[HTML][HTML] Methods for ChIP-seq analysis: A practical workflow and advanced applications
R Nakato, T Sakata - Methods, 2021 - Elsevier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with
implications across many fields of biology. In plant ecology, recent studies have attempted to …
implications across many fields of biology. In plant ecology, recent studies have attempted to …
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
Abstract The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …
[HTML][HTML] Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Recent developments in stem cell biology have enabled the study of cell fate decisions in
early human development that are impossible to study in vivo. However, understanding how …
early human development that are impossible to study in vivo. However, understanding how …
[HTML][HTML] Histone methylation dynamics and gene regulation occur through the sensing of one-carbon metabolism
Summary S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) link one-
carbon metabolism to methylation status. However, it is unknown whether regulation of SAM …
carbon metabolism to methylation status. However, it is unknown whether regulation of SAM …
[HTML][HTML] ChIP-Hub provides an integrative platform for exploring plant regulome
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms
the basis for most life on earth. A wealth of regulome and epigenome data have been …
the basis for most life on earth. A wealth of regulome and epigenome data have been …
The changing paradigm of intron retention: regulation, ramifications and recipes
Intron retention (IR) is a form of alternative splicing that has long been neglected in
mammalian systems although it has been studied for decades in non-mammalian species …
mammalian systems although it has been studied for decades in non-mammalian species …
Refactoring transcription factors for metabolic engineering
C Deng, Y Wu, X Lv, J Li, Y Liu, G Du, J Chen… - Biotechnology …, 2022 - Elsevier
Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic
regulation systems composed of transcription factors have been widely used in metabolic …
regulation systems composed of transcription factors have been widely used in metabolic …
[HTML][HTML] Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
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 throughput, the development of working standards for the quality assessment of ChIP …
Motif-based analysis of large nucleotide data sets using MEME-ChIP
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can
analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and …
analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and …