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Khabre desk
Recent reporting, analysis and explainers from the Bioinformatics desk.
science
A bioRxiv preprint presents Sma3s v3, a scalable workflow for assigning functions to proteins in proteomes, pangenomes and metagenomes. In tests on a Vibrio cholerae pangenome and a metagenomic catalogue, it reported higher annotation coverage than the cited comparator tools.
science
A bioRxiv preprint presents Rsearch, an R package that integrates VSEARCH with visualisation, parameter optimisation and conversion tools for metabarcoding analysis. In a mock-community comparison with DADA2, the two pipelines produced abundance profiles that closely matched the expected composition, with differences in OTU counts and computational performance.
science
A bioRxiv preprint reports that incomplete reference profiles can leave bulk RNA deconvolution targets non-identifiable even when an algorithm returns precise estimates. The authors propose measuring coverage and false-certification risk, and estimate the measurement precision needed for a decisive result in peripheral blood mononuclear cells.
science
A bioRxiv preprint presents POME, a self-supervised model that represents incomplete mixed-type biomedical data as a graph. The authors report improved missing-data imputation and useful sample representations across three biomedical datasets.
science
A bioRxiv preprint finds that randomly dividing single-cell data can leak information between training and test sets when related cells share labels. The authors propose eakcheck, a tool that estimates this leakage before a predictive model is trained.