AIMC Topic: Evolution, Molecular
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Evolution of gene regulatory networks in insects.
Current opinion in insect science
Jun 1, 2025
Changes in gene regulatory networks (GRNs) underlying the evolution of traits have been intensively studied, with insects providing excellent model cases. In studies using Drosophila, butterflies, and other insects, several well-known cases have show...
Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.
Genome biology and evolution
May 30, 2025
Plant DNA methylation changes occur hundreds to thousands of times faster than DNA mutations and can be transmitted transgenerationally, making them useful for studying population-scale patterns in clonal or selfing species. However, a state-of-the-a...
EVOLVE: A Web Platform for AI-Based Protein Mutation Prediction and Evolutionary Phase Exploration.
Journal of chemical information and modeling
May 12, 2025
While predicting structure-function relationships from sequence data is fundamental in biophysical chemistry, identifying prospective single-point and collective mutation sites in proteins can help us stay ahead in understanding their potential effec...
Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks.
Molecular biology and evolution
Apr 1, 2025
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their us...
Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.
Nucleic acids research
Feb 8, 2025
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been sele...
An efficient deep learning method for amino acid substitution model selection.
Journal of evolutionary biology
Jan 3, 2025
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...
Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.
Nucleic acids research
Nov 27, 2024
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced D...
Do protein language models learn phylogeny?
Briefings in bioinformatics
Nov 22, 2024
Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the ca...
CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution.
Briefings in bioinformatics
Jul 25, 2024
Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine lear...
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