AIMC Topic: Evolution, Molecular

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Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles.

Computational and mathematical methods in medicine Aug 7, 2021
Antioxidant proteins (AOPs) play important roles in the management and prevention of several human diseases due to their ability to neutralize excess free radicals. However, the identification of AOPs by using wet-lab experimental techniques is often...
Proteins Databases, Protein Amino Acids Computational Biology Markov Chains Antioxidants Peroxiredoxins Evolution, Molecular Humans Machine Learning Algorithms
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Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.

Scientific reports Jun 16, 2021
Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection ...
Humans Machine Learning Algorithms Alleles Streptococcal Infections Genetic Variation Streptococcus pyogenes Carrier Proteins Evolution, Molecular Bacterial Proteins Genome, Bacterial Regulon Genes, Bacterial Bacterial Outer Membrane Proteins Antigens, Bacterial
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Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.

Nature communications Jun 10, 2021
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere...
Pedigree Meiosis Computer Simulation Machine Learning Models, Genetic Phylogeny Eukaryota Evolution, Molecular Genome-Wide Association Study Genome Genomics Retroelements Genetic Variation Polymorphism, Single Nucleotide INDEL Mutation Crossing Over, Genetic Polymorphism, Genetic Chromosomes Genes, Duplicate Ascomycota Arabidopsis Sequence Inversion
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Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction.

International journal of molecular sciences Jun 2, 2021
The new advances in deep learning methods have influenced many aspects of scientific research, including the study of the protein system. The prediction of proteins' 3D structural components is now heavily dependent on machine learning techniques tha...
Amino Acid Sequence Protein Conformation Sequence Alignment Neural Networks, Computer Machine Learning Software Evolution, Molecular Databases, Protein Deep Learning Computational Biology Humans
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Detecting adaptive introgression in human evolution using convolutional neural networks.

eLife May 25, 2021
Studies in a variety of species have shown evidence for positively selected variants introduced into a population via introgression from another, distantly related population-a process known as adaptive introgression. However, there are few explicit ...
Mutation Gene Frequency Neural Networks, Computer Genotype Evolution, Molecular Humans
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Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning.

International journal of molecular sciences May 11, 2021
Experimental studies of and have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are esse...
Genes, Essential Drosophila Proteins Drosophila melanogaster Caenorhabditis elegans Proteins Gene Ontology Caenorhabditis elegans Machine Learning Animals Genomics Evolution, Molecular
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Automatic Search-and-Replace From Examples With Coevolutionary Genetic Programming.

IEEE transactions on cybernetics Apr 15, 2021
We describe the design and implementation of a system for executing search-and-replace text processing tasks automatically, based only on examples of the desired behavior. The examples consist of pairs describing the original string and the desired m...
Software Algorithms Machine Learning Models, Genetic Evolution, Molecular Data Mining
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On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't.

Genes Apr 5, 2021
In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transfor...
Selection, Genetic Adaptation, Physiological Genetics, Population Genetic Drift Algorithms Evolution, Molecular Humans Genome, Human Artificial Intelligence Machine Learning
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Harnessing machine learning to guide phylogenetic-tree search algorithms.

Nature communications Mar 31, 2021
Inferring a phylogenetic tree is a fundamental challenge in evolutionary studies. Current paradigms for phylogenetic tree reconstruction rely on performing costly likelihood optimizations. With the aim of making tree inference feasible for problems i...
Models, Genetic Humans Databases, Genetic Machine Learning Evolution, Molecular Databases, Protein Algorithms Animals Phylogeny
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Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches.

Scientific reports Mar 25, 2021
The problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were ...
Evolution, Molecular Proteins Sequence Alignment Biological Coevolution Machine Learning Models, Genetic
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