Results 11 to 20 of about 604,881 (306)
WACS: improving ChIP-seq peak calling by optimally weighting controls
BMC Bioinformatics, 2021 Background Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome.
Aseel Awdeh +2 more
doaj +1 more source
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
G3: Genes, Genomes, Genetics, 2021 Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone ...
Cheryl A Keller +11 more
doaj +1 more source
dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data. [PDF]
PLoS Computational Biology, 2013 Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) has been successfully used for genome-wide profiling of transcription factor binding sites, histone modifications, and nucleosome occupancy in many model organisms and humans.
Dongjun Chung +6 more
doaj +1 more source
MER41 repeat sequences contain inducible STAT1 binding sites. [PDF]
PLoS ONE, 2010 Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences.
Christoph D Schmid, Philipp Bucher
doaj +1 more source
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
openaire +5 more sources
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
openaire +6 more sources
BMC Bioinformatics, 2021 Background Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure.
Lélia Polit +5 more
doaj +1 more source
Evaluation of algorithm performance in ChIP-seq peak detection. [PDF]
PLoS ONE, 2010 Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions.
Elizabeth G Wilbanks, Marc T Facciotti
doaj +1 more source
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
core +1 more source
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
doaj +1 more source