Roberto Spreafico

RNA evidence supports clinical stage antibody drug targets in oncology

The paper evaluates whether single-cell RNA-seq improves the prioritization of antibody-based oncology targets by combining tumor specificity, normal safety, and blood sink features.

EpiRanha: Hunting for Epitope Similarity with a Structure- and Residue-Aware Graph Neural Network

EpiRanha identifies epitope similarities using a structure- and residue-aware graph neural network, improving detection of cross-reactive epitopes and off-target interactions.

Effects of protein interface mutations on protein quality and affinity

The paper disentangles protein-interaction and protein-quality effects in antibody-antigen binding using deep mutational scanning and evaluates models for their ability to predict these effects.

NAStructuralDB : Structural database to facilitate computational studies of molecular modeling and recognition of proteins with special focus on antibody-antigen interactions.

NAStructuralDB provides a processed dataset of antibody, Nanobody, and protein structures with molecular contact information and annotations to aid in predictive tasks.

ASD: Antigen-Specific Antibody Database

The paper develops the ASD database to aggregate antibody-antigen interaction data from multiple sources, providing a standardized resource for computational model development.

Chronic sensing of host-derived lipids is an all-in-one signal that primes and activates NLRP3.

The paper shows that chronic exposure to oxidized phospholipids primes and activates NLRP3 via NRF2, independent of microbial cues, contributing to atherogenesis.

AbDesign: Database of point mutants of antibodies with associated structures reveals poor generalization of binding predictions from machine learning models.

The paper creates a dataset of antibody-antigen complexes with mutations and evaluates affinity prediction methods, finding that current models poorly predict binding effects compared to empirical methods.

Distinct components of nucleoside-modified messenger RNA vaccines cooperate to instruct efficient germinal center responses

This study identifies distinct roles of nucleoside-modified mRNA and lipid nanoparticles in promoting Tfh cell responses through different mechanisms.

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

Language models trained on high-throughput affinity data predict KD of unseen antibody variants across three orders of magnitude, and a "naturalness" score can be optimised alongside affinity.

NFκB dynamics determine stimulus-responsive epigenomic reprogramming in macrophages

This study shows that NFκB activity dynamics determine stimulus-specific epigenomic reprogramming in macrophages by promoting de novo enhancer formation.

Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing

The paper develops ImReP, a computational method to profile TCR and BCR repertoires from RNA-seq data, creating a large atlas of immunological sequences across 53 tissues.

Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

This paper introduces ROP to identify the source of unmapped RNA-Seq reads across diverse tissues, showing it can account for 99.9% of 1 trillion reads and reveals immune and microbial correlations.