Results 31 to 40 of about 16,252 (205)
Ribocutter: Cas9-mediated rRNA depletion from multiplexed Ribo-seq libraries [PDF]
, 2021 AbstractRNA sequencing libraries produced from fragmented RNA, especially Ribo-seq libraries, contain high proportions of reads from abundant non-coding RNAs. Here, we describe a streamlined Cas9-based protocol for removing abundant rRNA/ncRNA contaminants from Ribo-seq (or other small RNA-seq) libraries and an easy-to-use software tool, ribocutter ...
Oscar G. Wilkins, Jernej Ule
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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.
Giorgia Giacomini +8 more
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Variational inference for detecting differential translation in ribosome profiling studies
Frontiers in Genetics, 2023 Translational efficiency change is an important mechanism for regulating protein synthesis. Experiments with paired ribosome profiling (Ribo-seq) and mRNA-sequencing (RNA-seq) allow the study of translational efficiency by simultaneously quantifying the ...
David C. Walker +5 more
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Repurposing Ribo-Seq to provide insights into structured RNAs [PDF]
, 2020 AbstractRibosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, this method can enrich RNAs that are not bound by ribosomes, but rather, are protected from degradation in another way. For example, Escherichia coli Ribo-Seq libraries also capture reads from most non-coding RNAs (ncRNAs).
Brayon J. Fremin, Ami S. Bhatt
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A custom library construction method for super-resolution ribosome profiling in Arabidopsis
Plant Methods, 2022 Background Ribosome profiling, also known as Ribo-seq, is a powerful technique to study genome-wide mRNA translation. It reveals the precise positions and quantification of ribosomes on mRNAs through deep sequencing of ribosome footprints.
Hsin-Yen Larry Wu, Polly Yingshan Hsu
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Bacterial riboproteogenomics : the era of N-terminal proteoform existence revealed [PDF]
, 2020 With the rapid increase in the number of sequenced prokaryotic genomes, relying on automated gene annotation became a necessity. Multiple lines of evidence, however, suggest that current bacterial genome annotations may contain inconsistencies and are ...
Fijalkowska, Daria +3 more
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, 2017 The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the ...
Baranov, Pavel V. +4 more
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Frontiers in Oncology, 2021 Cutaneous melanoma (CMM) is a skin tumor with a high degree of malignancy. BRAF resistance imposes great difficulty to the treatment of CMM, and partially contributes to the poor prognosis of CMM.
Tianhong Wei, Lan Li, Zhiyou He
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An update on sORFs.org : a repository of small ORFs identified by ribosome profiling [PDF]
, 2017 sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release.
Menschaert, Gerben +2 more
core +1 more source
Reliable detection of translational regulation with Ribo-seq [PDF]
, 2017 Ribosome profiling (Ribo-Seq) reveals genome-wide translation rates via the quantification of ribosome protected fragments (RPFs) of mRNAs. Several methods have recently been developed to detect differentially translated genes (DTGs) using Ribo-seq: Xtail, Ribodiff and Riborex. At their core, all of these approaches either utilize existing differential
Chothani, Sonia P +6 more
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