Susan J. Thomson

The paper develops microhaplotype-based kinship estimation methods for autopolyploid populations and shows they outperform SNP-based methods in Actinidia.

TEgenomeSimulator generates synthetic genomes with configurable transposable element landscapes, offering greater flexibility and realism compared to existing simulators.

This study evaluates protein-coding sequence detection tools, finding most are inaccurate and inefficient, with only three out of nine performing better than a naive scheme.

PrinTE simulates genome evolution driven by transposable elements, revealing that genome size is strongly correlated with LTR retrotransposon dynamics and suggesting genome expansion followed by contraction in A. psidii.

The paper evaluates low-pass nanopore sequencing for global methylation measurement in plants, finding that higher coverage is needed for accuracy compared to vertebrates and demonstrating consistent results across sample conditions.

This study identifies and characterizes innate immunity in Actinidia melanandra against Pseudomonas syringae pv. actinidiae, revealing PTI triggered by the T3S system.

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

TriPoly improves haplotype estimation in polyploids using parent-offspring trios and Mendelian inheritance, achieving higher accuracy at lower coverage than single-individual methods.