Nicola Calonaci

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

The paper introduces ctDNAmer, a reference-free tool for detecting ctDNA from WGS data by analyzing k-mers, showing improved tumor fraction estimation and detection compared to traditional methods.

CONGAS+ is a Bayesian method that maps single-cell RNA and ATAC data to copy number clones, revealing subclonal architectures and genotype-phenotype relationships in cancer.

CONGAS clusters single-cell RNA sequencing data using copy number alterations to infer subclonal composition and RNA phenotypes in cancer data.

This paper introduces CNAqc, a toolset for validating clonal and subclonal copy number alterations in bulk tumor sequencing by addressing tumor purity, ploidy, and heterogeneity using simulations and single-cell data.