ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Z Zou, T Ohta, F Miura, S Oki - Nucleic acids research, 2022 - academic.oup.com
… with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to
explore the epigenomic landscape … This epigenomic landscape can also be characterized for …

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

S Ma, Y Zhang - Molecular biomedicine, 2020 - Springer
Epigenome sequencing technologies have evolved from low-throughput … epigenome biology,
we discuss the development of epigenome sequencing technologies, especially ChIP-seq

[HTML][HTML] Methods for ChIP-seq analysis: A practical workflow and advanced applications

R Nakato, T Sakata - Methods, 2021 - Elsevier
epigenomic landscape contributes to cell identity, development, lineage specification, and
disease. In this review, we first present a typical ChIP-seq … advanced ChIP-seq applications …

Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses

Z Zou, M Iwata, Y Yamanishi, S Oki - BMC bioinformatics, 2022 - Springer
epigenetic landscape of drug responses, in terms of transcription factors (TFs), through
large-scale ChIP-seq … and almost all publicly available ChIP-seq data (consisting of 13,558 …

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

G Lomberk, Y Blum, R Nicolle, A Nair… - Nature …, 2018 - nature.com
… ), and DNA methylation to define epigenomic landscapes for … that the distinct epigenomic
landscapes are regulated by … new insight into the epigenetic landscapes associated with the …

[HTML][HTML] Comprehensive characterization of the epigenetic landscape in multiple myeloma

E Alaterre, S Ovejero, L Herviou, H de Boussac… - Theranostics, 2022 - ncbi.nlm.nih.gov
… A comprehensive characterization of the epigenetic landscape of HMCLs would … epigenetic
landscape of HMCLs. We generated chromatin immunoprecipitation sequencing (ChIP-seq) …

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

A Griffon, Q Barbier, J Dalino, J van Helden… - Nucleic acids …, 2015 - academic.oup.com
… The large collections of ChIP-seq data rapidly accumulating … fully apprehended by integrating
public ChIP-seq data sets and … and retained 395 available ChIP-seq data sets merged with …

Epigenetic landscape during coronavirus infection

A Schäfer, RS Baric - Pathogens, 2017 - mdpi.com
… regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus
infections as a model. By combining measures of epigenome reorganization with RNA and …

Epigenetic landscape reveals MECOM as an endothelial lineage regulator

J Lv, S Meng, Q Gu, R Zheng, X Gao, J Kim… - Nature …, 2023 - nature.com
… To systematically investigate the epigenetic landscapes of ECs, we … ChIP-Seq data of 11
distinct histone modifications, DNase-Seq data that indicate chromatin openness, and ChIP-Seq

Identifying dispersed epigenomic domains from ChIP-Seq data

Q Song, AD Smith - Bioinformatics, 2011 - academic.oup.com
… like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, …
Results: We present the RSEG method for identifying epigenomic domains from ChIP-Seq data …