AIMC Topic: Evolution, Molecular
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Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.
PLoS computational biology
Mar 22, 2021
Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally ch...
Artificial intelligence in health data analysis: The Darwinian evolution theory suggests an extremely simple and zero-cost large-scale screening tool for prediabetes and type 2 diabetes.
Diabetes research and clinical practice
Feb 27, 2021
AIMS: The effective identification of individuals with early dysglycemia status is key to reduce the incidence of type 2 diabetes. We develop and validate a novel zero-cost tool that significantly simplifies the screening of undiagnosed dysglycemia.
An Elite Gene Guided Reproduction Operator for Many-Objective Optimization.
IEEE transactions on cybernetics
Jan 15, 2021
Traditional reproduction operators in many-objective evolutionary algorithms (MaOEAs) seem to not be so effective to tackle many-objective optimization problems (MaOPs). This is mainly because the population size cannot be set to an arbitrarily large...
Evolution of drug resistance in HIV protease.
BMC bioinformatics
Dec 30, 2020
BACKGROUND: Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques...
Inter-protein residue covariation information unravels physically interacting protein dimers.
BMC bioinformatics
Dec 17, 2020
BACKGROUND: Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synthetic peptides with unknown in...
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.
Nature communications
Dec 1, 2020
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression leve...
Evolutionary insights into the active-site structures of the metallo-β-lactamase superfamily from a classification study with support vector machine.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry
Sep 18, 2020
The metallo-β-lactamase (MβL) superfamily, which is intriguing due to its enzyme promiscuity, is a good model enzyme superfamily for studies of catalytic function evolution. Our previous study traced the evolution of the phosphotriesterase activity o...
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Open biology
Sep 2, 2020
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionall...
A novel fusion based on the evolutionary features for protein fold recognition using support vector machines.
Scientific reports
Sep 1, 2020
Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting fe...
Genes, the brain, and artificial intelligence in evolution.
Journal of human genetics
Jul 27, 2020
Three important systems, genes, the brain, and artificial intelligence (especially deep learning) have similar goals, namely, the maximization of likelihood or minimization of cross-entropy. Animal brains have evolved through predator-prey interactio...
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