Xiaofan Zhou

Receptor-like kinase RLK15 binds a fungal RNase effector to enhance autophosphorylation and activate host defense

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

Contrasting gene gain and loss shape metabolic diversification in the Ralstonia solanacearum species complex

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

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

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.

Ancient co-option of LTR retrotransposons as yeast centromeres

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.

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

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

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.

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.

Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species

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.

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.

Genomic factors shaping codon usage across the Saccharomycotina subphylum

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.

Visualization and review of reads alignment on the graphical pan-genome with VAG

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.

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss

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.

Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage

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.

Olfactory Receptors Are Required For Social Behavior And Neural Plasticity In Ants, As Evidenced By CRISPR-Mediated Gene Knockout

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

in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

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.

Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

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

RNAseq in the mosquito maxillary palp: a little antennal RNA goes a long way

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.