ArticlePLoS computational biology2011
Genome-scale analysis of translation elongation with a ribosome flow model.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed, 203 citations in OpenAlex.
- Article
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- Negative feedback and oscillations in a model for mRNA translation.Journal of the Royal Society, Interface · 2025Article
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- Codon usage modulates the relationship between the burden and yield of protein overexpression.Journal of biological engineering · 2025Article
- A data-driven estimation of the ribosome drop-off rate inNAR genomics and bioinformatics · 2024Article
- A mathematical framework for analysing particle flow in a network with multiple pools.Royal Society open science · 2024Article
- Specific codons control cellular resources and fitness.Science advances · 2024Article
- Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells.Nucleic acids research · 2023Article
- Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.PLoS computational biology · 2023Article
- eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content.The EMBO journal · 2023Article
- On the gain of entrainment in theJournal of the Royal Society, Interface · 2023Article
- Persistence and stability of generalized ribosome flow models with time-varying transition rates.PloS one · 2023Article
- Translation in the cell under fierce competition for shared resources: a mathematical model.Journal of the Royal Society, Interface · 2022Article
- A theoretical framework to analyse the flow of particles in a dynamical system with stochastic transition rates and site capacities.Royal Society open science · 2022Article
- The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation.RNA (New York, N.Y.) · 2022Article
- Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes.Journal of the Royal Society, Interface · 2022Article
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
- Article
- Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance levels, ribosomal densities and the relation between all these variables, better than alternative ('non-physical') approaches. In addition, we show that the RFM can be used for accurate inference of various other quantities including genes' initiation rates and translation costs. These quantities could not be inferred by previous predictors. We find that increasing the number of available ribosomes (or equivalently the initiation rate) increases the genomic translation rate and the mean ribosome density only up to a certain point, beyond which both saturate. Strikingly, assuming that the translation system is tuned to work at the pre-saturation point maximizes the predictive power of the model with respect to experimental data. This result suggests that in all organisms that were analyzed (from bacteria to Human), the global initiation rate is optimized to attain the pre-saturation point. The fact that similar results were not observed for heterologous genes indicates that this feature is under selection. Remarkably, the gap between the performance of the RFM and alternative predictors is strikingly large in the case of heterologous genes, testifying to the model's promising biotechnological value in predicting the abundance of heterologous proteins before expressing them in the desired host.
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