[HTML][HTML] Chromatin accessibility: a window into the genome
M Tsompana, MJ Buck - Epigenetics & chromatin, 2014 - Springer
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with
disruption of nucleosome organization at promoters, enhancers, silencers, insulators and …
disruption of nucleosome organization at promoters, enhancers, silencers, insulators and …
[HTML][HTML] Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research
The advent of high throughput next generation sequencing (NGS) has accelerated the pace
of discovery of disease-associated genetic variants and genomewide profiling of expressed …
of discovery of disease-associated genetic variants and genomewide profiling of expressed …
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework
B Liu, R Long, KC Chou - Bioinformatics, 2016 - academic.oup.com
Motivation: Regulatory DNA elements are associated with DNase I hypersensitive sites
(DHSs). Accordingly, identification of DHSs will provide useful insights for in-depth …
(DHSs). Accordingly, identification of DHSs will provide useful insights for in-depth …
Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data
The expression of eukaryotic genes is regulated by cis-regulatory elements such as
promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the …
promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the …
[HTML][HTML] DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
Background Due to the complexity of the biological systems, the prediction of the potential
DNA binding sites for transcription factors remains a difficult problem in computational …
DNA binding sites for transcription factors remains a difficult problem in computational …
Bioinformatics tools for genome-wide epigenetic research
VE Angarica, A Del Sol - Neuroepigenomics in Aging and Disease, 2017 - Springer
Epigenetics play a central role in the regulation of many important cellular processes, and
dysregulations at the epigenetic level could be the source of serious pathologies, such as …
dysregulations at the epigenetic level could be the source of serious pathologies, such as …
[HTML][HTML] A comparison of peak callers used for DNase-Seq data
Genome-wide profiling of open chromatin regions using DNase I and high-throughput
sequencing (DNase-seq) is an increasingly popular approach for finding and studying …
sequencing (DNase-seq) is an increasingly popular approach for finding and studying …
Use Chou's 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting
S Zhang, T Xue - Molecular Genetics and Genomics, 2020 - Springer
DNase I hypersensitive sites (DHSs) are highly sensitive active chromatin regions to DNase
I enzymes, which provide the basis for the study of gene transcriptional regulation …
I enzymes, which provide the basis for the study of gene transcriptional regulation …
Predicting DNase I hypersensitive sites via un-biased pseudo trinucleotide composition
Abstract DNase I Hypersensitive sites (DHS) are the regions that are sensitive to cleavage
by the DNase I enzyme. Knowledge regarding these sites is helpful for decryption of the …
by the DNase I enzyme. Knowledge regarding these sites is helpful for decryption of the …
[HTML][HTML] On accounting for sequence-specific bias in genome-wide chromatin accessibility experiments: recent advances and contradictions
P Madrigal - Frontiers in bioengineering and biotechnology, 2015 - frontiersin.org
Uncovering the protein–DNA interactions involved in cell fate, development, and disease in
a time-and cell-specific manner is a fundamental goal of molecular biology. The advent of …
a time-and cell-specific manner is a fundamental goal of molecular biology. The advent of …