AIMC Topic: Phylogeny

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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 ...
Sequence Alignment Neural Networks, Computer Machine Learning Models, Genetic Phylogeny Evolution, Molecular Likelihood Functions
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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...
Machine Learning Algorithms Phylogeny Neural Networks, Computer Evolution, Molecular Deep Learning Likelihood Functions Computational Biology Sequence Alignment Models, Genetic
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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...
Algorithms Phylogeny Models, Genetic Machine Learning Hybridization, Genetic
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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...
Deep Learning Genomics Polymorphism, Single Nucleotide Animals Phylogeny Ants Chickens Genetics, Population Bees
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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...
Gene Dosage Phylogeny Deep Learning Computational Biology RNA, Ribosomal, 16S Microbiota Neural Networks, Computer Algorithms
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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 Seawater Salinity DNA, Bacterial RNA, Ribosomal, 16S Sequence Analysis, DNA Supervised Machine Learning Microbiota Biodiversity Phylogeny India Bacteria
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Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08.

Environmental research Apr 18, 2024
Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sedi...
Streptomyces Artificial Intelligence Algeria RNA, Ribosomal, 16S Phylogeny Indoleacetic Acids
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Phylogenetic and Molecular Characteristics of Wild Bird-Origin Avian Influenza Viruses Circulating in Poland in 2018-2022: Reassortment, Multiple Introductions, and Wild Bird-Poultry Epidemiological Links.

Transboundary and emerging diseases Apr 12, 2024
Since 2020, a significant increase in the severity of H5N highly pathogenic avian influenza (HPAI) epidemics in poultry and wild birds has been observed in Poland. To further investigate the genetic diversity of HPAI H5N viruses of clade 2.3.4.4b, HP...
Poland Phylogeny Influenza A virus Reassortant Viruses Birds Animals Poultry Diseases Animals, Wild Influenza in Birds Poultry
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DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.

PLoS computational biology Apr 10, 2024
In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in opti...
Florida HIV Infections Computational Biology Epidemics Phylogeny Deep Learning Humans Algorithms Software Computer Simulation Disease Outbreaks
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Genomic language model predicts protein co-regulation and function.

Nature communications Apr 3, 2024
Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function par...
Machine Learning Semantics Operon Phylogeny Proteins Metagenomics
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