AIMC Topic: Phylogeny

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Investigating genetic, antigenic, and structural diversity in the outer membrane protein, PorB: implications for vaccine design.

mBio
UNLABELLED: Vaccines targeting are needed to reduce disease burden and help address the problem of antimicrobial resistance, with an understanding of relationships between gonococcal genetics and molecules influencing diversity, infection, and the i...

Predicting hydrocarbon presence in marine cold seep sediments using machine learning models trained with benthic bacterial 16S rRNA taxonomy.

Microbiology spectrum
UNLABELLED: Hydrocarbon seepage in marine sediments exerts selective pressure on benthic microbiomes. Accordingly, microbial community composition in these sediments can reflect the presence of hydrocarbons, with specific groups being more prolific i...

Integrative machine learning and RT-qPCR analysis identify key stress-responsive genes in Thermus thermophilus HB8.

Genetica
Bacteria are constantly exposed to diverse environmental stresses, necessitating complex adaptive mechanisms for survival. Thermus thermophilus, a thermophilic extremophile, serves as an excellent model for investigating these responses due to its re...

Species richness is an important mediator of multifunctionality changes in Hobq desert shrub ecosystem.

Scientific reports
Studying the biodiversity and multifunctionality relationships of the Hobq Desert shrub ecosystem and its response to environmental factors is crucial for ecological restoration in the region. In this study, we examined variations in biodiversity and...

Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds.

BMC genomics
BACKGROUND: Shandong's local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China's waterfowl germplasm. Understanding the genetic characteristics of these populations, along with moni...

Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing.

BMC microbiology
BACKGROUND: Identifying key characteristics of unknown suspects, such as age, height, and drug use, is essential for advancing forensic investigations.

Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.

Archives of microbiology
The study of fungal genetics has undergone transformative advancements in recent decades, profoundly reshaping our understanding of fungal diversity, evolution, and pathogenesis. This review synthesizes cutting-edge molecular techniques revolutionizi...

Morphological traits and machine learning for genetic lineage prediction of two reef-building corals.

PloS one
Integrating multiple lines of evidence that support molecular taxonomy analysis has proven to be a robust method for species delimitation in scleractinian corals. However, morphology often conflicts with genetic approaches due to high phenotypic plas...

Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species.

Planta
Through multi-faceted comparative analysis of MITEs across six pear genomes, we revealed their distribution patterns, functional impacts and their significant role as genomic origins for miRNAs, with copy number being the most critical factor for MIT...

Pollen morphology, deep learning, phylogenetics, and the evolution of environmental adaptations in Podocarpus.

The New phytologist
Podocarpus pollen morphology is shaped by both phylogenetic history and the environment. We analyzed the relationship between pollen traits quantified using deep learning and environmental factors within a comparative phylogenetic framework. We inves...