Nobuhiko Tokuriki

Nov 14, 2024 | biorxiv.org | John Chen |Barnabas Gall |Nobuhiko Tokuriki |Colin Jackson

AbstractExploration of protein sequence space can offer insight into protein sequence-function relationships, benefitting both basic science and industrial applications. The use of sequence similarity networks (SSNs) is a standard method for exploring large sequence datasets, but is currently limited when scaling to very large datasets and when viewing more than one level (hierarchy) of homology.

Mar 4, 2024 | biorxiv.org | John Chen |Dongkyu Lee |Nobuhiko Tokuriki |Sevan Gholipour

AbstractMost antibiotic-resistance genes (ARGs) evolved in environmental microbes long before humanity's antibiotic breakthrough, and widespread antibiotic use expedited the dissemination of ARGs among clinical pathogens. While widely discussed, the investigation of environmental ARG distributions lacks the scalability and taxonomic information necessary for a comprehensive analysis. Here, we present a global distribution of all five classes of β-lactamases among microbes and environments.