AIMC Topic: Phylogeny

Clear Filters Showing 11 to 20 of 212 articles

Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference.

mSphere Dec 19, 2024
The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographi...
Bacteria DNA, Bacterial RNA, Ribosomal, 16S Middle Aged Phylogeny China Microbiota Mouth Nasal Cavity Sequence Analysis, DNA Skin Hand Humans Machine Learning Female Young Adult Adult Male
View on PubMed DOI

Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistant from whole genome sequencing and gene expression.

Antimicrobial agents and chemotherapy Nov 14, 2024
Whole genome sequencing (WGS) potentially represents a rapid approach for antimicrobial resistance genotype-to-phenotype prediction. However, the challenge still exists to predict fully minimum inhibitory concentrations (MICs) and antimicrobial susce...
Acinetobacter baumannii Multilocus Sequence Typing Genome, Bacterial Genotype Whole Genome Sequencing Acinetobacter Infections Neural Networks, Computer Anti-Bacterial Agents Phenotype Phylogeny Microbial Sensitivity Tests Drug Resistance, Multiple, Bacterial Humans
View on PubMed DOI

Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia.

Molecular ecology Oct 19, 2024
Multiple-island endemics (MIE) are considered ideal natural subjects to study patterns of island colonization that involve recent population-level genetic processes. Kleinia neriifolia is a Canarian MIE widespread across the archipelago, which exhibi...
Phylogeography Genetics, Population Islands Neural Networks, Computer Phylogeny Polymorphism, Single Nucleotide Plastids
View on PubMed DOI

Deep learning to capture leaf shape in plant images: Validation by geometric morphometrics.

The Plant journal : for cell and molecular biology Oct 9, 2024
Plant leaves play a pivotal role in automated species identification using deep learning (DL). However, achieving reproducible capture of leaf variation remains challenging due to the inherent "black box" problem of DL models. To evaluate the effecti...
Deep Learning Neural Networks, Computer Image Processing, Computer-Assisted Phylogeny Plant Leaves
View on PubMed DOI

Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments.

Molecular phylogenetics and evolution Aug 30, 2024
Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the phylogenetic tree reconstruction based on the Maximum Likelihood method. In this study, we present ...
Neural Networks, Computer Evolution, Molecular Likelihood Functions Sequence Alignment Machine Learning Phylogeny Models, Genetic
View on PubMed DOI

Reliable estimation of tree branch lengths using deep neural networks.

PLoS computational biology Aug 5, 2024
A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the t...
Likelihood Functions Sequence Alignment Models, Genetic Evolution, Molecular Neural Networks, Computer Phylogeny Machine Learning Deep Learning Algorithms Computational Biology
View on PubMed DOI

Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning.

Molecular phylogenetics and evolution Jul 17, 2024
The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to...
Machine Learning Models, Genetic Algorithms Hybridization, Genetic Phylogeny
View on PubMed DOI

Tracing the genealogy origin of geographic populations based on genomic variation and deep learning.

Molecular phylogenetics and evolution Jul 2, 2024
Assigning a query individual animal or plant to its derived population is a prime task in diverse applications related to organismal genealogy. Such endeavors have conventionally relied on short DNA sequences under a phylogenetic framework. These met...
Polymorphism, Single Nucleotide Phylogeny Chickens Ants Animals Bees Deep Learning Genetics, Population Genomics
View on PubMed DOI

Deep learning for predicting 16S rRNA gene copy number.

Scientific reports Jun 20, 2024
Culture-independent 16S rRNA gene metabarcoding is a commonly used method for microbiome profiling. To achieve more quantitative cell fraction estimates, it is important to account for the 16S rRNA gene copy number (hereafter 16S GCN) of different co...
Phylogeny Deep Learning Neural Networks, Computer Computational Biology RNA, Ribosomal, 16S Algorithms Microbiota Gene Dosage
View on PubMed DOI

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.

BMC microbiology May 10, 2024
BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic acti...
Bays Sequence Analysis, DNA Biodiversity Bacteria Phylogeny Seawater Supervised Machine Learning DNA, Bacterial India Salinity Microbiota RNA, Ribosomal, 16S
View on PubMed DOI
Popular Topics
Recent Journals