Claudio Bassot

Balancing spatial resolution and proteome depth in LC-MS based spatialproteomics

This study evaluates the trade-off between spatial resolution and proteome depth in spatial proteomics using SLACS, showing that few-cell sampling maintains proteomic information while increasing spatial specificity.

Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay.

The paper shows that ribosomes modulate transcriptome abundance through frameshifts and out-of-frame mRNA decay in yeast under poor nutritional conditions, with conservation across species.

Limits and potential of combined folding and docking using PconsDock.

This paper introduces PconsDock, a fold-and-dock method that predicts tertiary and quaternary structures of protein pairs without prior structural information, achieving comparable performance to traditional methods.

The evolutionary history of topological variations in the CPA/AT superfamily

The paper identifies novel topologies in CPA/AT transporters using an integrated method and presents a database with structural classifications.

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.

Identification of a novel fold type in CPA/AT transporters by ab-initio structure prediction

This study identifies a novel reentrant-helix-reentrant fold in CPA/AT transporters using ab-initio structure prediction, revealing structural adaptations and the utility of deep-learning-based modeling.

Accurate contact-based modelling of repeat proteins predicts the structure of Curlin and SPW repeats.

The paper predicts the structure of repeat proteins using contact-based deep learning, achieving high accuracy for five PFAM families without known structures.

Why do eukaryotic proteins contain more intrinsically disordered regions?

The paper investigates why eukaryotic proteins have more intrinsically disordered regions by comparing linker regions between eukaryotic and prokaryotic proteomes.