Fabrizio Angaroni

Kinbiont: From time series to ecological and evolutionary responses in microbial systems

Kinbiont provides a model-based analysis pipeline for microbial kinetics data, enabling ecological and evolutionary insights through numerical methods and machine learning.

Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients

This study identifies cancer type-specific evolutionary signatures using genomic data from over 35,000 patients, revealing patterns of driver mutation acquisition linked to prognosis.

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.

PMCE: efficient inference of expressive models of cancer evolution with high prognostic power

PMCE infers probabilistic graphical models of cancer evolution from mutational profiles, showing a significant correlation between predicted evolutionary paths and patient survival.

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.