Results 11 to 20 of about 69,491 (204)

Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data

Frontiers in Genetics, 2012
Pedro Madrigal, Paweł Krajewski, Krajewski Paweł   +2 more
exaly   +3 more sources

Correction: A Comparison of Peak Callers Used for DNase-Seq Data [PDF]

PLoS ONE, 2014
doaj   +4 more sources

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. [PDF]

PLoS ONE, 2015
Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue ...
Anil Raj, Heejung Shim, Yoav Gilad, Jonathan K Pritchard, Matthew Stephens   +4 more
doaj   +1 more source

Differential chromatin profiles partially determine transcription factor binding. [PDF]

PLoS ONE, 2017
We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts condition specific factor binding more accurately than other methods based on DNase-seq data ...
Rujian Chen, David K Gifford
doaj   +1 more source

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Genome Biology, 2020
Background Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases.
Hainan Zhao, Wenli Zhang, Tao Zhang, Yuan Lin, Yaodong Hu, Chao Fang, Jiming Jiang   +6 more
doaj   +1 more source

DNase-capture reveals differential transcription factor binding modalities. [PDF]

PLoS ONE, 2017
We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions.
Daniel Kang, Richard Sherwood, Amira Barkal, Tatsunori Hashimoto, Logan Engstrom, David Gifford   +5 more
doaj   +1 more source

Integrated bioinformatics analysis of the transcription factor-mediated gene regulatory networks in the formation of spermatogonial stem cells

Frontiers in Physiology, 2022
Background:In vitro induction of spermatogonial stem cells (SSCs) from embryonic stem cells (ESCs) provides a promising tool for the treatment of male infertility.
Kesong Shi, Baoluri Wang, Le Dou, Shu Wang, Xinrui Fu, Haiquan Yu   +5 more
doaj   +1 more source

Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana [PDF]

Plant Methods, 2015
Sergei A Filichkin, Molly Megraw
exaly   +2 more sources

Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis-regulation in human and mouse

Molecular Therapy: Nucleic Acids, 2023
Cis-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network.
Chao Song, Yuexin Zhang, Hong Huang, Yuezhu Wang, Xilong Zhao, Guorui Zhang, Mingxue Yin, Chenchen Feng, Qiuyu Wang, Fengcui Qian, Desi Shang, Jian Zhang, Jiaqi Liu, Chunquan Li, Huifang Tang   +14 more
doaj   +1 more source

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA

Nature Communications, 2022
Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites.
Shengen Shawn Hu, Lin Liu, Qi Li, Wenjing Ma, Michael J. Guertin, Clifford A. Meyer, Ke Deng, Tingting Zhang, Chongzhi Zang   +8 more
doaj   +1 more source