Author

Alice Antonello

University of Trieste

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Research Focus:variant calling· 4 Assay:whole-genome sequencing· 4 Approach:statistical model· 2 Research Focus:trajectory inference· 2 Research Focus:variant effect prediction· 2 Approach:Bayesian inference· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Giulio CaravagnaiD· 4 shared Giovanni SantacatterinaiD· 3 shared Nicola CalonaciiD· 3 shared Riccardo Bergamin· 3 shared Salvatore MiliteiD· 2 shared Alberto CasagrandeiD· 1 shared Alberto CazzanigaiD· 1 shared Alberto d’OnofrioiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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4 shared papersBioinformatics

Giulio CaravagnaORCID

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4 papers

Recent·Most cited

Tumour evolution as ground truth for cancer whole-genome sequencing

Valeriani Lucrezia, Giorgia Gandolfi, Elena Buscaroli, Katsiaryna Davydzenka, Giovanni Santacatterina, Alice Antonello, Azad Sadr, Virginia Anna Gazziero, Salvatore Milite, Elena Rivaroli, Anna Kabanova, Guido Sanguinetti, Alessio Ansuini, Leonardo Egidi, Stefano Cozzini, , Giulio Caravagna

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.

bioRxiv · Jun 11, 2026 · PreprintBioinformatics

A reference-free strategy for circulating tumor DNA detection from whole-genome sequencing data

Carmen Oroperv, Amanda Frydendahl, Tenna Vesterman Henriksen, Giovanni Santacatterina, Alice Antonello, Nicola Calonaci, Mads Heilskov Rasmussen, Giulio Caravagna, IMPROVE-consortia, Claus L. Andersen, Søren Besenbacher

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.

bioRxiv · Jul 23, 2025 · PreprintBioinformatics

Timing and clustering co-occurring genome amplifications incancers

Sara Cocomello, Giovanni Santacatterina, Riccardo Bergamin, Alice Antonello, Giulio Caravagna

This paper introduces TickTack, a Bayesian model to time and cluster co-occurring genome amplifications in cancer, revealing insights into tumor evolution and genomic instability.

bioRxiv · Mar 31, 2025 · PreprintCancer Biology

Computational validation of clonal and subclonal copy number alterations from bulk tumour sequencing

Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J. Williams, Fabio Anselmi, Alberto d’Onofrio, Vasavi Sundaram, Alona Sosinsky, William C. H. Cross, Giulio Caravagna

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.

bioRxiv · Feb 13, 2021 · PreprintBioinformatics