Antonis Rokas

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.

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

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 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.

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

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

The paper expands mitochondrial genome sampling across Saccharomycotina yeasts by extracting sequences from nuclear genome datasets, revealing trends in size, GC content, and gene presence.

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

The paper maps de novo telomere addition hotspots in yeast using a high-throughput method and computational analysis, showing enrichment in subtelomeres and Cdc13 binding.

This study identifies genetic loci associated with gestational duration and preterm delivery, showing maternal and fetal genetic effects and antagonistic pleiotropy with birth weight.

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.

BioKIT provides a unified toolkit for processing and analyzing diverse sequence data, demonstrating its utility through quality assessments and codon usage analysis across multiple datasets.

The paper identifies AlkZ and AlkX DNA glycosylases involved in bacterial resistance to genotoxins, linking them to specific antimicrobial production.

The paper shows that galactose metabolism genes can be horizontally transferred between yeast species, allowing for the reacquisition of a lost trait after millions of years.

This study analyzes the distribution and evolution of clusters of tandemly duplicated genes (CTDGs) across 18 mammalian genomes, revealing their enrichment in environmental interaction processes and chromosome-specific patterns.

integRATE prioritizes candidate genes across heterogeneous omics data by using desirability functions, identifying known and novel genes in preterm birth.

The paper constructs a robust phylogenomic timetree for Aspergillus and Penicillium fungi using multiple genome datasets and phylogenetic methods to identify incongruent branches and estimate divergence times.

The paper compares the wetA gene regulatory network across three Aspergillus species, finding conserved regulatory roles but divergent network structures.

The paper shows that fructophilic yeasts in the W/S clade lost and reacquired alcoholic fermentation genes via horizontal gene transfer, adapting to high sugar environments.

This study identifies five types of genetic variation in secondary metabolic gene clusters across 66 strains of Aspergillus fumigatus and links them to evolutionary drivers like mutation, recombination, and horizontal gene transfer.

iWGS is a computational pipeline that guides the design and analysis of de novo genome sequencing projects by simulating data generation, quality control, assembly, and evaluation.

This paper reconstructs the Saccharomycotina yeast phylogeny using genome-scale data from 86 yeast genomes and identifies robust and conflicting relationships among major lineages.

The paper challenges the findings of a previous RNAseq study on mosquito olfactory tissues, suggesting contamination led to spurious results and failed to replicate the original conclusions.