.002 · Cited by 18

Cis-regulatory chromatin loops analysis identifies GRHL3 as a master regulator of surface epithelium commitment

Huang, H., Liu, J., Li, M., Guo, H., Zhu, J., Zhu, L., Wu, S., Mo, K., Huang, Y., Tan, J., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo5668 · Cited by 17

DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes

Wang, S., Zhang, Q., He, Y., Cui, Z., Guo, Z., Han, K., & Huang, D.-S. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010572 · Cited by 16

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction

Schuette, G., Ding, X., & Zhang, B. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2023.07.017 · Cited by 15

Predicting the spatial organization of chromosomes using epigenetic data

Mourad, R., & Cuvier, O. (2015) · Genome biology · doi:10.1186/s13059-015-0752-8 · Cited by 17

A sequence level model of an intact locus predicts the location and function of nonadditive enhancers

Barr, K. A., & Reinitz, J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0180861 · Cited by 17

Cardiovascular Disease and Long Noncoding RNAs

Hennessy, E. J. (2017) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.117.001556 · Cited by 17

Topology of polymer chains under nanoscale confinement

Satarifard, V., Heidari, M., Mashaghi, S., Tans, S. J., Ejtehadi, M. R., & Mashaghi, A. (2017) · Nanoscale · doi:10.1039/c7nr04220e · Cited by 17

Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C

Nagano, T., Wingett, S., & Fraser, P. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7231-9_6 · Cited by 16

Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins

Sobhy, H., Kumar, R., Lewerentz, J., Lizana, L., & Stenberg, P. (2019) · Scientific Reports · doi:10.1038/s41598-019-40770-9 · Cited by 17

Role of histone deacetylases in bone development and skeletal disorders

Wang, J. S., Yoon, S.-H., & Wein, M. N. (2020) · Bone · doi:10.1016/j.bone.2020.115606 · Cited by 19

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics

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

3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines

Kocanova, S., Goiffon, I., & Bystricky, K. (2018) · Methods · doi:10.1016/j.ymeth.2018.02.013 · Cited by 16

Chromatin accessibility dynamics of myogenesis at single cell resolution

Pliner, H. A., Packer, J., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., et al. (2017) · doi:10.1101/155473 · Cited by 16

Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges

Liu, M., & Darling, A. E. (2015) · F1000Research · doi:10.12688/f1000research.7281.1 · Cited by 16

DNA loop domain organization in nucleoids from cells of different types

Afanasieva, K. S., Chopei, M., Lozovik, A., Semenova, A., Лукаш, Л. Л., & Sivolob, A. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2016.12.177 · Cited by 16

Chromatin Organization and Function in Drosophila

Llorens‐Giralt, P., Camilleri‐Robles, C., Corominas, M., & Climent‐Cantó, P. (2021) · Cells · doi:10.3390/cells10092362 · Cited by 16

Sister chromatid–sensitive Hi-C to map the conformation of replicated genomes

Mitter, M., Takács, Z., Köcher, T., Micura, R., Langer, C. C. H., & Gerlich, D. W. (2022) · Nature Protocols · doi:10.1038/s41596-022-00687-6 · Cited by 16

EPI-Mind: Identifying Enhancer–Promoter Interactions Based on Transformer Mechanism

Ni, Y., Fan, L.-P., Wang, M., Zhang, N., Zuo, Y.-C., & Liao, M. (2022) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-022-00525-z · Cited by 16

Tracing cancer evolution and heterogeneity using Hi-C

Erdmann-Pham, D. D., Batra, S. S., Turkalo, T. K., Durbin, J., Blanchette, M., Yeh, I., Shain, A. H., Bastian, B. C., Song, Y. S., Rokhsar, D. S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42651-2 · Cited by 16

3D genome remodeling and homologous pairing during meiotic prophase of mouse oogenesis and spermatogenesis.

He, J., Yan, A., Chen, B., Huang, J., & Kee, K. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.10.009 · Cited by 16

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

Li, Z., & Tamar Schlick, A. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1121 · Cited by 16

Fluidification of entangled polymers by loop extrusion

Conforto, F., Fosado, Y. A. G., & Michieletto, D. (2024) · Physical Review Research · doi:10.1103/physrevresearch.6.033160 · Cited by 16

Evolution of 3D Chromatin Folding

Álvarez-González, L., & Ruiz‐Herrera, A. (2024) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-111523-102233 · Cited by 18

Genome maintenance in the context of 4D chromatin condensation

Yu, S., Yang, F., & Shen, W. H. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2221-2 · Cited by 17

Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale

Szczurek, A., Xing, J. W., Birk, U. J., & Cremer, C. G. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00114 · Cited by 16

Anatomy of Mammalian Replication Domains

Takebayashi, S., Ogata, M., & Okumura, K. (2017) · Genes · doi:10.3390/genes8040110 · Cited by 17

Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S‐phase transition

Ghule, P. N., Seward, D. J., Fritz, A. J., Boyd, J. R., van Wijnen, A. J., Lian, J. B., Stein, J. L., & Stein, G. S. (2018) · Journal of Cellular Physiology · doi:10.1002/jcp.26741 · Cited by 16

Interpreting 4C-Seq Data: how far can we go?

Raviram, R., Rocha, P. P., Bonneau, R., & Skok, J. A. (2014) · Epigenomics · doi:10.2217/epi.14.47 · Cited by 16

Statistical Challenges in Analyzing Methylation and Long-Range Chromosomal Interaction Data

Qin, Z. S., Li, B., Conneely, K. N., Wu, H., Hu, M., Ayyala, D. N., Park, Y., Jin, V. X., Zhang, F., Zhang, H., et al. (2016) · Statistics in Biosciences · doi:10.1007/s12561-016-9145-0 · Cited by 16

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

Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

Moisan, S., Nabec, A. L., Quillévéré, A., Maréchal, C. L., & Férec, C. (2019) · Human Genetics · doi:10.1007/s00439-019-02068-8 · Cited by 16

Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulationPreprint

Huang, N., Seow, W. Q., Appert, A., Yan, D., Stempor, P., & Ahringer, J. (2021) · Genome Research · doi:10.1101/gr.275669.121 · Cited by 16

3D Genome Organization: Causes and Consequences for DNA Damage and Repair

Simon, À. C., & Fabre, E. (2021) · Genes · doi:10.3390/genes13010007 · Cited by 15

Complex chromosomal rearrangements induced by transposons in maize

Sharma, S. P., & Peterson, T. (2022) · Genetics · doi:10.1093/genetics/iyac124 · Cited by 14

Disruption of regulatory domains and novel transcripts as disease‐causing mechanisms

Allou, L., & Mundlos, S. (2023) · BioEssays · doi:10.1002/bies.202300010 · Cited by 15

Chromosomes captured one by one

Dekker, J., & Mirny, L. A. (2013) · Nature · doi:10.1038/nature12691 · Cited by 15

Chromatin Dynamics during Differentiation of Myeloid Cells

Schönheit, J., Leutz, A., & Rosenbauer, F. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.08.015 · Cited by 15

Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex

Mitchell, A., Javidfar, B., Bicks, L. K., Neve, R. L., Garbett, K. A., Lander, S. S., Mirnics, K., Morishita, H., Wood, M. A., Jiang, Y. P., et al. (2016) · Nature Communications · doi:10.1038/ncomms12743 · Cited by 15

Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution

Spill, Y. G., Castillo, D., Vidal, E., & Martí-Renom, M. (2019) · Nature Communications · doi:10.1038/s41467-019-09907-2 · Cited by 14

CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities

Tarbell, E., Jiang, K., Hennon, T., Holmes, L., Williams, S., Fu, Y., Gaffney, P. M., Liu, T., & Jarvis, J. N. (2021) · Scientific Reports · doi:10.1038/s41598-021-82989-5 · Cited by 12

Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation

Wu, N., Yuan, F., Yue, S., Jiang, F., Ren, D., Liu, L., Bi, Y., Guo, Z., Ji, L., Han, K. Q., et al. (2021) · Cell & Bioscience · doi:10.1186/s13578-021-00701-6 · Cited by 15

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Jia, B., Jin, J., Han, M., Li, B., & Yuan, Y. (2022) · Science China Life Sciences · doi:10.1007/s11427-021-2084-1 · Cited by 15

Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition

Aran, D., & Hellman, A. (2013) · BioEssays · doi:10.1002/bies.201300119 · Cited by 15

Epigenetic interplay at the β-globin locus

Lee, W. S., McColl, B., Maksimovic, J., & Vadolas, J. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2017.01.014 · Cited by 14

DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses

Hadwiger, L. A., & Tanaka, K. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01056 · Cited by 14

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

A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions

Vanhaeren, T., Divina, F., García-Torres, M., Gómez-Vela, F., Vanhoof, W., & Martínez‐García, P. M. (2020) · Genes · doi:10.3390/genes11090985 · Cited by 15

Epigenomic Characterization of Lymphoid Neoplasms

Duran‐Ferrer, M., & Martín-Subero, J. I. (2023) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-051122-100856 · Cited by 16

Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line

Fujita, T., Kitaura, F., Yuno, M., Suzuki, Y., Sugano, S., & Fujii, H. (2017) · DNA Research · doi:10.1093/dnares/dsx023 · Cited by 14

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

DNA dioxygenases Tet2/3 regulate gene promoter accessibility and chromatin topology in lineage-specific loci to control epithelial differentiation

Chen, G., Fatima, I., Xu, Q., Rozhkova, E., Fessing, M. Y., Mardaryev, A. N., Sharov, A. A., Xu, G., & Botchkarev, V. A. (2023) · Science Advances · doi:10.1126/sciadv.abo7605 · Cited by 15

Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis

Chen, Y., Xie, D., Ma, X., Xue, X., Liu, M., Xiao, X., Lai, C., Xu, X., Chen, X., Chen, Y., et al. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad348 · Cited by 14

CCSI: a database providing chromatin–chromatin spatial interaction information

Xie, X., Ma, W., Songyang, Z., Luo, Z., Huang, J., Dai, Z., & Xiong, Y. (2016) · Database · doi:10.1093/database/bav124 · Cited by 14

Capture Hi‐C Library Generation and Analysis to Detect Chromatin Interactions

Orlando, G., Kinnersley, B., & Houlston, R. (2018) · Current Protocols in Human Genetics · doi:10.1002/cphg.63 · Cited by 16

The 3D genome: From fundamental principles to disease and cancer

Umlauf, D., & Mourad, R. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.002 · Cited by 15

Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications

Federico, C., Brancato, D., Bruno, F., Coniglio, E., Sturiale, V., & Saccone, S. (2025) · Genes · doi:10.3390/genes16070780 · Cited by 16

Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues

Chen, F., Zhang, Q., Deng, X., Zhang, X., Chen, C., Lv, D., Li, Y., Li, D., Zhang, Y., Li, P., et al. (2018) · Epigenetics · doi:10.1080/15592294.2018.1500057 · Cited by 13

Bifractal structure of chromatin in rat lymphocyte nuclei

Iashina, E. G., Varfolomeeva, E. Y., Pantina, R. A., Bairamukov, V. Y., Kovalev, R. A., Fedorova, N. D., Pipich, V., Radulescu, A., & Григорьев, С. В. (2021) · Physical review. E · doi:10.1103/physreve.104.064409 · Cited by 13

Identification of Genomic Safe Harbors in the Anhydrobiotic Cell Line, Pv11

Miyata, Y., Tokumoto, S., Arai, T., Shaikhutdinov, N., Deviatiiarov, R. M., Fuse, H., Gogoleva, N. E., Garushyants, S. K., Cherkasov, A. V., Ryabova, A., et al. (2022) · Genes · doi:10.3390/genes13030406 · Cited by 13

Consistencies and contradictions in different polymer models of chromatin architecture

Câmara, A. S., & Mascher, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.033 · Cited by 13

3D genome organization and epigenetic regulation in autoimmune diseases

Qiu, Y., Feng, D., Jiang, W., Zhang, T., Lu, Q., & Zhao, M. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1196123 · Cited by 12

The Network Architecture of the Saccharomyces cerevisiae Genome

Hoang, S. A., & Bekiranov, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081972 · Cited by 12

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Daban, J. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.1043 · Cited by 13

Tuning DNA Condensation with Zwitterionic Polyamidoamine (zPAMAM) Dendrimers

An, M., Tonga, G. Y., Parkin, S., Rotello, V. M., & DeRouchey, J. E. (2017) · Macromolecules · doi:10.1021/acs.macromol.7b01470 · Cited by 13

Observation of nucleic acid and protein correlation in chromatin of HeLa nuclei using small-angle neutron scattering with D2O−H2O contrast variation

Григорьев, С. В., Iashina, E. G., Wu, B., Pipich, V., Lang, C., Rădulescu, A., Bairamukov, V. Y., Filatov, M. V., Pantina, R. A., & Varfolomeeva, E. Y. (2021) · Physical review. E · doi:10.1103/physreve.104.044404 · Cited by 13

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

Maslova, A., & Krasikova, A. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.753097 · Cited by 16

The interplay of supercoiling and thymine dimers in DNA

Lim, W., Randisi, F., Doye, J. P. K., & Louis, A. A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac082 · Cited by 13

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation

Golkaram, M., Jang, J., Hellander, S., Kosik, K. S., & Petzold, L. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-13731-3 · Cited by 14

Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling

Zhang, X., Branciamore, S., Gogoshin, G., Rodin, A. S., & Riggs, A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620425114 · Cited by 12

Viral Chromosome Conformation Capture (V3C) Assays for Identifying Trans-interaction Sites between Lytic Viruses and the Cellular Genome

Majumder, K., Boftsi, M., & Pintel, D. J. (2019) · BIO-PROTOCOL · doi:10.21769/bioprotoc.3198 · Cited by 13

Discovery of a stable expression hot spot in the genome of Chinese hamster ovary cells using lentivirus-based random integration

Zhou, S., Ding, X., Yang, L., Chen, Y., Gong, X., Jin, J., & Li, H. (2019) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2019.1601998 · Cited by 13

Varying the Resolution of the Rouse Model on Temporal and Spatial Scales: Application to Multiscale Modeling of DNA Dynamics

Rolls, E., Togashi, Y., & Radek Erban, A. (2017) · Multiscale Modeling and Simulation · doi:10.1137/16m108700x · Cited by 13

From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer GenomesPreprint

Zhang, C., & Pellman, D. S. (2015) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2015.80.027623 · Cited by 15

Optimization of Genome Knock-In Method: Search for the Most Efficient Genome Regions for Transgene Expression in Plants

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