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Nuc3DMap delineates finer nucleosome-based three-dimensional chromatin architecture

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inferredcites →https://doi.org/10.1016/0001-8708(75)90149-8openalex-snapshot
Renormalization group methods
inferredcites →https://doi.org/10.1016/0771-050x(75)90034-0openalex-snapshot
An algorithm for smoothing, differentiation and integration of experimental data using spline functions
inferredcites →https://doi.org/10.1016/j.ajhg.2015.12.002openalex-snapshot
Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus
inferredcites →https://doi.org/10.1016/j.cell.2008.02.022openalex-snapshot
Dynamic Regulation of Nucleosome Positioning in the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2011.12.014openalex-snapshot
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
inferredcites →https://doi.org/10.1016/j.cell.2012.01.010openalex-snapshot
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
inferredcites →https://doi.org/10.1016/j.cell.2013.04.053openalex-snapshot
Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2015.01.054openalex-snapshot
Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo
inferredcites →https://doi.org/10.1016/j.cell.2015.05.048openalex-snapshot
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
inferredcites →https://doi.org/10.1016/j.cell.2015.11.024openalex-snapshot
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
inferredcites →https://doi.org/10.1016/j.cell.2017.09.043openalex-snapshot
Multiscale 3D Genome Rewiring during Mouse Neural Development
inferredcites →https://doi.org/10.1016/j.cell.2017.11.008openalex-snapshot
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
inferredcites →https://doi.org/10.1016/j.cell.2018.12.014openalex-snapshot
Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs
inferredcites →https://doi.org/10.1016/j.celrep.2016.04.085openalex-snapshot
Formation of Chromosomal Domains by Loop Extrusion
inferredcites →https://doi.org/10.1016/j.celrep.2020.107870openalex-snapshot
Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming
inferredcites →https://doi.org/10.1016/j.cels.2015.07.012openalex-snapshot
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
inferredcites →https://doi.org/10.1016/j.csbj.2022.07.037openalex-snapshot
Mapping nucleosome and chromatin architectures: A survey of computational methods
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.molcel.2020.03.002openalex-snapshot
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
inferredcites →https://doi.org/10.1016/j.molcel.2020.03.003openalex-snapshot
Ultrastructural Details of Mammalian Chromosome Architecture
inferredcites →https://doi.org/10.1016/j.molcel.2020.06.007openalex-snapshot
Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases
inferredcites →https://doi.org/10.1016/j.molcel.2023.06.018openalex-snapshot
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
inferredcites →https://doi.org/10.1016/j.molcel.2024.10.021openalex-snapshot
Long-range regulation of transcription scales with genomic distance in a gene-specific manner
inferredcites →https://doi.org/10.1016/j.stem.2015.11.010openalex-snapshot
Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
inferredcites →https://doi.org/10.1038/nature09380openalex-snapshot
Mediator and cohesin connect gene expression and chromatin architecture
inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot
Spatial partitioning of the regulatory landscape of the X-inactivation centre
inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot
Topological domains in mammalian genomes identified by analysis of chromatin interactions
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12753openalex-snapshot
Topology of mammalian developmental enhancers and their regulatory landscapes
inferredcites →https://doi.org/10.1038/nature23884openalex-snapshot
The 4D nucleome project
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
Integrative genomics viewer
inferredcites →https://doi.org/10.1038/ncomms5909openalex-snapshot
Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data
inferredcites →https://doi.org/10.1038/ng.3286openalex-snapshot
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
inferredcites →https://doi.org/10.1038/ng.3539openalex-snapshot
Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin
inferredcites →https://doi.org/10.1038/nmeth.2148openalex-snapshot
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
inferredcites →https://doi.org/10.1038/s41467-020-20282-1openalex-snapshot
ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function
inferredcites →https://doi.org/10.1038/s41467-023-38429-1openalex-snapshot
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
inferredcites →https://doi.org/10.1038/s41467-024-48593-7openalex-snapshot
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains
inferredcites →https://doi.org/10.1038/s41576-018-0060-8openalex-snapshot
Organizational principles of 3D genome architecture
inferredcites →https://doi.org/10.1038/s41580-019-0132-4openalex-snapshot
The role of 3D genome organization in development and cell differentiation
inferredcites →https://doi.org/10.1038/s41580-021-00362-wopenalex-snapshot
Understanding 3D genome organization by multidisciplinary methods
inferredcites →https://doi.org/10.1038/s41586-024-08333-9openalex-snapshot
Nucleosome fibre topology guides transcription factor binding to enhancers
inferredcites →https://doi.org/10.1038/s41587-022-01211-7openalex-snapshot
A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers
inferredcites →https://doi.org/10.1038/s41588-019-0561-1openalex-snapshot
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inferredcites →https://doi.org/10.1038/s41588-023-01442-7openalex-snapshot
RNA polymerase II dynamics shape enhancer–promoter interactions
inferredcites →https://doi.org/10.1038/s41588-023-01452-5openalex-snapshot
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells
inferredcites →https://doi.org/10.1038/s41588-023-01649-8openalex-snapshot
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization
inferredcites →https://doi.org/10.1038/s41592-019-0686-2openalex-snapshot
SciPy 1.0: fundamental algorithms for scientific computing in Python
inferredcites →https://doi.org/10.1038/s41596-019-0273-0openalex-snapshot
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btab698openalex-snapshot
iNucs: inter-nucleosome interactions
inferredcites →https://doi.org/10.1093/bioinformatics/btl647openalex-snapshot
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btz615openalex-snapshot
PyRanges: efficient comparison of genomic intervals in Python
inferredcites →https://doi.org/10.1093/imanum/drs019openalex-snapshot
A fast algorithm for matrix balancing
inferredcites →https://doi.org/10.1093/nar/gks501openalex-snapshot
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages
inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot
deepTools: a flexible platform for exploring deep-sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv1505openalex-snapshot
TopDom: an efficient and deterministic method for identifying topological domains in genomes
inferredcites →https://doi.org/10.1101/gr.185272.114openalex-snapshot
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
inferredcites →https://doi.org/10.1101/gr.215160.116openalex-snapshot
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
inferredcites →https://doi.org/10.1101/gr.5560806openalex-snapshot
Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1109/tau.1967.1161901openalex-snapshot
The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms
inferredcites →https://doi.org/10.1126/sciadv.aaw1668openalex-snapshot
Principles of genome folding into topologically associating domains
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.aaz1646openalex-snapshot
Single-molecule regulatory architectures captured by chromatin fiber sequencing
inferredcites →https://doi.org/10.1126/science.abn8131openalex-snapshot
Structures of +1 nucleosome–bound PIC-Mediator complex
inferredcites →https://doi.org/10.1177/0844562118786647openalex-snapshot
Univariate Outliers: A Conceptual Overview for the Nurse Researcher
inferredcites →https://doi.org/10.1186/1471-2164-14-778openalex-snapshot
Finding the active genes in deep RNA-seq gene expression studies
inferredcites →https://doi.org/10.1186/1748-7188-9-14openalex-snapshot
Identification of alternative topological domains in chromatin
inferredcites →https://doi.org/10.1186/gb-2003-4-5-p3openalex-snapshot
DAVID: Database for Annotation, Visualization, and Integrated Discovery
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s13059-016-1003-3openalex-snapshot
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
inferredcites →https://doi.org/10.1186/s13059-018-1596-9openalex-snapshot
Comparison of computational methods for the identification of topologically associating domains
inferredcites →https://doi.org/10.1186/s13059-019-1815-zopenalex-snapshot
Quantitative MNase-seq accurately maps nucleosome occupancy levels
inferredcites →https://doi.org/10.1186/s13059-020-02167-0openalex-snapshot
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
inferredcites →https://doi.org/10.1186/s13059-020-02215-9openalex-snapshot
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
inferredcites →https://doi.org/10.1186/s13059-020-02253-3openalex-snapshot
SPIN reveals genome-wide landscape of nuclear compartmentalization
inferredcites →https://doi.org/10.1186/s13059-021-02465-1openalex-snapshot
NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
inferredcites →https://doi.org/10.1186/s13072-022-00473-4openalex-snapshot
Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C
inferredcites →https://doi.org/10.1186/s13073-020-00769-8openalex-snapshot
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops
inferredcites →https://doi.org/10.1371/journal.pcbi.1012067openalex-snapshot
Cooltools: Enabling high-resolution Hi-C analysis in Python
inferredcites →https://doi.org/10.1371/journal.pcbi.1012164openalex-snapshot
Pairtools: From sequencing data to chromosome contacts
inferredcites →https://doi.org/10.1371/journal.pgen.1000138openalex-snapshot
The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome
inferredcites →https://doi.org/10.7554/elife.02042openalex-snapshot
The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1
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