(Q28601222)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

title

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

1 reference

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14 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Steven W Wingett

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Andrew Dimond

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Daniel R Zerbino

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Biola M. Javierre

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Cameron S. Osborne

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Peter Fraser

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Mikhail Spivakov

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

author name string

Paula Freire-Pritchett

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Csilla Várnai

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Vincent Plagnol

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

Stefan Schoenfelder

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

language of work or name

English

0 references

publication date

15 June 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

page(s)

127

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

14 March 2020

DESeq2

object named as

DESeq2

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Orchestrating high-throughput genomic analysis with Bioconductor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

CTCF: an architectural protein bridging genome topology and function

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

An integrated encyclopedia of DNA elements in the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Topological domains in mammalian genomes identified by analysis of chromatin interactions

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Differential expression analysis for sequence count data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Diffusion-driven looping provides a consistent framework for chromatin organization

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Cell cycle-regulated phosphorylation of p220(NPAT) by cyclin E/Cdk2 in Cajal bodies promotes histone gene transcription

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Systematic localization of common disease-associated variation in regulatory DNA

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

The long-range interaction landscape of gene promoters

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Cajal bodies are linked to genome conformation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

HiCUP: pipeline for mapping and processing Hi-C data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell 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=4908757

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

FourCSeq: analysis of 4C sequencing data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

The pluripotent regulatory circuitry connecting promoters to their long-range interacting 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=4908757

Capture Hi-C identifies the chromatin interactome of colorectal cancer 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=4908757

A comparative encyclopedia of DNA elements in the mouse 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=4908757

ArrayExpress update--simplifying data submissions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Using eQTL weights to improve power for genome-wide association studies: a genetic study of childhood asthma.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Iterative correction of Hi-C data reveals hallmarks of chromosome 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=4908757

Weighted multiple testing procedures for genomic studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Improving power of genome-wide association studies with weighted false discovery rate control and prioritized subset analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

ChromHMM: automating chromatin-state discovery and characterization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Genomics tools for unraveling chromosome architecture

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Genome-Wide Significance Levels and Weighted Hypothesis Testing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

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=4908757

sdef: an R package to synthesize lists of significant features in related experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Discovering collectively informative descriptors from high-throughput experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

The role of transcription factories in large-scale structure and dynamics of interphase chromatin.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4908757

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait 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=4908757

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

Chromatin position effects assayed by thousands of reporters integrated in parallel

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

A Simplex Method for Function Minimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

Exploring long-range genome interactions using the WashU Epigenome Browser

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

False discovery control with p-value weighting

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-0992-2

10.1186/S13059-016-0992-2

21 January 2018

Identifiers

DOI

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27306882%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

PubMed publication ID

27306882

2 references