Toni Gabaldón

PanTEon provides a cross-kingdom framework for reproducible TE classification, benchmarking machine learning methods and highlighting performance variations across TE superfamilies and lineages.

The paper tracks the spread of fluconazole-resistant Candida parapsilosis clones in Spain, identifying multiple resistance mechanisms and clonal lineages across 31 hospitals.

This study investigates the role of horizontal gene transfer versus host retargeting in the early integration of chromatophores in Paulinella micropora, finding that host retargeting predominated over gene transfer.

This study uses ancient whole-genome data to show geographically structured selection during the Neolithic transition in Western Eurasia, involving both farmer and hunter-gatherer alleles.

This study reconstructs the evolutionary history of temporal transcription factor series in insect visual brains, showing conserved patterns and species-specific variations that influence neuronal diversity.

The paper reconstructs the last eukaryotic common ancestor proteome and identifies multiple horizontal gene transfers from diverse bacterial donors, suggesting complex microbial associations in eukaryogenesis.

This study identifies convergent genomic strategies for antifungal resistance in Candida species through experimental evolution and genome sequencing.

The paper identifies genetic drivers of clinically relevant traits in Candida parapsilosis using genome-wide association studies and machine learning models.

This study analyzes Asgard archaea genomes to determine the roles of horizontal gene transfer and gene duplication in their evolution, finding gene duplication drives genome size increase.

This study characterizes the phenotypic and genomic diversity of Candida dubliniensis isolates from HIV-positive individuals, revealing significant variability in drug resistance and other clinically relevant traits.

The paper uses simulations to assess how unsampled lineages affect gene flow inference during eukaryogenesis, finding low misinterpretation probability but specific problematic cases.

This study identifies and characterizes lncRNAs in Mucorales fungi, revealing their roles in development and pathogenicity, and highlights their potential as antifungal targets.

The paper investigates how Erg3 loss-of-function contributes to echinocandin resistance in Candida species by analyzing combined mutations in ERG3 and FKS2.

This paper validates a probabilistic method for relative dating of evolutionary events using gene trees and shows it correlates strongly with fossil-calibrated molecular clocks.

The paper presents a chromosome-level genome assembly of the Hispid cotton rat, annotating 24,878 protein-coding genes and identifying genetic innovations.

This paper identifies a novel Ca2+-binding motif in MICU1 that functions as an early sensor, triggering structural changes that refine its regulatory role in mitochondrial Ca2+ uptake.

This study compares structure-based and sequence-based methods for phylogenetic reconstruction and finds that sequence-based methods still outperform structure-based ones in large-scale phylogenomics.

The paper assesses the stability of oral and fecal microbiome samples stored at room temperature for 15 days using different preservation methods, finding minimal changes in alpha diversity and relative abundances.

This study presents a multi-omics analysis of a supercentenarian, revealing that extreme age and poor health are distinct molecular processes.

The paper identifies hyper-multidrug-resistant Nakaseomyces glabratus strains with fitness trade-offs and explores nitroxoline as a potential alternative therapy for resistant UTIs.

This study investigates RNA structure in Candida pathogens using genome-wide probing, revealing structural conservation, SNP impacts, and conserved hairpin features in lncRNAs.

The paper sequenced and compared genomes of yeast species in the Pichia cactophila complex to show recurrent hybridizations and propose new species classifications.

JLOH infers LOH blocks from genomic data and assigns them to subgenomes in hybrids.

The paper examines genome-wide ortholog variation in 206 A. fumigatus isolates, finding no significant differences in ortholog distribution between clinical and environmental isolates after accounting for phylogeny.

This study profiles transcriptome and proteome of Candida parapsilosis assimilating hydroxyaromatic carbon sources, revealing pathway regulation and metabolic connections.

The paper compares chromatin activities in two A. fumigatus isolates, finding higher genome instability in Af293 and identifying a variant with chromosomal alterations linked to increased virulence.

Karyon diagnoses non-standard genomic architectures in assemblies using raw data and de novo assembly, identifying 17% of tested fungal assemblies as having unusual configurations.

PerSVade improves structural variant detection by optimizing parameters for each species, enhancing accuracy across diverse eukaryotes.

The paper presents the genome of Sitophilus oryzae, revealing high transposable element content and host-symbiont metabolic interactions.

The paper investigates whether loss of the mismatch repair protein Msh2 relaxes species boundaries between Cryptococcus neoformans and C. deneoformans, finding increased hybrid viability and aneuploidy but no increased recombination.