David Baker

The paper investigates genetic diversification in Staphylococcus epidermidis during orthopaedic device-related infections, finding that insertion sequence elements drive adaptation without affecting antimicrobial resistance or biofilm formation.

This study uses shotgun metagenomics to show that the gut microbiome of insectivorous bats remains stable during temporary managed care, with minimal changes in microbial composition.

This paper develops a murine model of Shigella sonnei intestinal colonization and identifies factors contributing to its persistence and immune response.

The paper describes a new secondary chromosome, EEC1, in the Embleya genus, which is distinct from other secondary replicons and plays a key role in the genus' metabolism and evolution.

The paper evaluates four TIS sequencing library generation protocols to reduce costs and improve efficiency for gene essentiality analysis in E. coli.

The paper evaluates DNA extraction and storage protocols for human faecal samples to optimize high-molecular weight DNA recovery for long-read metagenomics.

The paper introduces P3ANUT, a platform for analyzing DNA sequencing data to identify and correct errors in peptide phage display library screening.

This study sequenced K. pneumoniae isolates from Southern Ghana, identifying genetic diversity, antimicrobial resistance, and virulence traits, highlighting the need for genomic surveillance.

The paper compares Illumina and Oxford Nanopore sequencing for viral genome recovery from human gut samples, finding Illumina better for resolved genomes and hybrid approaches better for diversity.

The paper describes an optimized DNA extraction method for skin swabs suitable for shotgun metagenomics, validated on adult and baby samples to characterize bacterial microbiota effectively.

This study uses genomic data from 8746 SARS-CoV-2 genomes across 33 African countries to show that most epidemics were initiated by European importations and later driven by local transmission and mobility, leading to the spread of variants of concern.

The paper uses shotgun metagenomics to analyze equine fecal samples, revealing taxonomic and functional diversity in the horse gut microbiome, including novel bacterial genera and species.

This study analyzes genomic diversity and antimicrobial resistance in Escherichia coli isolates from non-human primates in the Gambia, identifying novel sequence types and potential human pathogen exchange.

CoronaHiT is a method for high-throughput SARS-CoV-2 genome sequencing that improves coverage and throughput compared to existing protocols.

The paper evaluates de novo genome assembly methods for a low-quality non-model mammal sample, finding that more data types do not always improve assembly quality.

This paper compares genome assembly technologies for the potato species S. verrucosum, evaluating their completeness, accuracy, cost, and computational requirements.