David A. Rasko

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

Deciphering Bacterial and Archaeal Transcriptional Dark Matter and Its Architectural Complexity

The paper predicts bacterial and archaeal transcripts using ONT direct RNA sequencing and public data, revealing novel and previously characterized transcripts across multiple strains.

Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa

This study analyzes spatial-temporal and phylogenetic data from typhoid fever cases in Samoa to identify transmission patterns and the role of asymptomatic carriers.

Persistence of rare Salmonella Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

This study characterizes the genomic structure and evolutionary history of Salmonella Typhi in Samoa, revealing dominant rare genotypes with low antimicrobial resistance.

Comparison of long read sequencing technologies in resolving bacteria and fly genomes

This study compares PacBio and Oxford Nanopore long-read sequencing technologies for bacterial and fly genome assembly and methylation detection, finding no single technology outperforms others across all metrics.

Cost Effective, Experimentally Robust Differential Expression Analysis for Human/Mammalian, Pathogen, and Dual-Species Transcriptomics

This study evaluates the impact of read length and pairing on differential expression analysis in host-pathogen interactions, finding 54-bp paired reads most robust and 36-bp single reads suitable for bacterial samples.

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

This study compares enrichment techniques for multi-species RNA-Seq, finding that targeted enrichment with Agilent SureSelect improves read mapping to target organisms.

FADU: A Feature Counting Tool for Prokaryotic RNA-Seq Analysis

FADU improves RNA-Seq quantification for prokaryotes by better detecting genes missed by HTSeq and featurecounts, especially in organisms with overlapping transcriptional units and polycistronic transcripts.

Population dynamics of Escherichia coli in the gastrointestinal tracts of Tanzanian children

This study examines E. coli population dynamics in Tanzanian children's gut over six months, finding high diversity and transient strains despite antibiotic exposure.