ArticleScientific reports2019
Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 2026Article
- Mechanism of RACK1-dependent ZAKα activation at stalled and collided ribosomes.Molecular cell · 2026Article
- seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.bioRxiv : the preprint server for biology · 2026Article
- ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data.bioRxiv : the preprint server for biology · 2025Article
- Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton.Journal of advanced research · 2024Article
- Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.Wellcome open research · 2024Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Implications of tRNA abundance on translation elongation across bovine tissues.Frontiers in genetics · 2023Article
- A critical period of translational control during brain development at codon resolution.Nature structural & molecular biology · 2022Article
- Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes.Computational and structural biotechnology journal · 2022Article
- Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force.Biochemistry · 2021Article
- ORFik: a comprehensive R toolkit for the analysis of translation.BMC bioinformatics · 2021Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- Selection of Cashmere Fineness Functional Genes by Translatomics.Frontiers in genetics · 2021Article
- Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
- Inferring efficiency of translation initiation and elongation from ribosome profiling.Nucleic acids research · 2020Article
- A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.PLoS computational biology · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Identifying the A- and P-site locations on ribosome-protected mRNA fragments from Ribo-Seq experiments is a fundamental step in the quantitative analysis of transcriptome-wide translation properties at the codon level. Many analyses of Ribo-Seq data have utilized heuristic approaches applied to a narrow range of fragment sizes to identify the A-site. In this study, we use Integer Programming to identify the A-site by maximizing an objective function that reflects the fact that the ribosome's A-site on ribosome-protected fragments must reside between the second and stop codons of an mRNA. This identifies the A-site location as a function of the fragment's size and its 5' end reading frame in Ribo-Seq data generated from S. cerevisiae and mouse embryonic stem cells. The correctness of the identified A-site locations is demonstrated by showing that this method, as compared to others, yields the largest ribosome density at established stalling sites. By providing greater accuracy and utilization of a wider range of fragment sizes, our approach increases the signal-to-noise ratio of underlying biological signals associated with translation elongation at the codon length scale.
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