Alessio Ansuini

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

BASCULE: Bayesian inference and clustering of mutational signatures leveraging biological priors

BASCULE uses a Bayesian framework to standardize and cluster mutational signatures across cancer types, identifying prognostic subtypes in over 8,000 samples.

Unsupervised domain classification of AlphaFold2-predicted protein structures

DPCstruct classifies AlphaFold2-predicted protein structures into domain clusters, recovering known folds and identifying novel structural motifs.

Enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models

The paper improves prediction of protein stability changes from single mutations using MSA-based language models and a curated dataset, achieving better performance than existing methods.

Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering

This paper annotates protein families in the Unified Human Gastrointestinal Proteome using DPCfam clustering, improving family coverage over Pfam.

The geometry of hidden representations of protein language models

The paper analyzes the geometric properties of hidden representations in protein language models and identifies three distinct phases that reveal a general strategy for reconstructing missing data.