(Q33699592)

28 July 2017

title

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions (English)

1 reference

28 July 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

18 July 2024

3

Jacques Rougemont

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

18 July 2024

author name string

Marion Leleu

series ordinal

1

1 reference

28 July 2017

Grégory Lefebvre

series ordinal

2

1 reference

28 July 2017

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=20861161

18 July 2024

publication date

22 September 2010

1 reference

full work available at URL

28 July 2017

https://europepmc.org/articles/pmc3080774?pdf=render

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20861161/?tool=EBI

18 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20861161/pdf/?tool=EBI

18 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

https://europepmc.org/articles/PMC3080774

18 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

https://europepmc.org/articles/PMC3080774?pdf=render

18 July 2024

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

https://doi.org/10.1093/bfgp/elq022

18 July 2024

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20861161

http://academic.oup.com/bfg/article-pdf/9/5-6/466/440034/elq022.pdf

18 July 2024

https://api.crossref.org/works/10.1093/BFGP/ELQ022

1 reference

Briefings in functional genomics

18 July 2024

published in

1 reference

28 July 2017

volume

9

1 reference

28 July 2017

issue

5-6

1 reference

28 July 2017

page(s)

466-476

1 reference

Differential expression analysis for sequence count data

28 July 2017

cites work

1 reference

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Evaluation of algorithm performance in ChIP-seq peak detection

21 June 2018

1 reference

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MER41 repeat sequences contain inducible STAT1 binding sites

21 June 2018

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HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

21 June 2018

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The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

21 June 2018

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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

21 June 2018

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A quantitative model of transcriptional regulation reveals the influence of binding location on expression

21 June 2018

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The value of position-specific priors in motif discovery using MEME.

21 June 2018

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Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

21 June 2018

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De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

21 June 2018

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Heritable individual-specific and allele-specific chromatin signatures in humans

21 June 2018

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A scaling normalization method for differential expression analysis of RNA-seq data

21 June 2018

1 reference

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On the detection and refinement of transcription factor binding sites using ChIP-Seq data

21 June 2018

1 reference

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A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

21 June 2018

1 reference

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A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

21 June 2018

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The UCSC Genome Browser database: update 2010

21 June 2018

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Computation for ChIP-seq and RNA-seq studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae 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=3080774

BayesPeak: Bayesian analysis of ChIP-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Exhaustive search for over-represented DNA sequence motifs with CisFinder

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

ChIP-seq: advantages and challenges of a maturing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Mapping accessible chromatin regions using Sono-Seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Impact of chromatin structures on DNA processing for genomic analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

CEAS: cis-regulatory element annotation system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Comparative study on ChIP-seq data: normalization and binding pattern characterization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Extracting transcription factor targets from ChIP-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

MEME SUITE: tools for motif discovery and searching

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

21 June 2018

1 reference

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

21 June 2018

1 reference

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EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Genomic location analysis by ChIP-Seq

21 June 2018

1 reference

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Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

21 June 2018

1 reference

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Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

21 June 2018

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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

21 June 2018

1 reference

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The DNA-encoded nucleosome organization of a eukaryotic genome

21 June 2018

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Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

21 June 2018

1 reference

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21 June 2018

1 reference

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Design and analysis of ChIP-seq experiments for DNA-binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

An integrated software system for analyzing ChIP-chip and ChIP-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

F-Seq: a feature density estimator for high-throughput sequence tags

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Modeling ChIP sequencing in silico with applications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Combinatorial patterns of histone acetylations and methylations in 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=3080774

Dynamic regulation of nucleosome positioning in 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=3080774

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

21 June 2018

1 reference

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Targeted high-throughput sequencing of tagged nucleic acid samples

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Genome-wide maps of chromatin state in pluripotent and lineage-committed 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=3080774

Indexing strategies for rapid searches of short words in genome sequences.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

21 June 2018

1 reference

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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

High-resolution profiling of histone methylations in 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=3080774

MAMMOT--a set of tools for the design, management and visualization of genomic tiling arrays

21 June 2018

1 reference

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EPD in its twentieth year: towards complete promoter coverage of selected model organisms

21 June 2018

1 reference

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P-Match: transcription factor binding site search by combining patterns and weight matrices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Gibbs Recursive Sampler: finding transcription factor binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

TRANSFAC: transcriptional regulation, from patterns to profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Physical constraints and functional characteristics of transcription factor-DNA interaction.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Using TESS to predict transcription factor binding sites in DNA sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

A universal classification of eukaryotic transposable elements implemented in Repbase.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

ChIP-Seq data reveal nucleosome architecture of human promoters.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

Predicting transcription factor affinities to DNA from a biophysical model

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3080774

30 October 2018

Identifiers

DOI

10.1093/BFGP/ELQ022

1 reference

28 July 2017

1 reference

28 July 2017

1 reference