Systematic evaluation of factors influencing ChIP-seq fidelity (Q34241267)

31 July 2017

Systematic evaluation of factors influencing ChIP-seq fidelity (English)

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31 July 2017

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31 July 2017

Tao Liu

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Housheng Hansen He

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Housheng Hansen He

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Barbara J. Wold

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Barbara J Wold

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Jason D Lieb

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Peter J Bickel

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31 July 2017

Yiwen Chen

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Nicolas Negre

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Qunhua Li

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Joanna O Mieczkowska

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Matthew Slattery

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31 July 2017

Tae-Kyung Kim

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Jennifer Zieba

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Yijun Ruan

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Richard M Myers

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Kevin P White

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X Shirley Liu

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22 April 2012

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609-614

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https://scigraph.springernature.com/pub.10.1038/nmeth.1985

31 July 2017

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

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

6 July 2018

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A user's guide to the encyclopedia of DNA elements (ENCODE)

6 July 2018

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A cis-regulatory map of the Drosophila genome.

6 July 2018

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X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila

6 July 2018

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ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

6 July 2018

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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

6 July 2018

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Identification of functional elements and regulatory circuits by Drosophila modENCODE

6 July 2018

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Evaluation of algorithm performance in ChIP-seq peak detection

6 July 2018

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Expression in aneuploid Drosophila S2 cells

6 July 2018

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BEDTools: a flexible suite of utilities for comparing genomic features

6 July 2018

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A comprehensive map of insulator elements for the Drosophila genome

6 July 2018

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

6 July 2018

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Computation for ChIP-seq and RNA-seq studies

6 July 2018

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Impact of chromatin structures on DNA processing for genomic analyses

6 July 2018

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CEAS: cis-regulatory element annotation system

6 July 2018

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Unlocking the secrets of the genome

6 July 2018

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Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Differential chromatin marking of introns and expressed exons by H3K36me3.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Model-based analysis of ChIP-Seq (MACS)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

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

6 July 2018

1 reference

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Genome-wide mapping of in vivo protein-DNA interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

High-resolution profiling of histone methylations in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Model-based analysis of tiling-arrays for ChIP-chip.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

Tandem repeats finder: a program to analyze DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477507

6 July 2018

Identifiers

DOI

10.1038/NMETH.1985

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Dimensions Publication ID

31 July 2017

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31 July 2017

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