HiCUP: pipeline for mapping and processing Hi-C data (Q31042123)

13 November 2017

HiCUP: pipeline for mapping and processing Hi-C data (English)

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13 November 2017

2

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13 November 2017

Steven Wingett

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Mayra Furlan-Magaril

object named as

Mayra Furlan-Magaril

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Peter Fraser

object named as

Peter Fraser

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author name string

Takashi Nagano

4

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PMCID

4706059

13 November 2017

Stefan Schoenfelder

5

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PMCID

4706059

13 November 2017

Simon Andrews

7

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13 November 2017

20 November 2015

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13 November 2017

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13 November 2017

4

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13 November 2017

1310

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Creative Commons Attribution 4.0 International

13 November 2017

start time

20 November 2015

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Global reorganization of the nuclear landscape in senescent cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

Cohesin complex promotes transcriptional termination between convergent genes in S. pombe

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706059

10.12688/F1000RESEARCH.7334.1

25 November 2018

Identifiers

DOI

1 reference

13 November 2017

1 reference

13 November 2017

1 reference

PMCID

4706059