Results 1 to 10 of about 14,752 (86)
RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data [PDF]
Nucleic Acids Research, 2020 Abstract Ribosome profiling, also known as Ribo-seq, has become a popular approach to investigate regulatory mechanisms of translation in a wide variety of biological contexts. Ribo-seq not only provides a measurement of translation efficiency based on the relative abundance of ribosomes bound to transcripts, but also has the capacity
Ji-Ping Wang, Wang Ji-Ping
exaly +5 more sources
A review of Ribosome profiling and tools used in Ribo-seq data analysis [PDF]
Computational and Structural Biotechnology JournalTranslational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of the methods to study translation and its regulation. It is a high throughput technology based on deep sequencing, which targets ribosome protected mRNA fragments to produce a 'global snapshot' of translatome.
Sufang Wang
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Trips-Viz: a transcriptome browser for exploring Ribo-Seq data [PDF]
Nucleic Acids Research, 2019 Ribosome profiling (Ribo-Seq) is a technique that allows for the isolation and sequencing of mRNA fragments protected from nuclease digestion by actively translating ribosomes. Mapping these ribosome footprints to a genome or transcriptome generates quantitative information on translated regions.
Stephen J Kiniry +2 more
exaly +6 more sources
Accurate detection of short and long active ORFs using Ribo-seq data [PDF]
Bioinformatics, 2020 Abstract Motivation Ribo-seq, a technique for deep-sequencing ribosome-protected mRNA fragments, has enabled transcriptome-wide monitoring of translation in vivo. It has opened avenues for re-evaluating the coding potential of open reading frames (ORFs), including many short ORFs that were previously ...
Saket Choudhary +2 more
exaly +5 more sources
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data [PDF]
BMC Genomics, 2019 Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell's transcriptome. In practice, Ribo-seq data analysis can be sensitive to quality issues such as read length variation, low read periodicities, and ...
Anna N Stepanova +2 more
exaly +6 more sources
RiboPlotR: a visualization tool for periodic Ribo-seq reads. [PDF]
Plant Methods, 2021 Abstract Background: Ribo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time. While 3-nt periodicity has been widely used to study novel translation events such as upstream ORFs in 5’
Wu HL, Hsu PY.
europepmc +6 more sources
A tool for analyzing and visualizing ribo-seq data at the isoform level. [PDF]
BMC Bioinformatics, 2021 Abstract Background Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation.
Wu WS +5 more
europepmc +5 more sources
Structured RNA Contaminants in Bacterial Ribo-Seq. [PDF]
mSphere, 2020 Structured ncRNAs are pivotal mediators of bioregulation in bacteria, and their functions are often reliant on their specific structures. Here, we first inspect Ribo-Seq reads across noncoding regions, identifying contaminant reads in these libraries.
Fremin BJ, Bhatt AS.
europepmc +4 more sources
STATR: A simple analysis pipeline of Ribo-Seq in bacteria. [PDF]
J Microbiol, 2020 Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of
Choe D, Palsson B, Cho BK.
europepmc +3 more sources
Normalized Ribo-Seq for Quantifying Absolute Global and Specific Changes in Translation. [PDF]
Bio Protoc, 2022 Ribosome profiling (Ribo-Seq) is a highly sensitive method to quantify ribosome occupancies along individual mRNAs on a genome-wide scale. Hereby, ribosome-protected fragments (= footprints) are generated by nuclease digestion, isolated, and sequenced together with the corresponding randomly fragmented input samples, to determine ribosome densities (RD)
Hoerth K, Reitter S, Schott J.
europepmc +4 more sources