Daniel Croll

Earl Grey ParTEA annotates transposable elements across multiple genomes, revealing shared and private TE families and improving annotation consistency.

This study compares 3D genome architectures across 55 fungal species, identifying novel configurations and challenging existing classifications.

The paper analyzes genome sequencing data of Zymoseptoria tritici to show that new regulatory mutations predominantly cause gene downregulation.

This study identifies retrotransposon proliferation as a driver of genome size expansion in Pseudocercospora species, with species-specific TE families and ongoing activity in some strains.

The paper identifies transposable elements and repeat-induced point mutation as triggers of chromosomal instability and degeneration in a fungal pathogen through experimental progeny analysis.

MycoMobilome is a non-redundant fungal TE consensus sequence database curated from 4,309 genomes, providing standardized naming and metadata for TE classification and curation.

This study investigates the functional domains of the transcription factor PnPf2 in Parastagonospora nodorum, revealing the MHR's role in protein-protein interactions and virulence.

This study analyzes a large European diversity panel of Zymoseptoria tritici to uncover genetic mechanisms underlying azole fungicide resistance across space and time.

The paper analyzes TE dynamics in Zymoseptoria tritici genomes to show how historical TE mobilization waves contribute to adaptive variation in a fungal pathogen.

This study investigates RIP-like mutation signatures across fungi, finding a 30-fold genome size increase in leotiomycetes linked to loss of RIP-related genes and identifying a zinc-finger protein as a novel genome defense mechanism.

This study shows how transposable elements create distinct genomic niches for effector evolution in Magnaporthe oryzae, contributing to diversification and host resistance evasion.

The paper examines intra-population variability in H3K27me3 histone marks in Zymoseptoria tritici and links it to gene expression variation.

This study uses high-resolution microbial network analysis to identify biocontrol consortia in the wheat phyllosphere that can suppress fungal pathogens in field conditions.

This study develops a high-throughput pipeline to discover antifungal resistance in crop pathogens, identifying 2192 resistance-associated genes across a thousand-genome panel of Zymoseptoria tritici.

The paper develops a qPCR method to predict Ustilago nuda infection levels in barley seeds, showing better correlation with field observations than visual embryo analysis.

The paper tests if specific fungal communities cause grapevine dieback disease using landscape-scale sampling and finds no such causal link.

This study examines the evolution and function of NIP2 paralogs in Rhynchosporium commune, showing their genomic distribution, expression during infection, and potential virulence roles.

This study identifies giant transposons called Starships in Aspergillus fumigatus that generate genomic and phenotypic heterogeneity across strains.

The paper uses population genomics and transcriptomics to reveal a cryptic virulent group and adaptive effectorome in Puccinia polysora, a fungal pathogen causing southern corn rust.

The paper identifies a non-recombining genomic region in the invasive fungus Cryphonectria parasitica linked to the mating-type locus, showing balanced haplotype segregation and potential adaptation through mobile elements.

The paper improves gene annotation of Zymoseptoria tritici by combining Iso-Seq and RNA-Seq data, resulting in more accurate gene models and new insights into its transcriptional landscape.

This paper develops a method using near-infrared spectroscopy and machine learning to rapidly detect biological agents in the field, achieving high accuracy in distinguishing them from non-biological substances.

The paper analyzes the global evolution of the effector gene AvrStb6 in Zymoseptoria tritici, showing diversification, loss, and virulence gains linked to host resistance deployment.

This study identifies genomic signatures of domestication in a fungus farmed by leafcutter ants using long-read sequencing, revealing gene expansions and losses linked to cultivation adaptation.

The paper estimates hybridization load in Alpine ibex due to hybridization with domestic goats, finding increased loss-of-function mutations in hybrids compared to non-hybrids.

This study develops a highly multiplexed amplicon sequencing assay for detecting genetically modified organisms, identifying 10 known modifications per GM event and assessing its performance in mixed and diluted samples.

This study uses whole-genome sequencing to identify genetic factors underlying quantitative pathogenicity and host adaptation in the fungal plant pathogen Zymoseptoria tritici.

The paper examines TE expression dynamics in a fungal pathogen, finding that TE activity influences trait variation and adaptation.

This study identifies and characterizes lncRNAs in Zymoseptoria tritici using machine learning, revealing their expression patterns and potential roles in pathogenicity and host interaction.