A. Rokas

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.

Rooting the animal tree of life

This paper investigates the root placement in the animal tree of life by analyzing 15 phylogenomic studies and finding that Ctenophora-sister is supported under constrained site-heterogeneous models.

Transcriptomic, protein-DNA interaction, and metabolomic studies of VosA, VelB, and WetA in Aspergillus nidulans asexual spores

The paper investigates the regulatory roles of VosA, VelB, and WetA in asexual spore formation in Aspergillus nidulans using transcriptomic, protein-DNA interaction, and metabolomic analyses.

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

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

Aspergillus fumigatus G-protein coupled receptors GprM and GprJ are important for the regulation of the cell wall integrity pathway, secondary metabolite production, and virulence

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

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.

Feature Frequency Profile-based phylogenies are inaccurate

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

ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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

Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits

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.

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.

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

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

Biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence in the closest nonpathogenic relatives of Aspergillus fumigatus

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.

Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis

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.

Gliotoxin, a known virulence factor in the major human pathogen Aspergillus fumigatus, is also biosynthesized by the non-pathogenic relative A. fischeri

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.

Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans

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

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.

Rapid phenotypic and metabolomic domestication of wild Penicillium molds on cheese

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

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.

Signatures of recent positive selection in enhancers across 41 human tissues

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

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.

Genome wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication

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

Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, a close relative of the major human fungal pathogen Aspergillus fumigatus

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.

Eukaryotic acquisition of a bacterial operon

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.

Examination of signatures of recent positive selection on genes involved in human sialic acid biology

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.

Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation

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

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

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.

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

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.

A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus

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.

Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

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.