Giulia Babbi

On the state of protein function prediction: a report on the fourth CAFA challenge

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants

The paper identifies Acinetobacter sp. as a dominant bacterium in tomato plant microbiota and shows its functional role in nutrient mobilization and stress adaptation, while decoupling its presence from antimicrobial resistance genes.

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

The paper evaluates variant effect predictions for ARSA gene variants, finding that a bootcamp-trained model outperformed others and that deep learning slightly improved performance over simpler methods.

Critical assessment of missense variant effect predictors on disease-relevant variant data

The paper evaluates missense variant effect predictors using CAGI6 data, finding strong performance across settings and highlighting biases in some predictors.

Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project

The paper evaluates variant prioritization methods for rare disease diagnosis using data from the Rare Genomes Project, finding that top models identify causal variants in most solved families and uncover potential candidates in unsolved ones.

Mouse Genomic Associations with Ex Vivo Sensitivity to Simulated Space Radiation

The paper identifies genomic associations with ex vivo DNA damage responses to ionizing radiation in mice, highlighting pathway differences across radiation types and timing.