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Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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UCSF Chimera—A visualization system for exploratory research and analysis

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The Meaning of Gene Positioning

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Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

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Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

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Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

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Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Restraint‐based three‐dimensional modeling of genomes and genomic domains

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Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

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Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

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Chromosome territories, nuclear architecture and gene regulation in mammalian cells

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A three-dimensional model of the yeast genome

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

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Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

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Fast gapped-read alignment with Bowtie 2

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Iterative correction of Hi-C data reveals hallmarks of chromosome organization

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The GEM mapper: fast, accurate and versatile alignment by filtration

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3D genome reconstruction from chromosomal contacts

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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

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3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

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A statistical approach for inferring the 3D structure of the genome

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Circular binary segmentation for the analysis of array-based DNA copy number data

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An efficient algorithm for large-scale detection of protein families

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Recovering ensembles of chromatin conformations from contact probabilities

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The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling

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Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

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Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

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Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

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Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment

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Matplotlib: A 2D Graphics Environment

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Capturing Chromosome Conformation

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

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Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

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Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

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Bayesian Inference of Spatial Organizations of Chromosomes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

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Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles

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Computational tools for Hi‐C data analysis

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Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells

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Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells

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Higher order assembly: folding the chromosome

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Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

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Comparison of computational methods for Hi-C data analysis

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Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

inferred← citeshttps://doi.org/10.1038/s41467-018-04130-xopenalex-snapshot

Theoretical principles of transcription factor traffic on folded chromatin

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Pre-mitotic genome re-organisation bookends the B cell differentiation process

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Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

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Transcription-factor-mediated supervision of global genome architecture maintains B cell identity

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The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

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Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

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Multi-level remodelling of chromatin underlying activation of human T cells

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Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

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OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes

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HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

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Single-cell absolute contact probability detection reveals that chromosomes are organized by multiple, low-frequency yet specific interactions

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Activation-induced re-organization of chromatin in human T cells

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

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chroGPS2: differential analysis of epigenome maps in R

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AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

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NF-κB–Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis

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HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

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HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure

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Software tools for visualizing Hi-C data

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The three-dimensional genome organization of Drosophila melanogaster through data integration

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HiGlass: web-based visual exploration and analysis of genome interaction maps

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DeepHiC: A generative adversarial network for enhancing Hi-C data resolution

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Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

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The functional and spatial organization of chromatin during Thymocyte development

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