Closing the loop: 3C versus DNA FISH (Q28075312)

language of work or name

1 reference

19 October 2016

5 references

2 August 2019

19 September 2019

12 October 2019

23 July 2020

5 references

2 August 2019

19 September 2019

12 October 2019

23 July 2020

17

1 reference

issue

1

1 reference

page(s)

215

1 reference

Creative Commons Attribution 4.0 International

copyright license

4 references

2 August 2019

19 September 2019

12 October 2019

describes a project that uses

23 July 2020

copyright status

copyrighted

0 references

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5072311/fullTextXML

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-016-1081-2

0 references

cites work

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Getting the genome in shape: the formation of loops, domains and compartments

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Expanding the Biologist's Toolkit with CRISPR-Cas9

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Large-scale chromatin organization: the good, the surprising, and the still perplexing

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Topological domains in mammalian genomes identified by analysis of chromatin interactions

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Structural organization of the inactive X chromosome in the mouse.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The 3D Genome as Moderator of Chromosomal Communication

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Condensin-driven remodelling of X chromosome topology during dosage compensation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

High-resolution 3D DNA FISH using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Robust image registration of biological microscopic images

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Organization of the mitotic chromosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The hierarchy of the 3D genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Hi-C: a comprehensive technique to capture the conformation of genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Three-dimensional folding and functional organization principles of the Drosophila genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

A decade of 3C technologies: insights into nuclear organization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The proteomes of transcription factories containing RNA polymerases I, II or III.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Cellular decision making and biological noise: from microbes to mammals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

CryoFISH: fluorescence in situ hybridization on ultrathin cryosections

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Fluorescence in situ hybridization (FISH), basic principles and methodology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Looping probabilities in model interphase chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

A three-dimensional model of the yeast genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Structural characterization of formaldehyde-induced cross-links between amino acids and deoxynucleosides and their oligomers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Dynamics of chromatin, proteins, and bodies within the cell nucleus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH).

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

A random-walk/giant-loop model for interphase chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5072311

Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation.

2 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

3D genome reconstruction from chromosomal contacts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

In vivo formaldehyde cross-linking: it is time for black box analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Elastic registration of biological images using vector-spline regularization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1081-2

Cell Preparation and Multicolor FISH in 3D Preserved Cultured Mammalian Cells

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/27760553

12 December 2020

inferred from PubMed ID database lookup

Factors affecting the timing and imprinting of replication on a mammalian chromosome

1 reference

https://pubmed.ncbi.nlm.nih.gov/27760553

12 December 2020

inferred from PubMed ID database lookup

3D-FISH on Cultured Cells Combined with Immunostaining

1 reference

https://pubmed.ncbi.nlm.nih.gov/27760553

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/S13059-016-1081-2

1 reference

Dimensions Publication ID

2906611

1049562986

0 references

2906611

1 reference

1 reference

1 reference