ArticleNucleic acids research2016
Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Combined statistical-biophysical modeling links ion channel genes to physiology of cortical neuron types.Patterns (New York, N.Y.) · 2025Article
- Negative feedback and oscillations in a model for mRNA translation.Journal of the Royal Society, Interface · 2025Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Translation in the cell under fierce competition for shared resources: a mathematical model.Journal of the Royal Society, Interface · 2022Article
- Model of Processive Catalysis with Site Clustering and Blocking and Its Application to Cellulose Hydrolysis.The journal of physical chemistry. B · 2022Article
- Translational buffering by ribosome stalling in upstream open reading frames.PLoS genetics · 2022Article
- Article
- Review: Emerging roles of the signaling network of the protein kinase GCN2 in the plant stress response.Plant science : an international journal of experimental plant biology · 2022Review
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
- Article
- Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware.ACS synthetic biology · 2021Article
- EGGTART: A tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP.Biophysical journal · 2021Article
- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Article
- A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs.Biology · 2021Article
- Inferring efficiency of translation initiation and elongation from ribosome profiling.Nucleic acids research · 2020Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field.
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