Results 11 to 20 of about 673,559 (305)
Cold Spring Harbor Protocols, 2018 Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein ...
Kim, Tae Hoon, Dekker, Job
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Normalization of ChIP-seq data with control [PDF]
BMC Bioinformatics, 2012 Background ChIP-seq has become an important tool for identifying genome-wide protein-DNA interactions, including transcription factor binding and histone modifications. In ChIP-seq experiments, ChIP samples are usually coupled with their matching control
Liang Kun, Keleş Sündüz
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Epigenetics, 2019 Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to obtain high-quality epigenomic maps using chromatin-immunoprecipitation-coupled deep ...
Wenbin Liu +5 more
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Transcriptomic and ChIP seq data
, 2021 Transcriptomic and ChIP seq ...
Wicky, Chantal +3 more
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ChIPulate: A comprehensive ChIP-seq simulation pipeline.
PLoS Computational Biology, 2019 ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a high-throughput technique to identify genomic regions that are bound in vivo by a particular protein, e.g., a transcription factor (TF).
Vishaka Datta +2 more
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In silico pooling of ChIP-seq control experiments.
PLoS ONE, 2014 As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation.
Guannan Sun +5 more
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ChIPseqR: analysis of ChIP-seq experiments [PDF]
BMC Bioinformatics, 2011 The use of high-throughput sequencing in combination with chromatin immunoprecipitation (ChIP-seq) has enabled the study of genome-wide protein binding at high resolution. While the amount of data generated from such experiments is steadily increasing, the methods available for their analysis remain limited. Although several algorithms for the analysis
Peter Humburg +3 more
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De novo ChIP-seq analysis [PDF]
Genome Biology, 2015 Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data.
He, Xin +5 more
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ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions [PDF]
, 2011 Background In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed
Muino, J.M. +14 more
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