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 +7 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
Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni [PDF]
Nature CommunicationsIn contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here,
Kathrin Froschauer +13 more
doaj +3 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 +6 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
Ribo-seq enlightens codon usage bias. [PDF]
DNA Res, 2017 International audienceCodon 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.
Paulet D, David A, Rivals E.
europepmc +6 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.
Marks J, Meydan S.
europepmc +4 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.
Joana Silva +2 more
exaly +3 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
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.
Thomas Martinez
exaly +4 more sources