Search the literature by keyword, topic, or author. Filter to articles with full text available.
1201 results
<h4>Motivation</h4>Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling …
Read PDF<h4>Background</h4>The analysis of ortholog genes derived from metagenomic experiments provides an invaluable opportunity to assess the functional role of microbial communities towards, for example, antimicrobial resistance or biochemical pathways under different experimental conditions. Nevertheless, the …
Read PDFThe aquaculture industry is undergoing a critical transition from marine-based to plant-based and novel protein sources. However, the physiological impacts of these dietary shifts remain largely obscured when evaluated solely by traditional performance metrics such …
Read PDF<h4>Motivation</h4>Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragments. Apart from their core use in assemblers, …
Read PDF<h4>Summary</h4>Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce …
Read PDFAntimicrobial resistance (AMR) is a global health and environmental challenge, driven by complex interactions among microbial communities, resistance genes, and selective pressures in various ecological niches. Traditional surveillance procedures often fall short in capturing the …
Read PDF<h4>Motivation</h4>Network analysis has become a central strategy for dissecting complex biological and environmental systems, particularly as modern omics technologies generate increasingly large and heterogeneous datasets. However, current tools often lack the scalability, flexibility, and native …
Read PDFDNA from microbial communities can be sequenced and assembled to gain insight into the microbes that may be present in unique environments. Powerful computational tools, combined with more accessible sequencing technologies, have enabled metagenome-assembled genome …
Read PDF<h4>Motivation</h4>Testing for differences in within-group dispersion is a fundamental problem in multivariate data analysis, with direct implications for interpreting group structure and validating statistical assumptions of other analysis such as ANOVA. Existing methods typically construct …
Read PDFThe metagenomic approach based on high-throughput sequencing is becoming increasingly prevalent for the detection of viral infections in plants. This method allows us to study the species composition of viruses associated with the plant, including …
Read PDF<h4>Motivation</h4>Metabolism occurs in a cell type-specific manner, but which cells regulate metabolite levels remains unclear.<h4>Results</h4>Here, we integrate some of the largest metabolite quantitative trait loci datasets, TOPMed and UK Biobank, with one of the most …
Read PDFBats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. …
Read PDF[This corrects the article DOI: 10.1371/journal.pone.0200095.].
Read PDFLaguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to …
Read PDFHere we report the 16S rRNA gene amplicon analysis of the gut microbiota of three frugivorous cave bat species from the Cathedral Cave in Cavinti, Laguna, Philippines. Among the bat species, the most abundant phyla …
Read PDF<h4>Motivation</h4>Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from …
Read PDF<h4>Motivation</h4>Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-species genetic variation can reveal adaptive evolution, selection pressures, and ecological dynamics that …
Read PDF<h4>Background and aim</h4>Despite its role in healthcare delivery and accessibility, the potential of bioinformatics to transform disease diagnosis in SSA remains unknown. This narrative review aims to assess the current status of bioinformatics initiatives in …
Read PDF<h4>Motivation</h4>Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose …
Read PDFUnderstanding biological communities is essential for elucidating ecosystem structure and function. Metabarcoding based on ribosomal RNA (rRNA) genes, particularly 16S and 23S, is widely used to characterise bacterial and microalgal communities. However, analysing high-throughput sequencing …
Read PDF