Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection
Genome Biology, 2022 Background The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq).
Thomas Eder, Florian Grebien
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Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
Frontiers in Genetics, 2014 With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention.
Thomas Samuel Carroll +4 more
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A flexible ChIP-sequencing simulation toolkit
BMC Bioinformatics, 2021 Background A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data.
An Zheng +5 more
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A simple method for generating high-resolution maps of genome-wide protein binding
eLife, 2015 Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require ...
Peter J Skene, Steven Henikoff
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CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis. [PDF]
PLoS ONE, 2014 Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. ChIP-Seq technology offers many advantages over ChIP-chip arrays, including but not limited to less noise, higher resolution, and more ...
Iman Rezaeian, Luis Rueda
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Low-Cell-Number Epigenome Profiling Aids the Study of Lens Aging and Hematopoiesis
Cell Reports, 2015 Understanding how chromatin modification regulates development and disease can be limited by available material. Despite recent progress, balancing high-quality and reliable mapping using chromatin-immunoprecipitation-based deep sequencing (ChIP-seq ...
Xiaobin Zheng +5 more
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intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
BMC Genomics, 2020 Background RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions.
Yingying Cao +2 more
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An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition. [PDF]
PLoS ONE, 2016 Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require ...
Brian Egan +16 more
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Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique
Frontiers in Cellular and Infection Microbiology, 2023 IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion.
Ronald J. Nowling +3 more
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CSA: a web service for the complete process of ChIP-Seq analysis
BMC Bioinformatics, 2019 Background Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA.
Min Li +4 more
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