A review of Ribosome profiling and tools used in Ribo-seq data analysis [PDF]
Computational and Structural Biotechnology JournalTranslational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of the methods to study translation and its regulation.
Sufang Wang
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Structured RNA Contaminants in Bacterial Ribo-Seq [PDF]
MSphere, 2020 Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes.
Ami Bhatt
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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 +2 more
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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.
José Alonso +2 more
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Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases [PDF]
Cells, 2022 RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases.
Atefeh Bagheri +3 more
doaj +2 more sources
Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq [PDF]
STAR Protocols, 2023 Summary: Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the “translational fitness” of a given mRNA in response to environmental or developmental cues with high resolution.
Isabel Cristina Vélez-Bermúdez +4 more
doaj +2 more sources
RiboPlotR: a visualization tool for periodic Ribo-seq reads [PDF]
Plant Methods, 2021 Background Ribo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time.
Hsin-Yen Larry Wu, Polly Yingshan Hsu
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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 +3 more
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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.
Angelo Valleriani +2 more
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Ribo-Seq and RNA-Seq of TMA46 (DFRP1) and GIR2 (DFRP2) knockout yeast strains [version 1; peer review: 3 approved] [PDF]
F1000Research, 2021 In eukaryotes, stalled and collided ribosomes are recognized by several conserved multicomponent systems, which either block protein synthesis in situ and resolve the collision locally, or trigger a general stress response. Yeast ribosome-binding GTPases
Alexander I. Alexandrov +9 more
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