AIMC Topic: Phylogeny

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EvoRator: Prediction of Residue-level Evolutionary Rates from Protein Structures Using Machine Learning.

Journal of molecular biology Mar 11, 2022
Measuring evolutionary rates at the residue level is indispensable for gaining structural and functional insights into proteins. State-of-the-art tools for estimating rates take as input a large set of homologous proteins, a probabilistic model of ev...
Machine Learning Software Algorithms Humans Protein Conformation Sequence Alignment Internet Use Phylogeny Proteins
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Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN.

Scientific reports Feb 14, 2022
Effective and timely antibiotic treatment depends on accurate and rapid in silico antimicrobial-resistant (AMR) predictions. Existing statistical rule-based Mycobacterium tuberculosis (MTB) drug resistance prediction methods using bacterial genomic s...
Phenotype Prognosis Phylogeny Humans Genome, Bacterial Antitubercular Agents Tuberculosis, Multidrug-Resistant Mycobacterium tuberculosis Data Accuracy Whole Genome Sequencing Deep Learning Cohort Studies Mutation Microbial Sensitivity Tests Drug Resistance, Multiple, Bacterial
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NIFtHool: an informatics program for identification of NifH proteins using deep neural networks.

F1000Research Feb 9, 2022
Atmospheric nitrogen fixation carried out by microorganisms has environmental and industrial importance, related to the increase of soil fertility and productivity. The present work proposes the development of a new high precision system that allows ...
Phylogeny Bacteria Informatics Neural Networks, Computer Oxidoreductases Bacterial Proteins
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Machine learning accurately predicts the multivariate performance phenotype from morphology in lizards.

PloS one Jan 21, 2022
Completing the genotype-to-phenotype map requires rigorous measurement of the entire multivariate organismal phenotype. However, phenotyping on a large scale is not feasible for many kinds of traits, resulting in missing data that can also cause prob...
Multivariate Analysis Lizards Animals Phylogeny Machine Learning Phenotype
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Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling.

Journal of computational biology : a journal of computational molecular cell biology Jan 5, 2022
Deep neural networks (DNNs) have been recently proposed for quartet tree phylogeny estimation. Here, we present a study evaluating recently trained DNNs in comparison to a collection of standard phylogeny estimation methods on a heterogeneous collect...
Databases, Genetic Evolution, Molecular Amino Acid Sequence Deep Learning Computational Biology Classification Computer Simulation Phylogeny Neural Networks, Computer
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Classification and Identification of Archaea Using Single-Cell Raman Ejection and Artificial Intelligence: Implications for Investigating Uncultivated Microorganisms.

Analytical chemistry Dec 15, 2021
Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing c...
Artificial Intelligence Lipids Phylogeny In Situ Hybridization, Fluorescence RNA, Ribosomal, 16S
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Employing phylogenetic tree shape statistics to resolve the underlying host population structure.

BMC bioinformatics Nov 10, 2021
BACKGROUND: Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. Determining whether a populat...
ROC Curve Support Vector Machine Machine Learning Algorithms Phylogeny
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Co-evolution based machine-learning for predicting functional interactions between human genes.

Nature communications Nov 9, 2021
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary question...
Phylogeny Sequence Analysis, DNA DNA Repair Evolution, Molecular Humans Machine Learning
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Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system.

Molecular ecology resources Oct 31, 2021
Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and de...
Bayes Theorem Species Specificity Biological Evolution Phylogeny Deep Learning Gene Flow Cactaceae
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Machine Learning Data Augmentation as a Tool to Enhance Quantitative Composition-Activity Relationships of Complex Mixtures. A New Application to Dissect the Role of Main Chemical Components in Bioactive Essential Oils.

Molecules (Basel, Switzerland) Oct 17, 2021
Scientific investigation on essential oils composition and the related biological profile are continuously growing. Nevertheless, only a few studies have been performed on the relationships between chemical composition and biological data. Herein, th...
Structure-Activity Relationship Data Collection Phylogeny Microsporum Machine Learning Oils, Volatile Complex Mixtures Arthrodermataceae Anti-Infective Agents
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