AIMC Topic: Phylogeny

Clear Filters Showing 41 to 50 of 212 articles

PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences.

Journal of bioinformatics and computational biology Feb 10, 2023
This work proposes a machine learning-based phylogenetic tree generation model based on agglomerative clustering (PTGAC) that compares protein sequences considering all known chemical properties of amino acids. The proposed model can serve as a suita...
Machine Learning Phylogeny Amino Acids Cluster Analysis Amino Acid Sequence
View on PubMed DOI

Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life.

Scientific reports Feb 6, 2023
In this study, we investigate how an organism's codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits across the domains of life. We perform secondary analysis of existing genetic datasets to build severa...
Machine Learning Reproducibility of Results Nucleotides Codon Phylogeny Genomics
View on PubMed DOI

Predicting Antigenic Distance from Genetic Data for PRRSV-Type 1: Applications of Machine Learning.

Microbiology spectrum Dec 13, 2022
The control of porcine reproductive and respiratory syndrome (PRRS) remains a significant challenge due to the genetic and antigenic variability of the causative virus (PRRSV). Predominantly, PRRSV management includes using vaccines and live virus in...
Machine Learning Animals Genetic Variation Cross Reactions Swine Phylogeny Porcine respiratory and reproductive syndrome virus Cross Protection Antigenic Variation Porcine Reproductive and Respiratory Syndrome
View on PubMed DOI

The impacts of fine-tuning, phylogenetic distance, and sample size on big-data bioacoustics.

PloS one Dec 7, 2022
Vocalizations in animals, particularly birds, are critically important behaviors that influence their reproductive fitness. While recordings of bioacoustic data have been captured and stored in collections for decades, the automated extraction of dat...
Artificial Intelligence Humans Phylogeny
View on PubMed DOI

A deep learning approach to real-time HIV outbreak detection using genetic data.

PLoS computational biology Oct 14, 2022
Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylo...
Europe HIV-1 Disease Outbreaks Phylogeny Deep Learning HIV Infections Humans
View on PubMed DOI

Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data.

Journal of computational biology : a journal of computational molecular cell biology Sep 1, 2022
Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene...
Genetic Speciation Genome Computer Simulation Deep Learning Phylogeny Models, Genetic
View on PubMed DOI

The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.

Nature communications Aug 17, 2022
Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth's history, likely replacing forested habitats in the second hal...
Ecosystem Phylogeny Deep Learning Biological Evolution Bayes Theorem Fossils
View on PubMed DOI

New feature extraction from phylogenetic profiles improved the performance of pathogen-host interactions.

Frontiers in cellular and infection microbiology Aug 2, 2022
MOTIVATION: The understanding of pathogen-host interactions (PHIs) is essential and challenging research because this potentially provides the mechanism of molecular interactions between different organisms. The experimental exploration of PHI is tim...
Machine Learning Computational Biology Phylogeny Host-Pathogen Interactions
View on PubMed DOI

bHLHDB: A next generation database of basic helix loop helix transcription factors based on deep learning model.

Journal of bioinformatics and computational biology Jul 25, 2022
The basic helix loop helix (bHLH) superfamily is a large and diverse protein family that plays a role in various vital functions in nearly all animals and plants. The bHLH proteins form one of the largest families of transcription factors found in pl...
Phylogeny Deep Learning Animals Plants Transcription Factors Amino Acid Sequence Basic Helix-Loop-Helix Transcription Factors
View on PubMed DOI

Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network.

Journal of bioinformatics and computational biology Jul 6, 2022
The evolutionary histories of genes are susceptible of differing greatly from each other which could be explained by evolutionary variations in horizontal gene transfers or biological recombinations. A phylogenetic tree would therefore represent the ...
Phylogeny Gene Transfer, Horizontal Software Algorithms Neural Networks, Computer
View on PubMed DOI
Popular Topics
Recent Journals