David Lewis

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes

EffectorGeneP improves gene annotation in pathogen genomes by predicting coding sequences from transcript data, outperforming existing methods and expanding the predicted secretome.

Virulence and genomic analysis of Puccinia coronata f. sp. avenae in Australia identifies new races and a new lineage in 2024

The paper analyzes 30 Puccinia coronata f. sp. avenae isolates from Australia to identify new races and a novel lineage, highlighting shifts in virulence and population structure.

Dehydrating microhabitats increase mite activity and intensify ectoparasitism of Drosophila

This study shows that dehydration increases mite activity and ectoparasitism of Drosophila in two fly-mite systems.

Haplotype-resolved genomes of diverse oat crown rust isolates reveal both global dispersion of long-lived clonal haplotypes and limited recombination between haplotypes.

Characterisation of virulence of Puccinia coronata f. sp. avenae in Australia in the 2023 growing season

The paper characterizes the virulence of Puccinia coronata f. sp. avenae isolates in Australia during the 2023 growing season and identifies new or increased virulence on resistance genes.

Radiolabeling Isolated Mitochondria with Tc-99m: A First-in-Field Protocol and Early Feasibility Findings

This paper develops a first-in-field protocol for radiolabeling isolated mitochondria with Tc-99m agents and shows early feasibility of tracking transplanted mitochondria in vivo.

A chromosome-scale genome assembly of the flax rust fungus reveals the two unusually large effector proteins, AvrM3 and AvrN

This study presents a chromosome-scale genome assembly of the flax rust fungus, revealing two large effector proteins, AvrM3 and AvrN, and providing insights into its mating system.

Impaired humidity sensing reduces tick survival by preventing water homeostasis

This study shows that impaired humidity sensing in ticks reduces survival by disrupting water homeostasis, particularly under variable environmental conditions.

Identification of diagnostic KASP markers for selection of crown rust resistance in oats

This study develops and validates KASP markers for crown rust resistance genes in oats, identifying new carriers and correcting previous classifications.

A high-resolution haplotype pangenome uncovers somatic hybridization, recombination and intercontinental migration in oat crown rust

This study constructs a high-resolution haplotype pangenome of oat crown rust, revealing somatic hybridization, recombination, and intercontinental migration as drivers of genetic diversity.

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.