Xiaofan Zhou

The paper identifies a fungal RNase effector recognized by a plant receptor kinase, triggering immune responses and enhancing disease resistance.

The paper identifies gene gain and loss mechanisms shaping metabolic diversity in Ralstonia solanacearum by analyzing genomic data and phylogenomics.

The paper uses machine learning to identify genomic signatures of antifungal drug resistance in Saccharomycotina yeasts, finding that natural resistance patterns differ from clinical isolates.

The paper identifies proto-point centromeres in Saccharomycodales yeast, showing they evolved from retrotransposon LTRs, supporting the hypothesis that point centromeres originated from ancestral retrotransposons.

The paper identifies genomic factors limiting Saccharomycotina fungi's ability to infect plants, finding they lack metabolic enzymes used by other phytopathogens.

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

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.

The paper identifies three yeast lineages with reduced DNA repair genes and high evolutionary rates, showing how gene loss can lead to persistent hypermutator phenotypes.

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

The paper analyzes codon usage patterns across 1,154 Saccharomycotina strains, identifying biases, correlations with GC content and tRNA-ome size, and order-specific classification using machine learning.

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 paper introduces VAG, a tool for visualizing and analyzing read alignments on graph pangenomes, and demonstrates its application in identifying genetic variations in rice and other species.

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.

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 uses CRISPR to knock out the Orco gene in ants, showing its role in olfaction, social behavior, and neural plasticity.

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.