Results 21 to 30 of about 574,745 (303)

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, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley, Robert Landick, Sündüz Keleş   +6 more
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, Chris A. Helliwell, David W. Bulger, Glenn Stone   +3 more
openaire   +5 more sources

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes

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, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva   +5 more
doaj   +1 more source

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, Cicek, A. Ercument, Wang, Yuhao, Schulz, Marcel H., Le, Hai-Son, Bar-Joseph, Ziv   +5 more
openaire   +6 more sources

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

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data [PDF]

, 2013
Background: ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody.
Bao, Yanchun,, ’t Hoen, Peter AC, Bao, Yanchun, Veronica Vinciotti, Hoen, P.A.C. 't, Vinciotti, V., Vinciotti, Veronica,, Yanchun Bao, Wit, Ernst,, Bao, Y.C., Ernst Wit, Wit, Ernst, Vinciotti, V, Peter AC ’t Hoen, 't Hoen, Peter A C, Vinciotti, Veronica, Hoen, Peter A.C. ’t,, Bao, Y, 't Hoen, PAC, Wit, E, Wit, E.   +20 more
core   +2 more sources

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, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek   +5 more
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., Angenent, G.C., Krajewski Pawel, Angenent Gerco C, Roeland CHJ van Ham, Pawel Krajewski, Muiño Jose M, Ham, R.C.H.J., van, Kaufmann, K., van Ham Roeland CHJ, Jose M Muiño, Kaufmann Kerstin, van Ham, R.C.H.J., Krajewski, P., Kerstin Kaufmann, Gerco C Angenent   +15 more
core   +1 more source

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, Ziwei eLiang, Rafik eSalama, Rory eStark, Ines ede Santiago   +4 more
doaj   +1 more source

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
doaj   +1 more source