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Capturing Chromosome Conformation

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Active genes dynamically colocalize to shared sites of ongoing transcription

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An Overview of Genome Organization and How We Got There: from FISH to Hi-C

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Identification of alternative topological domains in chromatin

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Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

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Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomesPreprint

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Single-Cell Analysis in Cancer Genomics

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Coolpup.py: versatile pile-up analysis of Hi-C data

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Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

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Heterogeneity in immune responses: from populations to single cells

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Understanding tumor ecosystems by single-cell sequencing: promises and limitations

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Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activationPreprint

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Single-Cell (Multi)omics Technologies

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Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

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Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation

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In situ genome sequencing resolves DNA sequence and structure in intact biological samples

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Polymer physics of chromosome large-scale 3D organisation

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Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

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Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

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Single-cell sequencing in stem cell biology

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Epigenetics of Atherosclerosis: Emerging Mechanisms and Methods

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Advances in single-cell omics and multiomics for high-resolution molecular profiling

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Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

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Single Cell Multi-Omics Technology: Methodology and Application

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Systematic Mapping of RNA-Chromatin Interactions In Vivo

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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

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Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

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Chromosome conformation capture technologies and their impact in understanding genome function

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In search of the determinants of enhancer–promoter interaction specificity

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Multiscale and integrative single-cell Hi-C analysis with Higashi

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ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

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Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

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Machine learning meets omics: applications and perspectives

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Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

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Epigenomics

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The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

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Analysis methods for studying the 3D architecture of the genome

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Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

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Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution

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Comparison of Hi-C results using in-solution versus in-nucleus ligation

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Measuring the reproducibility and quality of Hi-C data

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Functional genomics of the CDKN2A/B locus in cardiovascular and metabolic disease: what have we learned from GWASs?

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Multi-omics of single cells: strategies and applications

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MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

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Epigenome Maintenance in Response to DNA Damage

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Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution

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Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

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Interphase human chromosome exhibits out of equilibrium glassy dynamics

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Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

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C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2

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Stem cell quiescence: the challenging path to activation

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Origins of DNA replication in eukaryotes

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Transcription organizes euchromatin via microphase separation

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Three-dimensional chromatin packing and positioning of plant genomes

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PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription

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The X chromosome in space

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Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

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Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

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Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

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3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

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Mechanical Regulation of Transcription: Recent Advances

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Single-cell genomics meets human genetics

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Closing the loop: 3C versus DNA FISH

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Mechanisms of kidney fibrosis and routes towards therapy

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Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

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Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

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Interchromosomal interactions: A genomic love story of kissing chromosomes

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Single-cell measurement of higher-order 3D genome organization with scSPRITE

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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination

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