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Chromatin Immunoprecipitation for ChIP-chip and ChIP-seq
2014Bacterial adaptation to given environmental conditions is largely achieved by complex gene regulatory processes. To address the question how and to what extend single transcriptional regulators modulate gene expression, chromatin immunoprecipitation (ChIP) coupled to DNA microarrays (ChIP-chip) or to next-generation sequencing (ChIP-seq) is one of the ...
Sebastian Schulz, Susanne Häussler
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Computational Analysis of ChIP-seq Data
2010Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics
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Modelling ChIP-seq Data Using HMMs
2017Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this chapter, we show how hidden Markov models can be used for the analysis of data generated by ChIP-seq experiments.
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ChIP-Seq and the Complexity of Bacterial Transcriptional Regulation
2012Transcription factors (TFs) play a central role in regulating gene expression in all bacteria. Yet, until recently, studies of TF binding were limited to a small number of factors at a few genomic locations. Chromatin immunoprecipitation followed by sequencing enables mapping of binding sites for TFs in a global and high-throughput fashion.
James, Galagan +2 more
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2015
Introduction to ChIP-seq data analysis. Overview of quality control, mapping, peak calling and downstream analysis methods.
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Introduction to ChIP-seq data analysis. Overview of quality control, mapping, peak calling and downstream analysis methods.
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Methods for ChIP-seq analysis: A practical workflow and advanced applications
Methods, 2021Ryuichiro Nakato, Toyonori Sakata
exaly
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis
Genomics, Proteomics and Bioinformatics, 2021Xintao Qiu, Avery Feit, Yingtian Xie
exaly
ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates
Genomics, 2021Brad Balderson +2 more
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