A. Rokas

The paper constructs a genome-scale fungal phylogeny using 1,644 species and multiple data matrices, finding robust relationships and identifying taxonomic discrepancies.

This paper investigates the role of GprM and GprJ GPCRs in A. fumigatus, showing they regulate cell wall integrity, secondary metabolite production, and virulence.

This study shows that optimal codon usage in metabolic pathways correlates with ecological niches in budding yeasts, suggesting codon optimization can reveal metabolic ecology.

This paper evaluates the accuracy of FFP-based phylogenies and finds they perform poorly compared to standard methods like concatenation and coalescence.

ClipKIT trims multiple sequence alignments to retain phylogenetically-informative sites, improving phylogenomic inference accuracy and efficiency.

The paper investigates the loss of abaA, a master regulator of asexual development in fungi, and shows its correlation with morphological changes in asexual fruiting bodies across multiple fungal lineages.

This study constructs a genome-scale phylogeny of Ascomycota fungi, revealing contrasting modes of genome evolution across subphyla.

This study characterizes two clinical isolates of A. nidulans, showing differences in growth, metabolism, stress response, and virulence compared to a reference strain.

The paper identifies four factors causing outlier genes in phylogenomic matrices and shows how excluding them can mislead evolutionary inferences.

The paper compares secondary metabolite profiles and biosynthetic gene clusters between the pathogenic Aspergillus fumigatus and its nonpathogenic relatives A. fischeri and A. oerlinghausenensis, identifying conserved and diverged virulence-associated traits.

The paper characterizes the virulence and drug susceptibility of clinical isolates of Aspergillus fumigatus, A. lentulus, and A. fumigatiaffinis, revealing genomic and phenotypic heterogeneity across species and strains.

This study shows that the non-pathogenic Aspergillus fischeri produces gliotoxin like the pathogenic A. fumigatus, but losing secondary metabolite production does not affect its virulence.

The paper develops an approach to analyze evolutionary forces on genomic regions linked to preterm birth and finds diverse signatures like negative and positive selection.

This study shows that wild Penicillium molds rapidly evolve phenotypic and metabolomic traits similar to industrial cheese cultures when repeatedly passaged on cheese.

This study examines codon usage bias across 327 budding yeast species, finding that while genetic drift drives global patterns, translational selection influences many genes and codons.

This study identifies two lineages in Hanseniaspora yeasts, showing the FEL lineage lost more cell cycle and DNA repair genes than the SEL lineage, likely due to accelerated evolution and increased mutational load.

The paper identifies enhancers under recent positive selection across 41 human tissues and finds tissue-specific patterns, particularly in brain and testis enhancers.

This study examines the molecular evolution of placental galectins across mammals and humans, identifying signatures of natural selection and structural differences in a common haplotype.

This study identifies genetic variants associated with reproductive traits in dogs and links them to domestication-related traits.

This study compares Aspergillus fischeri and Aspergillus fumigatus to understand differences in pathogenicity, finding A. fischeri is less virulent, grows slower under stress, and has divergent secondary metabolism.

The paper reports the horizontal transfer of a bacterial operon into yeast, showing its adaptation to eukaryotic gene expression and iron acquisition in an insect gut environment.

The paper examines recent positive selection on sialic acid biology genes using whole genome data and finds few genes show signatures of recent adaptive evolution.

This paper reviews copy number variation in fungi, focusing on its role in wine yeast genetic diversity and adaptation, particularly in fermentation-related genes.

This study investigates the genomic features and evolution of a conditionally dispensable chromosome (CDC) in the tangerine pathotype of Alternaria alternata, revealing its role in pathogenicity and horizontal gene transfer.

This study evaluates four maximum likelihood phylogenetic programs on empirical data sets, finding that exhaustive methods outperform faster ones for single-gene trees and IQ-TREE excels in concatenation-based species tree inference.

The paper investigates the role of LaeA and BrlA in regulating secondary metabolism and hypoxia stress response in Aspergillus fumigatus, showing their coordinated control over metabolic and developmental processes.

The paper introduces quartet-based measures to quantify phylogenetic incongruence, showing they are more accurate and robust than bipartition-based methods, especially with partial trees and missing data.

The paper examines copy number variation in fermentation-related genes across 132 Saccharomyces cerevisiae wine strains, finding substantial CN diversity in gene families linked to adaptation to the wine fermentation environment.

The paper uses global co-expression networks to identify modules of genes associated with specialized metabolic pathways in plants, finding that these modules contain known biosynthetic genes and validated pathways.