Ribo-seq enlightens codon usage bias. [PDF]
DNA Res, 2017 Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of
Paulet D, David A, Rivals E.
europepmc +6 more sources
A Neural Network Approach for the Analysis of Reproducible Ribo–Seq Profiles
Algorithms, 2022 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 to obtain profiles that reflect the time spent by ribosomes in translating each part of an open reading frame ...
Caterina Graziani +2 more
exaly +10 more sources
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. [PDF]
F1000Res, 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.
Popa A +6 more
europepmc +6 more sources
Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture [PDF]
Plant Methods, 2021 Background: Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational ...
Amir Mahboubi +2 more
exaly +5 more sources
Ribo-ODDR : oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq [PDF]
Bioinformatics, 2021 MotivationRibosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution.
Ferhat Alkan +2 more
exaly +3 more sources
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq [PDF]
Briefings in BioinformaticsAccurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease.
Nasun Hah +2 more
exaly +4 more sources
Ribo-seq and RNA-seq analyses enrich the regulatory network of tomato fruit cracking. [PDF]
BMC Plant Biol, 2023 Abstract Tomato (Solanum lycopersicum), 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 through affecting the appearance and quality of the fruit.
Zhong Z +7 more
europepmc +5 more sources
How tailored Ribo-seq methods probe unique translation events. [PDF]
RNARibosome profiling (Ribo-seq) is a next-generation, high-resolution sequencing technique that captures ribosome-protected mRNA fragments to map ribosome positions across the transcriptome. This method serves as a powerful proxy for global translational activity by revealing where ribosomes engage with mRNAs. Recent advances have expanded the utility of
Marks J, Meydan S.
europepmc +3 more sources
InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data. [PDF]
Bioinform AdvAbstract Motivation The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our understanding of what parts of the transcriptome are translated. Many alternative open reading frames (ORFs) are now regularly being detected
Ward EL +4 more
europepmc +4 more sources
Improved Ribo-seq enables identification of cryptic translation events. [PDF]
Nat 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 ...
Erhard F +8 more
europepmc +5 more sources