A. L. LaBella

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.

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.

Saccharomycotina yeasts defy longstanding macroecological patterns

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

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.

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.

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.

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.

Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus

The paper analyzes the genomes and phenotypes of four Aspergillus fumigatus isolates from COVID-19 patients, finding minor genomic differences and variable virulence traits.

PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data

PhyKIT provides a UNIX shell toolkit for processing and analyzing phylogenomic data, offering functions to evaluate sequence alignments, trees, and evolutionary relationships.

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

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

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

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

Accounting for diverse evolutionary forces reveals the mosaic nature of selection on genomic regions associated with human preterm birth

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.

Variation and selection on codon usage bias across an entire subphylum

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.

Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

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 impact of natural selection on the evolution and function of placentally expressed galectins

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.