The Hitchhiker's guide to Hi-C analysis: practical guidelines (Q35140940)

6 August 2017

title

The Hitchhiker's guide to Hi-C analysis: practical guidelines (English)

1 reference

6 August 2017

Noam Kaplan

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Bryan R Lajoie

1 reference

6 August 2017

Job Dekker

series ordinal

1 reference

6 August 2017

publication date

6 November 2014

1 reference

6 August 2017

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6 August 2017

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6 August 2017

page(s)

65-75

1 reference

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

6 August 2017

cites work

1 reference

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Insulator function and topological domain border strength scale with architectural protein occupancy

13 July 2018

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

13 July 2018

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Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

13 July 2018

1 reference

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The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

13 July 2018

1 reference

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The 3D genome in transcriptional regulation and pluripotency

13 July 2018

1 reference

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Identification of alternative topological domains in chromatin

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps

13 July 2018

1 reference

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

13 July 2018

1 reference

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Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Functional and topological characteristics of mammalian regulatory domains.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

High-throughput genome scaffolding from in vivo DNA interaction frequency

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Organization of the mitotic chromosome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

3D chromosome modeling with semi-definite programming and Hi-C data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

High-resolution mapping of the spatial organization of a bacterial chromosome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Topology of mammalian developmental enhancers and their regulatory landscapes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

A high-resolution map of the three-dimensional chromatin interactome in human cells

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Communication of genome regulatory elements in a folded chromosome.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Genome architecture: domain organization of interphase chromosomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

The hierarchy of the 3D genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Bayesian inference of spatial organizations of chromosomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

HiCNorm: removing biases in Hi-C data via Poisson regression

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

The long-range interaction landscape of gene promoters

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Normalization of a chromosomal contact map.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

A map of the cis-regulatory sequences in the mouse genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Topological domains in mammalian genomes identified by analysis of chromatin interactions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Fast gapped-read alignment with Bowtie 2

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Higher-order chromatin structure: bridging physics and biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Enhancer and promoter interactions-long distance calls

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Bridging the resolution gap in structural modeling of 3D genome organization

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

A three-dimensional model of the yeast genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Looping and interaction between hypersensitive sites in the active beta-globin locus

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Capturing chromosome conformation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4347522

Power-Law Distributions in Empirical Data

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FJ.YMETH.2014.10.031

10.1016/J.YMETH.2014.10.031

7 January 2021

Identifiers

DOI

1 reference

6 August 2017

1 reference

6 August 2017

1 reference