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Andres M. Alonso

dblp:311/1644 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2023
0000-0002-2896-7147ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › molecular evolution
codon usage bias
0.712023
Dicodon-based measures for modeling gene expression · Bioinform. 2023
Bioinformatics and computational biology
gene expression
0.712023
Dicodon-based measures for modeling gene expression · Bioinform. 2023
Bioinformatics and computational biology
translation efficiency
0.712023
Dicodon-based measures for modeling gene expression · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

weighting strategy · 0.7correlation analysis · 0.7
YearPublicationVenuePosition
2023 Dicodon-based measures for modeling gene expression
abstract
MOTIVATION: Codon usage preference patterns have been associated with modulation of translation efficiency, protein folding, and mRNA decay. However, new studies support that codon pair usage has also a remarkable effect at the gene expression level. Here, we expand the concept of CAI to answer if codon pair usage patterns can be understood in terms of codon usage bias, or if they offer new information regarding coding translation efficiency. RESULTS: Through the implementation of a weighting strategy to consider the dicodon contributions, we observe that the dicodon-based measure has greater correlations with gene expression level than CAI. Interestingly, we have noted that dicodons associated with a low value of adaptiveness are related to dicodons which mediate strong translational inhibition in yeast. We have also noticed that some codon-pairs have a smaller dicodon contribution than estimated by the product of the respective codon contributions. AVAILABILITY AND IMPLEMENTATION: Scripts, implemented in Python, are freely available for download at https://zenodo.org/record/7738276#.ZBIDBtLMIdU.
Andres M. Alonso, Luis Diambra
Bioinform.1