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Phylogeny

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Application of machine learning algorithm and modified high resolution DNA melting curve analysis for molecular subtyping of Salmonella isolates from various epidemiological backgrounds in northern Thailand.

World journal of microbiology & biotechnology
Food poisoning from consumption of food contaminated with non-typhoidal Salmonella spp. is a global problem. A modified high resolution DNA melting curve analysis (m-HRMa) was introduced to provide effective discrimination among closely related HRM c...

Machine learning-based analyses support the existence of species complexes for and .

Parasitology
Human strongyloidiasis is a serious disease mostly attributable to Strongyloides stercoralis and to a lesser extent Strongyloides fuelleborni, a parasite mainly of non-human primates. The role of animals as reservoirs of human-infecting Strongyloides...

Predicting host taxonomic information from viral genomes: A comparison of feature representations.

PLoS computational biology
The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus...

Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data.

Viruses
The fast replication rate and lack of repair mechanisms of human immunodeficiency virus (HIV) contribute to its high mutation frequency, with some mutations resulting in the evolution of resistance to antiretroviral therapies (ART). As such, studying...

PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data.

IEEE journal of biomedical and health informatics
Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introdu...

An Application of Random Walk Resampling to Phylogenetic HMM Inference and Learning.

IEEE transactions on nanobioscience
Statistical resampling methods are widely used for confidence interval placement and as a data perturbation technique for statistical inference and learning. An important assumption of popular resampling methods such as the standard bootstrap is that...

TMTCPT: The Tree Method based on the Taxonomic Categorization and the Phylogenetic Tree for fine-grained categorization.

Bio Systems
Fine-grained categorization is one of the most challenging problems in machine vision. Recently, the presented methods have been based on convolutional neural networks, increasing the accuracy of classification very significantly. Inspired by these m...

Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution.

Communications biology
In contrast to the vast majority of reptiles, the skulls of adult crown birds are characterized by a high degree of integration due to bone fusion, e.g., an ontogenetic event generating a net reduction in the number of bones. To understand this proce...

gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.

Scientific reports
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromoso...

Predicting the short-term success of human influenza virus variants with machine learning.

Proceedings. Biological sciences
Seasonal influenza viruses are constantly changing and produce a different set of circulating strains each season. Small genetic changes can accumulate over time and result in antigenically different viruses; this may prevent the body's immune system...