Federica Quaglia

DOME Copilot: A resource to automate transparent reporting of artificial intelligence methods

DOME Copilot automates the generation of transparent AI methodology reports for life science publications, matching or exceeding manual quality while reducing creation time.

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.

Critical Assessment of Protein Intrinsic Disorder Prediction

The paper evaluates 43 methods for predicting intrinsically disordered regions and binding regions in proteins, finding that deep learning methods outperform older physicochemical approaches but binding prediction remains challenging.

APICURON: a database to credit and acknowledge the work of biocurators

APICURON credits biocurators by tracking their work across knowledgebases, using gamification and an API for resource integration.

Experimentally determined long intrinsically disordered protein regions are now abundant in the Protein Data Bank

The paper analyzes experimental evidence for long intrinsically disordered protein regions in the PDB, showing increased coverage of intrinsic disorder over the last decade.

Assessing predictors for new post translational modification sites: a case study on hydroxylation

The paper evaluates hydroxylation site predictors using independent datasets, finding they perform no better than random, highlighting issues with self-reported performance and generalization.