Results 41 to 50 of about 928,240 (334)

CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis. [PDF]

PLoS ONE, 2014
Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. ChIP-Seq technology offers many advantages over ChIP-chip arrays, including but not limited to less noise, higher resolution, and more ...
Iman Rezaeian, Luis Rueda
doaj   +1 more source

Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique

Frontiers in Cellular and Infection Microbiology, 2023
IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion.
Ronald J. Nowling, Kimani Njoya, John G. Peters, Michelle M. Riehle   +3 more
doaj   +1 more source

Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis. [PDF]

, 2018
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been widely used to discover
Chen, Chen, Chen, Huhui, Chen, Xuemei, Cui, Yuhai, Li, Chenlong, Wang, Suikang   +5 more
core   +2 more sources

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Nucleic Acids Res., 2017
We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors.
I. Kulakovskiy, I. Vorontsov, I. Yevshin, R. Sharipov, A. D. Fedorova, Eugene I. Rumynskiy, Y. Medvedeva, A. Magana-Mora, V. Bajic, Dmitri A. Papatsenko, F. Kolpakov, V. Makeev   +11 more
semanticscholar   +1 more source

Low-Cell-Number Epigenome Profiling Aids the Study of Lens Aging and Hematopoiesis

Cell Reports, 2015
Understanding how chromatin modification regulates development and disease can be limited by available material. Despite recent progress, balancing high-quality and reliable mapping using chromatin-immunoprecipitation-based deep sequencing (ChIP-seq ...
Xiaobin Zheng, Sibiao Yue, Haiyang Chen, Blake Weber, Junling Jia, Yixian Zheng   +5 more
doaj   +1 more source

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse [PDF]

, 2014
Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication.
Huang, Jinyan, Liu, Jing, Liu, X. Shirley, Mei, Shenglin, Qin, Qian, Sun, Hanfei, Wang, Juan, Wang, Qian, Wang, Qixuan, Yang, Xiaoqin, Zhang, Yong, Zhao, Chengchen   +11 more
core   +1 more source

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

Nucleic Acids Res., 2018
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230
C. Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang   +8 more
semanticscholar   +1 more source

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond [PDF]

, 2014
Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc.
Lu, Tao, Mundade, Rasika, Ozer, Hatice Gulcin, Prabhu, Lakshmi, Wei, Han   +4 more
core   +1 more source

MAnorm2 for quantitatively comparing groups of ChIP-seq samples

bioRxiv, 2020
Eukaryotic gene transcription is regulated by a large cohort of chromatin associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2,
Shiqi Tu, Mushan Li, Fengxiang Tan, Haojie Chen, Jian Xu, D. Waxman, Yijing Zhang, Zhen Shao   +7 more
semanticscholar   +1 more source

PeakPass: Automating ChIP-Seq Blacklist Creation [PDF]

Journal of Computational Biology, 2019
ChIP-Seq blacklists contain genomic regions that frequently produce artifacts and noise in ChIP-Seq experiments. To improve signal-to-noise ratio, ChIP-Seq pipelines often remove data points that map to blacklist regions. Existing blacklists have been compiled in a manual or semiautomated way.
Charles E, Wimberley, Steffen, Heber
openaire   +2 more sources