Paolo Ribeca

Mar 9, 2024 | biorxiv.org | Xavier Didelot |Paolo Ribeca

AbstractThe recent explosion in the amount of available sequencing data challenges existing analysis techniques. Here we introduce KPop, a novel versatile method based on full k-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike minimizer-based methods that produce distances and have lower resolution, KPop is able to accurately map sequences onto a low-dimensional space.

Mar 9, 2024 | biorxiv.org | Xavier Didelot |Paolo Ribeca

AbstractThe recent explosion in the amount of available sequencing data challenges existing analysis techniques. Here we introduce KPop, a novel versatile method based on full k-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike minimizer-based methods that produce distances and have lower resolution, KPop is able to accurately map sequences onto a low-dimensional space.

Sep 14, 2023 | nature.com | Chimaobi Chukwu |David King |Afolabi Akinpelu |Paolo Ribeca |Rebecca Sumner |Andrew Rambaut | +4 more

AbstractThe 2022 global mpox outbreak raises questions about how this zoonotic disease established effective human-to-human transmission and its potential for further adaptation. The 2022 outbreak virus is related to an ongoing outbreak in Nigeria originally reported in 2017, but the evolutionary path linking the two remains unclear due to a lack of genomic data between 2018, when virus exportations from Nigeria were first recorded, and 2022, when the global mpox outbreak began.

Jul 28, 2023 | biorxiv.org | Jake Carson |Matt J Keeling |David Wyllie |Paolo Ribeca

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