Results 21 to 30 of about 69,491 (204)

Functional Screenings Identify Regulatory Variants Associated with Breast Cancer Susceptibility

Current Issues in Molecular Biology, 2021
Genome-wide association studies (GWAS) have identified more than 2000 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility, most of which are located in the non-coding region.
Naixia Ren, Yingying Li, Yulong Xiong, Panfeng Li, Yutian Ren, Qilai Huang   +5 more
doaj   +1 more source

Universal count correction for high-throughput sequencing.

PLoS Computational Biology, 2014
We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions.
Tatsunori B Hashimoto, Matthew D Edwards, David K Gifford   +2 more
doaj   +1 more source

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

PLoS Computational Biology, 2023
Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular ...
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi   +14 more
doaj   +1 more source

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. [PDF]

PLoS Computational Biology, 2015
Genome-wide maps of transcription factor (TF) occupancy and regions of open chromatin implicitly contain DNA sequence signals for multiple factors. We present SeqGL, a novel de novo motif discovery algorithm to identify multiple TF sequence signals from ...
Manu Setty, Christina S Leslie
doaj   +1 more source

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

Molecular Biomedicine, 2020
Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high ...
Shaoqian Ma, Yongyou Zhang
doaj   +1 more source

NicE-seq: high resolution open chromatin profiling

Genome Biology, 2017
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking
V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf, Sriharsa Pradhan   +7 more
doaj   +1 more source

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction

BMC Bioinformatics, 2017
Background Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs.
Carlos Guzman, Iván D’Orso
doaj   +1 more source

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference

BMC Genomics, 2018
Background Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution.
Thomas J. F. Pranzatelli, Drew G. Michael, John A. Chiorini   +2 more
doaj   +1 more source

IGN: Invariable gene set-based normalization for chromatin accessibility profile data analysis

Computational and Structural Biotechnology Journal
Chromatin accessibility profiles generated using ATAC-seq or DNase-seq carry functional information of the regulatory genome that controls gene expression.
Shengen Shawn Hu, Hai-Hui Xue, Chongzhi Zang   +2 more
doaj   +1 more source

REPIC: a database for exploring the N 6-methyladenosine methylome

Genome Biology, 2020
The REPIC (RNA E PItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples of 49 studies, covering 61 cell lines or
Shun Liu, Allen Zhu, Chuan He, Mengjie Chen   +3 more
doaj   +1 more source