Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
R Nakato, K Shirahige - Briefings in bioinformatics, 2017 - academic.oup.com
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect
protein/DNA-binding and histone-modification sites across an entire genome. Recent …
protein/DNA-binding and histone-modification sites across an entire genome. Recent …
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Abstract Background Chromatin immunoprecipitation (ChIP) followed by high-throughput
sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have …
sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have …
Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1
JA Law, J Du, CJ Hale, S Feng, K Krajewski… - Nature, 2013 - nature.com
DNA methylation is an epigenetic modification that has critical roles in gene silencing,
development and genome integrity. In Arabidopsis, DNA methylation is established by …
development and genome integrity. In Arabidopsis, DNA methylation is established by …
Practical guidelines for the comprehensive analysis of ChIP-seq data
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
K Kaufmann, JM Muino, M Østerås, L Farinelli… - Nature protocols, 2010 - nature.com
Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between
transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF …
transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF …
Evaluation of algorithm performance in ChIP-seq peak detection
EG Wilbanks, MT Facciotti - PloS one, 2010 - journals.plos.org
Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq)
is revolutionizing our ability to interrogate whole genome protein-DNA interactions …
is revolutionizing our ability to interrogate whole genome protein-DNA interactions …
DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons
X Zhong, CJ Hale, JA Law, LM Johnson… - Nature structural & …, 2012 - nature.com
The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function
in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in …
in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in …
RNAmod: an integrated system for the annotation of mRNA modifications
Q Liu, RI Gregory - Nucleic acids research, 2019 - academic.oup.com
Dynamic and reversible RNA modifications such as N 6-methyladenosine (m6A) can play
important roles in regulating messenger RNA (mRNA) splicing, export, stability and …
important roles in regulating messenger RNA (mRNA) splicing, export, stability and …
Features that define the best ChIP-seq peak calling algorithms
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for
studying gene regulatory proteins, such as transcription factors and histones. Peak calling is …
studying gene regulatory proteins, such as transcription factors and histones. Peak calling is …
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12
AI Prieto, C Kahramanoglou, RM Ali… - Nucleic acids …, 2012 - academic.oup.com
IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the
same protein family but interact differently with the DNA. IHF is a sequence-specific DNA …
same protein family but interact differently with the DNA. IHF is a sequence-specific DNA …