Results 21 to 30 of about 928,240 (334)
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells-of-origin
Nature Biotechnology, 2021 Cell-free DNA (cfDNA) in human plasma provides access to molecular information about the pathological processes in the organs or tumors from which it originates.
R. Sadeh +30 more
semanticscholar +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
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
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
Genome Biology, 2020 We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles ...
Qian Qin +11 more
semanticscholar +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
Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors
Nature Communications, 2020 The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network.
Xiaoyu Tu +10 more
semanticscholar +1 more source
The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy [PDF]
, 2012 NF-kappaB transcriptional activation is required for skeletal muscle disuse atrophy. We are continuing to study how the activation of NF-kB regulates the genes that encode the protein products that cause atrophy. Using ChIP-sequencing we found that Bcl-3,
Jackman, Robert W. +2 more
core +5 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 +5 more
doaj +1 more source
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. [PDF]
, 2011 Although several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such data can be processed, analyzed, stored ...
Muino, J.M. +3 more
core +1 more source