A. Rokas

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

The paper investigates the relationship between gene family expansions and metabolic traits in yeasts, finding that keystone gene families drive multiple metabolic innovations.

Specialization restricts the evolutionary paths available to yeast sugar transporters

The paper investigates how specialization in yeast sugar transporters restricts evolutionary paths by analyzing sequence-function relationships and evolutionary history.

Pathogenicity is associated with population structure in a fungal pathogen of humans

The paper analyzes genomic data from 250 Aspergillus flavus isolates to show that pathogenicity is strongly linked to population structure, with population D containing most clinical isolates and harboring genes related to zinc ion binding and lipid metabolism.

Convergent reductive evolution in bee-associated lactic acid bacteria

This study identifies convergent gene loss in bee-associated lactic acid bacteria, linking it to phenotypic traits like fructophily through phylogenomic and machine learning analyses.

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

The paper analyzes gene family evolution across nearly all known Saccharomycotina yeast species, finding distinct evolutionary patterns with gene loss linked to metabolic and genomic changes.

Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence

This study examines strain variation in a non-pathogenic fungus, identifying factors linked to virulence differences across strains.

Genome-wide patterns of non-coding sequence variation in the major fungal pathogen Aspergillus fumigatus

This study identifies greater sequence variation in non-coding regions of A. fumigatus genes compared to protein-coding regions, suggesting a role in phenotypic differences between strains.

Functional and evolutionary integration of a fungal gene with a bacterial operon

The paper shows that the fungal gene ENB1, acquired from a bacterial operon, enables iron uptake in W/S clade yeasts and evolved through horizontal transfer and gene loss.

The evolution of gestation length in eutherian mammals

This study analyzes gestation length variation across eutherian mammals and identifies adaptive shifts linked to life history traits and evolutionary transitions.

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

The paper reconstructs a taxon-rich Opisthokonta tree of life using genome-scale data, suggesting a Mesoproterozoic origin and unresolved deep divergences within Holozoa.

Diverse signatures of convergent evolution in cacti-associated yeasts

This study identifies convergent evolution in cacti-associated yeasts using genomic and phenotypic data, finding thermotolerance and horizontal gene transfer as key adaptive traits.

Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning

This study uses machine learning to predict fungal secondary metabolite bioactivity from biosynthetic gene clusters, finding higher accuracy when combining bacterial and fungal data.

Saccharomycotina yeasts defy longstanding macroecological patterns

This study uses machine learning to model global yeast species distributions and finds they defy traditional macroecological patterns.

A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis

The paper identifies conidial surface proteins in Aspergillus fumigatus and shows their role in immune evasion during infection.

Machine learning illuminates how diet influences the evolution of yeast galactose metabolism

This study uses machine learning to analyze yeast genomes and growth data to uncover how diet influences the evolution of galactose metabolism.

Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen

This study identifies and characterizes the cryptic fungal pathogen Aspergillus latus, revealing its hybrid origin and developing genomic and phenotypic markers for accurate diagnosis.

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

The paper analyzes genomic, metabolic, and ecological data from nearly all Saccharomycotina yeast species to show that intrinsic genetic factors, not trade-offs or extrinsic factors, drive variation in niche breadth.

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi

This study examines the evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi across 35 genomes, finding conserved resistance genes and fragmented BGCs in most species.

COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses

This study analyzes 11 Aspergillus fumigatus isolates from COVID-19 patients with pulmonary aspergillosis, finding genomic diversity but similar stress responses to infection.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

The paper uses genome-scale phylogenomics to analyze 711 Aspergillus genomes, revealing taxonomic issues and strain misidentifications.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi

This study compares mitochondrial and nuclear genome evolution in Aspergillus section Flavi, finding differences in codon usage bias and evolutionary patterns between the two genomes.

Genomic and phenotypic trait variation of the opportunistic human pathogen Aspergillus flavus and its non-pathogenic close relatives

This study compares genomic and phenotypic traits of Aspergillus flavus and its non-pathogenic relatives to understand pathogenicity evolution.

Codon optimization, not gene content, predicts XYLose metabolism in budding yeasts

This study identifies codon optimization as the key predictor of xylose metabolism in budding yeasts, showing that gene content alone is insufficient.

Aspergillus fumigatus FhdA transcription factor is important for mitochondrial activity and codon usage regulation during the caspofungin paradoxical effect

This study shows that FhdA regulates mitochondrial activity and tRNA expression in Aspergillus fumigatus during caspofungin tolerance.

Mosaic patterns of selection in genomic regions associated with diverse human traits

The paper develops a computational framework to analyze selection patterns in genomic regions linked to human traits using GWAS summary statistics and evolutionary measures.

Lack of universal mutational biases in a fungal phylum

The paper analyzes mutational biases across 537 fungal strains from Ascomycota, finding variation in A|T and G|C substitution patterns and showing that genome composition is influenced by both mutational bias and selection.

Beyond the biosynthetic gene cluster paradigm: Genome-wide co-expression networks connect clustered and unclustered transcription factors to secondary metabolic pathways

This study identifies six transcription factors regulating secondary metabolism in Aspergillus niger by analyzing co-expression networks across 155 growth conditions.

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

OrthoSNAP identifies single-copy orthologs from gene family trees, increasing the number of markers for molecular evolution studies by splitting and pruning gene families.

Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives

The paper identifies extensive non-coding sequence divergence in A. fumigatus compared to related species, highlighting its potential role in virulence.

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

This study identifies conserved transcription factors and genes involved in gliotoxin protection in Aspergillus species through RNA-sequencing and deletion screening.