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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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Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity [PDF]
, 2012 We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments.
A Barski +52 more
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Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
BMC Research Notes, 2009 Background ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly ...
Sachs Laurent, Buisine Nicolas
doaj +1 more source
Imputation for transcription factor binding predictions based on deep learning. [PDF]
PLoS Computational Biology, 2017 Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard ...
Qian Qin, Jianxing Feng
doaj +1 more source
Functional diversity of CTCFs is encoded in their binding motifs [PDF]
, 2015 CTCF ChIP-seq data. Cell lines and statistics for the ChIP-seq data used in the study.
Chengqi Wang +3 more
core +3 more sources
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
Humburg, Peter +3 more
openaire +4 more sources
Nucleic Acids Res., 2016 Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation.
S. Mei +13 more
semanticscholar +1 more source
Defining bacterial regulons using ChIP-seq [PDF]
Methods, 2015 Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful method that identifies protein-DNA binding sites in vivo. Recent studies have illustrated the value of ChIP-seq in studying transcription factor binding in various bacterial species under a variety of growth conditions.
Myers, Kevin S. +3 more
openaire +2 more sources
PICS: Probabilistic Inference for ChIP-seq [PDF]
Biometrics, 2010 ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than ChIP-chip. While it presents new opportunities for research, ChIP-seq poses new challenges for statistical analysis ...
Zhang, Xuekui +6 more
openaire +4 more sources
Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency. [PDF]
, 2018 The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Case sequencing studies have revealed mutations to proteins that regulate chromatin state, known as chromatin remodeling ...
Catta-Preta, Rinaldo +3 more
core +6 more sources