Patrick J. Biggs

Genomic epidemiology of the 2017-2023 outbreak of Mycoplasma bovis sequence type ST21 in New Zealand

This paper uses genomic and epidemiological data to analyze the dynamics of a Mycoplasma bovis outbreak in New Zealand from 2017 to 2023, showing the impact of control measures and the persistence of infection.

Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered kakapo (Strigops habroptilus)

The paper identifies extraintestinal pathogenic Escherichia coli, Enterococcus faecalis, and Streptococcus gallolyticus as potential causative agents of exudative cloacitis in kakapos through metatranscriptomic analysis of lesions and cloacal swabs.

Genomic epidemiology of ESBL-producing Escherichia coli from humans and an Aotearoa New Zealand river

This study examines the genetic relationship between ESBL-producing E. coli from human clinical isolates and environmental samples in Aotearoa New Zealand, finding shared strains and highlighting environmental transmission pathways.

Lost In The Forest: Encoding Categorical Variables and the Absent Levels Problem

The paper addresses the absent levels problem in random forest models by proposing a novel ordinal encoding method using principal coordinates analysis, showing it is unbiased and performs as well as target-based approaches.

Species-wide genomics of kakapo provides transformational tools to accelerate recovery

This paper uses whole-genome sequencing of kakapo to analyze genetic diversity and breeding values, showing how conservation management has maintained genetic diversity and providing tools for future recovery efforts.

Visual integration of GWAS and differential expression results with the hidecan R package

The paper introduces the hidecan R package for visualizing GWAS and differential expression results along with manually curated candidate genes.