(Q51543538)

6 April 2018

title

A computational pipeline for comparative ChIP-seq analyses. (English)

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6 April 2018

author

Alexander Stark

4

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6 April 2018

Julia Zeitlinger

3

object named as

Julia Zeitlinger

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6 April 2018

author name string

Anaïs F Bardet

1

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6 April 2018

Qiye He

2

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6 April 2018

publication date

15 December 2011

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6 April 2018

number of pages

17

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based on heuristic

inferred from page(s)

published in

Nature Protocols

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6 April 2018

volume

7

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issue

1

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page(s)

45-61

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6 April 2018

https://scigraph.springernature.com/pub.10.1038/nprot.2011.420

exact match

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cites work

Genome-wide location and function of DNA binding proteins

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

A core transcriptional network for early mesoderm development in Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Combinatorial binding predicts spatio-temporal cis-regulatory activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Transposable elements have rewired the core regulatory network of human embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Comparative epigenomic analysis of murine and human adipogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Model-based analysis of ChIP-Seq (MACS)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Evaluation of algorithm performance in ChIP-seq peak detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

How does multiple testing correction work?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Shadow enhancers as a source of evolutionary novelty

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

A comprehensive map of insulator elements for the Drosophila genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

GONOME: measuring correlations between GO terms and genomic positions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Developmental gene regulation in the era of genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Divergence of transcription factor binding sites across related yeast species

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Genetic analysis of variation in transcription factor binding in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Genome-wide analysis of protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Gene ontology: tool for the unification of biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

TRANSFAC: transcriptional regulation, from patterns to profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

The Sequence Alignment/Map format and SAMtools

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

BEDTools: a flexible suite of utilities for comparing genomic features

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

MEME: discovering and analyzing DNA and protein sequence motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Combining evidence using p-values: application to sequence homology searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

A survey of DNA motif finding algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Assessing computational tools for the discovery of transcription factor binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Mapping accessible chromatin regions using Sono-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Impact of chromatin structures on DNA processing for genomic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

The human genome browser at UCSC

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2011.420

inferred from DOI database lookup

7 January 2021

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Identifiers

DOI

10.1038/NPROT.2011.420

1 reference

6 April 2018

PubMed ID

22179591

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6 April 2018