ArticleMethods in molecular biology (Clifton, N.J.)2022
Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- Analysis of stress-induced small proteins inScience signaling · 2025Article
- Analysis of stress-induced small proteins inbioRxiv : the preprint server for biology · 2025Article
- Article
- Translation initiation factor eIF1.2 promotes Toxoplasma stage conversion by regulating levels of key differentiation factors.Nature communications · 2024Article
- Intestinal transit-amplifying cells require METTL3 for growth factor signaling and cell survival.JCI insight · 2023Article
- Recent Advances in Our Molecular and Mechanistic Understanding of Misfolded Cellular Proteins in Alzheimer's Disease (AD) and Prion Disease (PrD).Biomolecules · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The emergence of ribosome profiling as a tool for measuring the translatome has provided researchers with valuable insights into the post-transcriptional regulation of gene expression. Despite the biological insights and technical improvements made since the technique was initially described by Ingolia et al. (Science 324(5924):218-223, 2009), ribosome profiling measurements and subsequent data analysis remain challenging. Here, we describe our lab's protocol for performing ribosome profiling in bacteria, yeast, and mammalian cells. This protocol has integrated elements from three published ribosome profiling methods. In addition, we describe a tool called RiboViz (Carja et al., BMC Bioinformatics 18:461, 2017) ( https://github.com/riboviz/riboviz ) for the analysis and visualization of ribosome profiling data. Given raw sequencing reads and transcriptome information (e.g., FASTA, GFF) for a species, RiboViz performs the necessary pre-processing and mapping of the raw sequencing reads. RiboViz also provides the user with various quality control visualizations.
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Registered trials
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