Davide Maspero

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

This study identifies MET signaling as a targetable vulnerability in rhabdoid tumors through integrated single-cell multi-omic and spatial transcriptomics analyses.

Spatial Flux Balance Analysis reveals region-specific cancer metabolic rewiring and metastatic mimicking

The paper develops spFBA to analyze spatial metabolic differences in cancer, revealing metastatic mimicking and lactate-consuming cells in colorectal tumors.

Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer

This study tracks T cell dynamics in a pediatric cancer patient post-ICI therapy to identify tumor-reactive TCRs for personalized TCR-T cell therapy.

Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data

This study identifies low-frequency mutations in SARS-CoV-2 deep sequencing data to detect variants earlier than consensus-based methods, using 220,788 samples.

Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines

The paper uses variant calling from scRNA-seq data to identify potential sample swaps between patient-derived cell lines.

Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution

The paper analyzes SARS-CoV-2 synonymous mutations across 400,000 samples, showing that mutations increasing codon similarity to human codons tend to persist, suggesting adaptation to human host codon usage.

Longitudinal cancer evolution from single cells

This paper introduces LACE, a framework for analyzing longitudinal single-cell mutation data to model cancer evolution and therapy response.

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

The paper analyzes SARS-CoV-2 genomic diversity to reveal mutational signatures and host responses, showing heterogeneous genomic architectures and the role of purifying selection and transmission dynamics.

VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

VERSO improves viral phylogenetic inference and quantifies intra-host diversity using clonal variant profiles and variant frequency patterns, outperforming existing tools on simulations and real data.

Personalized therapy design for liquid tumors via optimal control theory

This paper applies optimal control theory to design personalized cancer therapies, showing that individual pharmacokinetic differences significantly impact treatment outcomes.

Integration of single-cell RNA-seq data into metabolic models to characterize tumour cell populations

This paper integrates single-cell RNA-seq data into metabolic models to characterize tumour cell populations and identifies metabolic heterogeneity and interactions.

MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq data

MaREA identifies metabolic reactions significantly up-/down-regulated in cancer subgroups using RNAseq data and visualizes results on metabolic maps.