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

KDM6A knockout in human iPSCs alters the genome-wide histone methylation profile at active and poised enhancers, activating expression of ectoderm gene expression pathwaysPreprint

Maurya, S. S., Yang, W., Zhang, Q., Erdmann-Gilmore, P., Bystry, A., Townsend, R., & Druley, T. E. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.09.434633 · Cited by 1

OpenNucleome for high resolution nuclear structural and dynamical modelingPreprint

Lao, Z.-H., Kamat, K., Jiang, Z.-L., & Zhang, B. (2023) · bioRxiv · doi:10.1101/2023.10.16.562451 · Cited by 7

Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis -regulationPreprint

Thakur, R., Xu, M., Sowards, H., Yon, J., Jessop, L., Myers, T., Zhang, T., Chari, R., Long, E., Rehling, T., et al. (2024) · medRxiv · doi:10.1101/2024.11.14.24317204 · Cited by 1

How chromatin-binding proteins direct distinct folding pathways of tetra-nucleosomes: Insights from coarse-grained simulationsPreprint

Kapoor, U. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.27.667063 · Cited by 2

Algoritmos en bioinformática estructural

Contreras‐Moreira, B. (2018) · DIGITAL.CSIC (Spanish National Research Council (CSIC)) · doi:10.20350/digitalcsic/8544

Topology of contacts in interacting polymers

Dirschbacher, N. (2014) · PhDT · doi:10.7282/t3bg2mgh

The Recombination Enhancer Modulates the Conformation of Chr. III in Budding Yeast: A Dissertation

Belton, J.-M. (2014) · The Journal of the American Medical Association (JAMA) Network (American Medical Association) · doi:10.13028/m2f88z

Probing chromosome structure using multidimensional scaling of DNA contact matrices

Riley, A. D. (2014) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)

Choosing the target loci : heat shock factors HSF1 and HSF2 as regulators of cell stress and development

Vihervaara, A. (2014) · Doria (University of Helsinki)

Assessing modularity of developmental enhancers in Drosophila melanogaster

Martin, T. L. (2014) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

What does the study of intranuclear chromatin conformation tell us? Proximity? Yes. Interaction? No

Sverdlov, E. D. (2015) · BioEssays · doi:10.1002/bies.201500137

Regulation of Adipocyte Transcription by PPARgamma Ligands

Step, S. E. (2014) · ScholarlyCommons (University of Pennsylvania)

3D Genome Architecture in the Mammalian Nucleus

Enkhmandakh, B., & Bayarsaihan, D. (2013) · Epigenomics · doi:10.2217/epi.13.64

New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

Weston, D. J., Russell, R. A., Batty, E., Jensen, K., Stephens, D. A., Adams, N. M., & Freemont, P. S. (2015) · Journal of The Royal Society Interface · doi:10.1098/rsif.2014.0894

METHOD Open Access

Maretty, L., Sibbesen, J. A., & Krogh, A. (2014)

Parts and Methods in Synthetic Biology: An Investigation of Light Induced Gene Regulation in E. coli and the Design and Characterization of a Dual Mode Promoter in S. cerevisiae

Mazumder, M. (2014) · TSpace (University of Toronto)

Algorithms for Determining Differentially Expressed Genes and Chromosome Structures From High-Throughput Sequencing Data

Yang, Y. (2015) · eScholarship (California Digital Library)

Next-Generation Sequencing (NGS) in Biomarker Discovery and Applications in Nephrology

Mimura, I., & Nangaku, M. (2015) · Springer eBooks · doi:10.1007/978-94-007-7743-9_10-1

PRC-Mediated Interaction Networks of Repressed Genes: Emerging Insights and Possible Roles

Sanli, I., & Feil, R. (2016) · Epigenomics · doi:10.2217/epi-2016-0029

Genetics of Human Aging

Cho, M., & Suh, Y. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-411596-5.00012-5

Mechanisms Regulating Transcription in Plasmodium falciparum as Targets for Novel Antimalarial Drugs

Bunnik, E. M., & Roch, K. G. L. (2016) · doi:10.1002/9783527694082.ch18

Sensing and Remembering Cellular States Through Chromatin

Jiang, S., & Vondriska, T. M. (2016) · Springer eBooks · doi:10.1007/978-3-319-31828-8_15

Gene regulation in three dimensions

Wittek, K. T. (2016) · BIBSYS Brage (BIBSYS (Norway))

Analysis of Cohesin Function in Gene Regulation and Chromatin Organization in Interphase

Gupta, P., Lavagnolli, T., Mira-Bontenbal, H., & Merkenschlager, M. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6545-8_12

Transcriptional Regulation: When 1+1≠2

Thormann, V., Borschiwer, M., & Meijsing, S. H. (2016) · Springer eBooks · doi:10.1007/978-3-319-45723-9_1

A Constraint Logic Programming Approach to Predicting the Three-Dimensional Yeast Genome

MacKay, K. (2016) · University Library - University of Saskatchewan (University of Saskatchewan)

Chromatin in fractal globule state: evidence from comet assay

Afanasieva, K. S., Chopei, M., & Sivolob, A. (2015) · Biopolymers and Cell · doi:10.7124/bc.0008d2

Crossing Borders

Moore, B. L., & Semple, C. A. M. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803075-2.00003-9

Epigenetics of Malaria Parasites

Bunnik, E. M., & Roch, K. G. L. (2017) · Epigenetics and human health · doi:10.1007/978-3-319-55021-3_11

Three-dimensional Folding of Eukaryotic Genomes

Hsieh, T.-H. S. (2017) · eScholarship@UMassChan · doi:10.13028/m2mx01

Integrative understanding of transcription in animal cell mode

Rico, L. G., & Verónica, V. (2016) · TDX (Tesis Doctorals en Xarxa)

Chromosome Biology: The Sight of DNA, at Last!

Gligoris, T. G. (2018) · Current Biology · doi:10.1016/j.cub.2017.11.066

MADS floral integrators : Insights into molecular mechanisms of MADS domain proteins in the floral transition

Jamge, S. (2018) · doi:10.18174/430710

Chromatin 3D – will it make understanding of cancer transformation finally possible?

Drabik, G., Kaszuba-Zwoińska, J., Wiśniowski, Z., Konieczny, L., & Roterman, I. (2018) · Bio-Algorithms and Med-Systems · doi:10.1515/bams-2018-0002

Genome‐Wide Approaches to Identify the Interplay of Transcription Factors, Regulatory Elements and Target Genes

Qu, J., & Zhou, H. (2018) · Wiley eBooks · doi:10.1002/9780470015902.a0027370

All Roads Go to the Nucleus: Integration of Signaling/Transcription Factor-Mediated and Epigenetic Regulatory Mechanisms in the Control of Skin Development and Regeneration

Botchkarev, V. A., Sharov, A. A., & Fessing, M. Y. (2018) · Stem cell biology and regenerative medicine · doi:10.1007/978-3-319-16769-5_1

Embryogenic remodeling of global chromatin and its role on structure of corresponding lattice representation

Gunji, Y.-P., & Balaž, I. (2018) · Biosystems · doi:10.1016/j.biosystems.2018.09.013

Investigation of transcription factor binding at distal regulatory elements

Mitchelmore, J. (2017) · Apollo (University of Cambridge) · doi:10.17863/cam.25144

Analysis of Chromatin Interactions of BEAF-associated Promoters Using 4C

Shrestha, S. (2018) · doi:10.31390/gradschool_dissertations.4578

Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin

Pushkareva, O., Kurashenko, A., Moskvina, U., Rubinov, A. R., & Gelfand, M. S. (2018) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2018.8621097

Solution of the FISH-Hi-C paradox for Human Interphase ChromosomesPreprint

Shi, G., & Thirumalai, D. (2019) · arXiv (Cornell University)

The Review of Bioinformatics Tool for 3D Plant Genomics Research

Yang, X., Li, Z., Zhao, J., Ma, T., Li, P., & Zhang, L. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-20242-2_2

Computational Methods for Inferring Transcriptome Dynamics

Welch, J. D. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/yazw-zn17

Widespread selection against deleterious mutations in the Drosophila genomePreprint

Khromov, P., & Morozov, A. V. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.12.946392

The Pharmacoepigenomics Informatics Pipeline and H-GREEN Hi-C Compiler: Discovering Pharmacogenomic Variants and Pathways with the Epigenome and Spatial Genome

Allyn-Feuer, A. (2018) · Deep Blue (University of Michigan)

Changes in loop organization of chromatin at different stages of lymphocyte activation

Afanasieva, K. S., Lozovik, O. V., Olefirenko, V. V., & Sivolob, A. (1970) · Faktori eksperimental noi evolucii organizmiv · doi:10.7124/feeo.v20.733

Genetic Complexity of the Human Genome in Health and Disease: Basic Concepts

Athanassiadou, A. (2020) · Nonlinear Phenomena in Complex Systems · doi:10.33581/1561-4085-2020-23-2-113-120

Applications of CRISPR/Cas Beyond Simple Traits in Crops

Khan, S. H., Ghouri, M. Z., Aslam, S., Mubarik, M. S., Khan, Z., Ahmad, M. Q., & Sajjad, M. (2021) · Springer eBooks · doi:10.1007/978-981-15-7142-8_8

essHi-C: essential component analysis of Hi-C matrices

Franzini, S., Stefano, M. D., & Micheletti, C. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab062

Reconstruction of the Regulatory Network in a Minimal Bacterium Reveals Extensive Non-Transcription Factor Dependent RegulationPreprint

Yus, E., Lloréns‐Rico, V., Martínez, S., Gallo, C., Eilers, H., Blötz, C., Stülke, J., Lluch‐Senar, M., & Serrano, L. G. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3305580

DNA loop organization in dorsal root ganglion neurons: effects of peripheral inflammation

Afanasieva, K. S., Duzhyy, D. E., Belan, P. V., Voitenko, N. V., & Sivolob, A. (2021) · Biopolymers and Cell · doi:10.7124/bc.000a4f

Other omics approaches to the study of rare diseases

Gatta, G. D. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820140-4.00008-9

Insights into the Regulatory Activities of Chromatin Through Computational Analyses of Whole-Genome Data

Hoang, S. A. (2013) · doi:10.18130/v36n5m

Structural variation in genomes and its role in disease

Vlaar, J. M. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/902

Possibility of Uncoding Structural Organization of Genome in Rice Research: Prospects and Approaches by 3D Genome Sequencing

Bhowmick, B. K. (2021) · Springer eBooks · doi:10.1007/978-981-16-3997-5_1

Faculty Opinions recommendation of A high-resolution map of the three-dimensional chromatin interactome in human cells.

Lee, D. A., & Thorpe, S. D. (2013) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718148954.793487608

Faculty Opinions recommendation of The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.

Wutz, A. (2013) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718056084.793481369

Ação do ácido valproico e da tricostatina A na organização cromatínica e sua regulação por fatores epigenéticos em células HepG2 sob condições de hiperglicemia

Felisbino, M. B. (2016) · doi:10.47749/t/unicamp.2016.976565

Vorhersage, Analyse und Bedeutung charakteristischer Transkriptionsfaktor-Bindestellen und deren potentielle Masterkontrollfunktion in der transkriptionellen Genregulation

Haubrock, M. (2021) · doi:10.53846/goediss-8880

Pattern recognition for non-coding RNA promoters

Georgakilas, G. K. (2015) · doi:10.12681/eadd/38245

Chromatin reorganization, signaling responses and non-coding RNA regulators in homeostasis and senescence

Josipović, N. (2022) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9136

Faculty Opinions recommendation of Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers.

OHLSSON, R. I., & Göndör, A. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.732438469.793546047

Faculty Opinions recommendation of Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Kenter, A. L. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.731077751.793558057

Faculty Opinions recommendation of The 3D genome as moderator of chromosomal communication.

Kenter, A. L. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726211725.793558055

Next-Generation Sequencing (NGS) in Biomarker Discovery and Applications in Nephrology

Mimura, I., & Nangaku, M. (2016) · Springer eBooks · doi:10.1007/978-94-007-7699-9_10

Data mining and machine learning methods for chromosome conformation data analysis

Oluwadare, O. (2019) · MOspace Institutional Repository (University of Missouri) · doi:10.32469/10355/70076

Faculty Opinions recommendation of Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers.

Owen‐Hughes, T. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.732450599.793577162

Faculty Opinions recommendation of Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers.

Blelloch, R. H. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.732438469.793549702

GOntact: using chromatin contacts to infer target genes and Gene Ontology enrichments for cis -regulatory elementsPreprint

Laverré, A., Tannier, É., Veber, P., & Necşulea, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.13.495495

Structural and developmental dynamics of Matrix Associated Regions in Drosophila melanogaster genomePreprint

Sureka, R., Avvaru, A. K., Sowpati, D. T., Pathak, R. U., & Mishra, R. K. (2022) · Research Square · doi:10.21203/rs.3.rs-1766180/v1

Long Range Inter-Chromosomal Interaction of Oct4 Distal Enhancer Loci Regulates ESCs PluripotencyPreprint

Moon, B.-S., Huang, D., Gao, F., Cai, M., Lyu, G., Zhang, L., Chen, J., & Lu, W. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4099082

Probabilistic 3D-modelling of genomes and genomic domains by integrating high-throughput imaging and Hi-C using machine learningPreprint

Castillo, D., Mendieta-Esteban, J., & Martı́-Renom, M. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.19.508575

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Matoba, N., Quiroga, I. Y., Phanstiel, D. H., & Won, H. (2020) · Journal of Visualized Experiments · doi:10.3791/60428-v

Navigation and Use of Custom Tracks within the Axolotl Genome Browser

Nowoshilow, S., & Tanaka, E. M. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2659-7_19

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletionPreprint

Jeong, D., Shi, G., Li, X., & Thirumalai, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.22.513342

Single-Cell ATAC-seq analysis via Network Refinement with peaks location informationPreprint

Yu, J., Sun, D., Hou, Z., & Wu, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.18.517159

Analysis of Chromatin Interaction and Accessibility by Trac-Looping

Liu, S., Tang, Q., & Zhao, K. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2899-7_7

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin OrganizationPreprint

Lin, X., & Zhang, B. (2023) · eLife · doi:10.7554/elife.90073.1

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletionPreprint

Jeong, D., Shi, G., Li, X., & Thirumalai, D. (2023) · eLife · doi:10.7554/elife.88564.1

Spatial Architecture and Functional Characterization of Super Enhancer Associated Transcriptional Circuits in Aggressive Lymphomas

Serin, N. (2023) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-10102

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin OrganizationPreprint

Lin, X., & Zhang, B. (2024) · eLife · doi:10.7554/elife.90073.2

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletionPreprint

Jeong, D., Shi, G., Li, X., & Thirumalai, D. (2024) · eLife · doi:10.7554/elife.88564.2

The Role of Changes in Structure and Dynamics of Chromatin due to COVID-19

Bigildeev, A., Alekseev, V. I., Gribkova, A. K., Timokhin, G. S., Komarova, G. A., & Shaytan, A. К. (2024) · Russian Journal of Genetics · doi:10.1134/s1022795424010034

Functional and structural impacts of Ac/Ds transposon system in maize

Sharma, S. P. (2022) · doi:10.31274/td-20240329-352

Additional file 2 of De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.

Mao, Y., Cui, X., Wang, H., Qin, X., Liu, Y., Yin, Y., Su, X., Tang, J., Wang, F., Ma, F., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20098649

Additional file 5 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111126

Additional file 3 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111120

Additional file 5 of De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.

Mao, Y., Cui, X., Wang, H., Qin, X., Liu, Y., Yin, Y., Su, X., Tang, J., Wang, F., Ma, F., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20098658

Additional file 4 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111123

Additional file 3 of SPIN reveals genome-wide landscape of nuclear compartmentalization

Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579161

Additional file 3 of De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.

Mao, Y., Cui, X., Wang, H., Qin, X., Liu, Y., Yin, Y., Su, X., Tang, J., Wang, F., Ma, F., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20098652

Additional file 4 of De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L.

Mao, Y., Cui, X., Wang, H., Qin, X., Liu, Y., Yin, Y., Su, X., Tang, J., Wang, F., Ma, F., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20098655

Additional file 5 of SPIN reveals genome-wide landscape of nuclear compartmentalization

Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579167

Additional file 6 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111129

Additional file 4 of SPIN reveals genome-wide landscape of nuclear compartmentalization

Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579164

Additional file 2 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111117

Additional file 7 of Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14111132

Discovery of dynamic changes in 3D chromatin architecture through polymer physics modelPreprint

Anubhooti, Wasim, A., Narayan, P. K., Mondal, J., & Pongubala, J. M. R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.11.589000

Modeling and Analysis of Spatial Chromatin Interactions

Lin, S., Scholtens, D. M., & Datta, S. (2022) · Chapman & Hall/CRC eBooks · doi:10.1201/9781315153728-7

Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C

Rudan, M. V., Hadjur, S., & Sexton, T. (2016) · Methods in molecular biology · doi:10.1007/7651_2015_261 · Cited by 6

A (3D-Nuclear) Space Odyssey: Making Sense of Hi-C Maps

Mota-Gómez, I., & Lupiáñez, D. G. (2019) · Genes · doi:10.3390/genes10060415 · Cited by 16

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data

Meluzzi, D., & Arya, G. (2019) · Methods · doi:10.1016/j.ymeth.2019.08.008 · Cited by 10

Inferential analysis of genomic 3D organization

Paulsen, J. (2014) · NORA - Norwegian Open Research Archives · Cited by 1