AIMC Topic: Codon
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Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.
Scientific reports
Apr 10, 2025
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...
CodonTransformer: a multispecies codon optimizer using context-aware neural networks.
Nature communications
Apr 3, 2025
Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized thro...
Predicting lncRNA-protein interactions using a hybrid deep learning model with dinucleotide-codon fusion feature encoding.
BMC genomics
Dec 28, 2024
Long non-coding RNAs (lncRNAs) play crucial roles in numerous biological processes and are involved in complex human diseases through interactions with proteins. Accurate identification of lncRNA-protein interactions (LPI) can help elucidate the func...
Differentially used codons among essential genes in bacteria identified by machine learning-based analysis.
Molecular genetics and genomics : MGG
Jul 27, 2024
Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-express...
Riboformer: a deep learning framework for predicting context-dependent translation dynamics.
Nature communications
Mar 5, 2024
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. How...
Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life.
Scientific reports
Feb 6, 2023
In this study, we investigate how an organism's codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits across the domains of life. We perform secondary analysis of existing genetic datasets to build severa...
Using Machine Learning for Predicting the Effect of Mutations in the Initiation Codon.
IEEE journal of biomedical and health informatics
Nov 10, 2022
The effect of mutations has been traditionally predicted by studying what may happen due to the substitution of one amino acid for another one. This approach may be effective for mutations with impact in the function of the protein, but ineffective f...
Machine learning approach identifies prominent codons from different degenerate groups influencing gene expression in bacteria.
Genes to cells : devoted to molecular & cellular mechanisms
Aug 22, 2022
Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high-expression genes (HEG) and low-expression genes (LEG) in organisms is not yet adequately reported across different bacteria. In this ...
Codon Optimization Using a Recurrent Neural Network.
Journal of computational biology : a journal of computational molecular cell biology
Jun 21, 2022
Codon optimization of a DNA sequence can significantly increase efficiency of protein expression, reducing the cost to manufacture biologic pharmaceuticals. Although directed methods based on such factors as codon usage bias and GC nucleotide content...
CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation.
PLoS computational biology
Oct 22, 2021
MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accurately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates...
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