Nigel Peter French

Metatranscriptomics reveals diverse microbial communities in PCR-negative severe acute respiratory infections

The paper uses metatranscriptomics to analyze PCR-negative SARI samples, identifying microbial transcripts in 43% of cases and highlighting polymicrobial compositions and novel pathogens.

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.

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.