Andrea Porceddu

This study constructs a reference-free pangenome of Arabidopsis thaliana using 93 assemblies, revealing gene and pseudogene diversity across geographic regions.

Colora provides a Snakemake workflow for automated, high-quality chromosome-scale de novo genome assembly using PacBio HiFi, Hi-C, and optionally ONT reads.

This study identifies and characterizes pseudogenes in Fusarium graminearum, finding they are mostly in fast-evolving regions and some overlap with functional gene sequences.

This study compares genomic architectures across six Fusarium species, finding that genomic compartments with low collinearity are enriched for virulence-related genes and show signs of selective pressure.

The paper benchmarks three Hi-C scaffolding tools on Arabidopsis thaliana assemblies, finding YaHS performs best.

The paper introduces MCSeEd, a reference-free ddRAD method for whole-genome methylation profiling across multiple contexts, including 6mA, and provides a bioinformatic pipeline for differential methylation and SNP calling.