My5C: web tools for chromosome conformation capture studies

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Nature Methods

• Publication date

  2009-10-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1038/nmeth1009-690PMID 19789528PMCID PMC2859197
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Note: Supplementary information is available on the Nature Methods website.

  2009cited by this paper
• An evaluation of 3C-based methods to capture DNA interactions

  2007cited by this paper
• Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

  2006cited by this paper
• The three 'C' s of chromosome conformation capture: controls, controls, controls

  2005cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003cited by this paper
• Capturing Chromosome Conformation

  2002cited by this paper

• Mapping the 3D genome architecture

  2024cites this paper
• Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells

  2023cites this paper
• Cohesin-dependence of neuronal gene expression relates to chromatin loop length

  2022cites this paper
• Reliance of neuronal gene expression on cohesin scales with chromatin loop length

  2022cites this paper
• The Conformation of Yeast Chromosome III Is Mating Type The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer Dependent and Controlled by the Recombination Enhancer

  2022cites this paper
• Possibility of Uncoding Structural Organization of Genome in Rice Research: Prospects and Approaches by 3D Genome Sequencing

  2021cites this paper
• Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

  2021cites this paper
• Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons

  2021cites this paper
• Molecular and computational approaches to map regulatory elements in 3D chromatin structure

  2021cites this paper
• Targeted degradation of CTCF decouples local insulation of Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic chromosome domains from higher-order genomic compartmentalization [preprint] compartmentalization

  2021cites this paper
• The 3D Genome: From Structure to Function

  2021cites this paper
• Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

  2020cites this paper
• Sequence Analysis

  2020cites this paper
• Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

  2020cites this paper
• Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk

  2020cites this paper
• Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

  2019cites this paper
• Genome Informatics

  2019cites this paper
• Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

  2019cites this paper
• Integrative Modeling and Novel Technologies in Human Genomics

  2019cites this paper
• PRC2-Associated Chromatin Contacts in the Developing Limb Reveal a Possible Mechanism for the Atypical Role of PRC2 in HoxA Gene Expression.

  2019cites this paper
• Tasks, Techniques, and Tools for Genomic Data Visualization

  2019cites this paper
• Developmentally regulated Shh expression is robust to TAD perturbations

  2019cites this paper
• Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

  2019cites this paper
• 3C-Based Chromatin Interaction Analyses.

  2018cites this paper
• CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.

  2018cites this paper
• 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

  2018cites this paper
• Storage, visualization, and navigation of 3D genomics data.

  2018cites this paper
• ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C

  2018cites this paper
• Delta: a new web-based 3D genome visualization and analysis platform

  2018cites this paper
• 5C Analysis of 3C, ChIP-Loop, and Control Libraries.

  2018cites this paper
• Schizophrenia and a high-resolution map of the three-dimensional chromatin interactome of adult and fetal cortex

  2018cites this paper
• CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

  2018cites this paper
• Technical Review: A Hitchhiker's Guide to Chromosome Conformation Capture.

  2018cites this paper
• Novel long-range regulatory mechanisms controlling PKD2 gene expression

  2018cites this paper
• LADL: Light-activated dynamic looping for endogenous gene expression control

  2018cites this paper
• 5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

  2017cites this paper
• Dynamique de la chromatine et la régulation du changement du type sexuel chez la levure

  2017cites this paper
• Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

  2017influential citation
• Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure

  2017cites this paper
• Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

  2017cites this paper
• Delta integrates 3D physical structure with topology and genomic data of chromosomes

  2017cites this paper
• HiCcompare: a method for joint normalization of Hi-C datasets and differential chromatin interaction detection

  2017cites this paper
• Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters

  2017influential citation
• A User ' s Guide to the Encyclopedia of DNA Elements ( ENCODE )

  2017cites this paper
• Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

  2017cites this paper
• Edinburgh Research Explorer Spatial genome organization

  2017cites this paper
• Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization

  2017cites this paper
• Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

  2016cites this paper
• How computer science can help in understanding the 3D genome architecture

  2016cites this paper
• Software tools for visualizing Hi-C data

  2016cites this paper
• Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

  2016cites this paper
• Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity

  2016cites this paper
• Supplementary Materials and Methods for Polymer physics of chromosome large-scale 3 D organization

  2016cites this paper
• Chromosome conformation capture technologies and their impact in understanding genome function

  2016cites this paper
• Computational Approaches for the Analysis of Chromosome Conformation Capture Data and Their Application to Study Long-Range Gene Regulation: A Dissertation

  2016cites this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2016cites this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2016cites this paper
• Functional annotation of native enhancers with a Cas9 -histone demethylase fusion

  2015cites this paper
• In the loop: promoter–enhancer interactions and bioinformatics

  2015cites this paper
• Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements

  2015cites this paper
• Activation of proto-oncogenes by disruption of chromosome neighborhoods

  2015cites this paper
• Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.

  2015cites this paper
• An Overview of Genome Organization and How We Got There: from FISH to Hi-C

  2015cites this paper
• The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

  2015cites this paper
• The Three-Dimensional Structure of the Cystic Fibrosis Locus: A Dissertation

  2014influential citation
• Classifying leukemia types with chromatin conformation data

  2014cites this paper
• An integrated encyclopedia of DNA elements in the human genome

  2014cites this paper
• Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

  2014cites this paper
• The Impact of Next-Generation Sequencing Technology on Bacterial Genomics

  2014cites this paper
• Computational identification and analysis of evolutionary breakpoint regions in amniote genomes

  2014cites this paper
• The long-range interaction landscape of gene promoters

  2014cites this paper
• The Recombination Enhancer Modulates the Conformation of Chr. III in Budding Yeast: A Dissertation

  2014cites this paper
• Exploring the Interactions and Structural Organization of Genomes

  2014cites this paper
• Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

  2013cites this paper
• Exploring long-range genome interactions using the WashU Epigenome Browser

  2013cites this paper
• Long noncoding RNA programs active chromatin domain to coordinate homeotic gene activation

  2013cites this paper
• Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny

  2013cites this paper
• Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data

  2013cites this paper
• HiTC - Exploration of High Throughput ’C’ experiments

  2013cites this paper
• Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

  2013cites this paper
• Hox in motion: tracking HoxA cluster conformation during differentiation

  2013influential citation
• Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

  2013cites this paper
• QB-13016-LJ 156..174

  2013cites this paper
• Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

  2013cites this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2012cites this paper
• HiTC: exploration of high-throughput 'C' experiments

  2012cites this paper
• A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing.

  2012cites this paper
• Stamatoyannopoulos What does our genome encode ?

  2012cites this paper
• From cells to chromatin: capturing snapshots of genome organization with 5C technology.

  2012cites this paper
• What does our genome encode?

  2012cites this paper
• On the physical and chemical dynamics of chromatin

  2012cites this paper
• The long-range interaction landscape of gene promoters

  2012cites this paper
• Chromosome conformation capture assays in bacteria.

  2012cites this paper
• Cohesin Protects Genes against γH2AX Induced by DNA Double-Strand Breaks

  2012cites this paper
• 3C-based methods to detect long-range chromatin interactions

  2011cites this paper
• Three‐Dimensional Architecture of Genomes

  2011cites this paper
• A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

  2011cites this paper
• The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

  2011cites this paper
• A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

  2011cites this paper
• Structure determination of genomic domains by satisfaction of spatial restraints

  2010cites this paper