RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing [version 1; referees: 2 approved] [PDF]
F1000Research, 2016 The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential.
Alexandra Popa +6 more
doaj +5 more sources
Normalized Ribo-Seq for Quantifying Absolute Global and Specific Changes in Translation [PDF]
Bio-Protocol, 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 ...
Katharina Hoerth +2 more
doaj +4 more sources
DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data [PDF]
BMC Bioinformatics, 2019 Background Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mapped reads to similar isoforms ...
Hongfei Cui +3 more
doaj +5 more sources
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data [PDF]
BMC Genomics, 2019 Background 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.
Patrick Perkins +4 more
doaj +5 more sources
Ribo-seq and RNA-seq analyses enrich the regulatory network of tomato fruit cracking [PDF]
BMC Plant Biology, 2023 Tomato (Solanum lycopersicum L.), one of the most widely grown vegetable crops in the world, faces cracking problems before and after harvest. Fruit cracking reduces the commercial value and seriously affects the economic performance of the fruits by ...
Zhaojiang Zhong +7 more
doaj +5 more sources
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
exaly +5 more sources
Improved Ribo-seq enables identification of cryptic translation events [PDF]
Nature Methods, 2018 Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation ...
Florian Erhard +2 more
exaly +6 more sources
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
GWIPS-viz: development of a ribo-seq genome browser [PDF]
Nucleic Acids Research, 2013 We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis ...
Baranov, Pavel V. +9 more
core +8 more sources
Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes [PDF]
Computational and Structural Biotechnology Journal, 2022 Glucocorticoids such as dexamethasone (Dex) are widely used to treat both acute and chronic inflammatory conditions. They regulate immune responses by dampening cell-mediated immunity in a glucocorticoid receptor (GR)-dependent manner, by suppressing the
Suhail A. Ansari +7 more
doaj +2 more sources