A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-2297-1_6
Abstract: Protein production from mRNA is one of the fundamental molecular processes in a cell. Accurate genome-wide information on the levels of translation and ribosome distribution on mRNA can be gathered by carrying out ribosome footprinting,… read more here.
Keywords: translational regulation; ribo seq; genome wide; seq method ... See more keywords
Improved Ribo-seq enables identification of cryptic translation events
Sign Up to like & getrecommendations! Published in 2018 at "Nature methods"
DOI: 10.1038/nmeth.4631
Abstract: 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… read more here.
Keywords: improved ribo; enables identification; seq enables; translation ... See more keywords
RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa1049
Abstract: 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… read more here.
Keywords: pattern; ribo seq; analysis ribo; ribo ... See more keywords
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa395
Abstract: Abstract Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation; ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under various physiological… read more here.
Keywords: ribosome profiling; analysis; seq data; mrna translation ... See more keywords
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkab323
Abstract: Abstract Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified… read more here.
Keywords: seq; ribosome profiling; analysis; trips viz ... See more keywords
A Neural Network Approach for the Analysis of Reproducible Ribo-Seq Profiles
Sign Up to like & getrecommendations! Published in 2022 at "Algorithms"
DOI: 10.3390/a15080274
Abstract: In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for globally monitoring the translation process in vivo at single nucleotide resolution. Based on deep sequencing of mRNA fragments, Ribo–seq allows… read more here.
Keywords: seq profiles; neural network; ribo; reproducible ribo ... See more keywords