Practical guidelines for the comprehensive analysis of ChIP-seq data (Q21563477)

5 September 2022

7

Pedro Madrigal

Pedro

Madrigal

1 reference

5 September 2022

1

Timothy Bailey

Timothy

Bailey

1 reference

5 September 2022

9

Jie Zhang

Jie

Zhang

1 reference

5 September 2022

Pawel Krajewski

2

Pawel

Krajewski

1 reference

5 September 2022

Istvan Ladunga

3

Istvan

Ladunga

1 reference

5 September 2022

Qunhua Li

5

Qunhua

Li

1 reference

5 September 2022

Tao Liu

6

Tao

Liu

1 reference

5 September 2022

Cenny Taslim

8

Cenny

Taslim

1 reference

PLOS Computational Biology

5 September 2022

language of work or name

English

0 references

publication date

2013

0 references

published in

0 references

volume

9

0 references

issue

11

0 references

page(s)

e1003326

0 references

copyright license

Creative Commons Attribution 3.0 Unported

start time

14 November 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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19 March 2017

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19 March 2017

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

19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

19 March 2017

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

19 March 2017

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Quantifying similarity between motifs

19 March 2017

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

19 March 2017

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

19 March 2017

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High-resolution profiling of histone methylations in the human genome

19 March 2017

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High-resolution DNA-binding specificity analysis of yeast transcription factors

19 March 2017

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

19 March 2017

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The UCSC genome browser and associated tools

19 March 2017

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Galaxy: a web-based genome analysis tool for experimentalists

19 March 2017

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

19 March 2017

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19 March 2017

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19 March 2017

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Integrative genomics viewer

19 March 2017

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7 April 2017

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Genome-wide mapping of in vivo protein-DNA interactions

7 April 2017

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Galaxy: a platform for interactive large-scale genome analysis

7 April 2017

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

7 April 2017

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GREAT improves functional interpretation of cis-regulatory regions

7 April 2017

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

7 April 2017

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Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

7 April 2017

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A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

7 April 2017

1 reference

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A fast weak motif-finding algorithm based on community detection in graphs

10 May 2017

1 reference

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LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.

12 September 2017

1 reference

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Predicting the molecular complexity of sequencing libraries

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Combining multiple ChIP-seq peak detection systems using combinatorial fusion

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Normalization of ChIP-seq data with control

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Inferring direct DNA binding from ChIP-seq

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Systematic evaluation of factors influencing ChIP-seq fidelity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Normalization, bias correction, and peak calling for ChIP-seq

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Detecting differential binding of transcription factors with ChIP-seq

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Studying the epigenome using next generation sequencing

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Systematic bias in high-throughput sequencing data and its correction by BEADS.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Inferring transcription factor complexes from ChIP-seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

PeakRanger: a cloud-enabled peak caller for ChIP-seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

MEME-ChIP: motif analysis of large DNA datasets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

FIMO: scanning for occurrences of a given motif

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Identifying dispersed epigenomic domains from ChIP-Seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

RecMotif: a novel fast algorithm for weak motif discovery

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

An assessment of histone-modification antibody quality

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Discovering homotypic binding events at high spatial resolution.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Deep and wide digging for binding motifs in ChIP-Seq data.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

BigWig and BigBed: enabling browsing of large distributed datasets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

A signal-noise model for significance analysis of ChIP-seq with negative control

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Computation for ChIP-seq and RNA-seq studies

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

BayesPeak: Bayesian analysis of ChIP-seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

CEAS: cis-regulatory element annotation system

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

RNA Pol II accumulates at promoters of growth genes during developmental arrest.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Regulatory sequence analysis tools

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

STAMP: a web tool for exploring DNA-binding motif similarities

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828144

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts

30 May 2018

1 reference

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003326

A computational pipeline for comparative ChIP-seq analyses.

21 January 2018

1 reference

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003326

MULTOVL: fast multiple overlaps of genomic regions.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003326

10.1371/JOURNAL.PCBI.1003326

21 January 2018

Identifiers

DOI

1 reference

journals/ploscb/BaileyKLLLLMTZ13

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

1 reference