Vera van Noort

This study links genomic diversity to phenotypic virulence in Pseudomonas aeruginosa by analyzing multiple strains and their functional behaviors.

This paper develops AdventML, a model for predicting enzyme optimal temperature using transformer embeddings and resampling, achieving R2 ~0.64 and improved extreme temperature predictions.

This study improves OGT prediction for prokaryotes using machine learning with amino acid descriptors, achieving an R2 of 0.89.

This study examines CYP4 evolution in birds using 363 genomes to explore how gene variation relates to ecological traits and metabolic strategies, identifying positive selection in substrate recognition sites.

This study uses structure-informed methods to annotate hypothetical proteins from Pseudomonas phages, showing that combining structural and sequence-based approaches can annotate up to 43% of previously unannotated proteins.

This study investigates the evolutionary origins of proteins in the AHR signaling pathway, identifying gene losses and duplications that inform functional connectivity across species.

This study analyzes Pseudomonas aeruginosa virus PA5oct using hybrid sequencing and proteomics to reveal its genomic structure, transcription dynamics, and interactions with host bacteria.

The paper constructs a genome-based taxonomy for the Lactobacillus Genus Complex using 2,459 genomes, identifying new species and resolving misclassifications.

The paper predicts potential protein-peptide interactions for 530 SIPs in Arabidopsis thaliana using docking and energy calculations, suggesting they may modulate ligand/cofactor binding or protein complexes.