Marie‐Claire Harrison

FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning

FLASH predicts phenotype from sequence using deep learning, achieving high accuracy on unseen variants and identifying new virulence predictors across microbes.

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.

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

The paper examines filamentation morphology evolution in Saccharomycotina yeasts using integrated genomic, metabolic, and environmental data from 1,154 strains, finding that filamentation is common and linked to phylogeny and environmental factors.

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.

Convergent reductive evolution in bee-associated lactic acid bacteria

This study identifies convergent gene loss in bee-associated lactic acid bacteria, linking it to phenotypic traits like fructophily through phylogenomic and machine learning analyses.

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.

CBD-1 scaffolds two independent complexes required for eggshell vitelline layer formation and egg activation in C. elegans

The paper identifies CBD-1 as a scaffold protein in C. elegans that forms two distinct complexes for vitelline layer assembly and egg activation, revealing its multifaceted role in eggshell formation and fertilization.