Simone Ciccolella

22 papers B 1Journal 15Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
Cancer progression inference using a finite-state model to allow recurrences and losses of mutations.
Neural Comput. Appl.
Simone Ciccolella, Murray Patterson, Iman Hajirasouliha, Gianluca Della Vedova
2025 J jnl
Differential analysis of alternative splicing events in gene regions using residual neural networks.
Neural Comput. Appl.
Simone Ciccolella, Luca Denti, Jorge Avila Cartes, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Paola Bonizzoni
2025 B conf
Pangenome Graph Indexing via the Multidollar-BWT.
SEA
Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, Paola Bonizzoni
2024 J jnl
Differential quantification of alternative splicing events on spliced pangenome graphs.
PLoS Comput. Biol.
Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti
2024 J jnl
PangeBlocks: customized construction of pangenome graphs via maximal blocks.
BMC Bioinform.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
2024 J jnl
RecGraph: recombination-aware alignment of sequences to variation graphs.
Bioinform.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
2023 — conf
Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines.
ICCABS
Akshay Juyal, Zahra Tayebi, Alexander Zelikovsky, Mauricio Soto Gomez, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
2023 J jnl
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data.
J. Comput. Biol.
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
2023 J jnl
Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison.
Algorithms
Simone Ciccolella, Gianluca Della Vedova, Vladimir Filipovic, Mauricio Soto Gomez
2022 — —
Practical algorithms for Computational Phylogenetics.
Simone Ciccolella
2022 J jnl
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data.
CoRR
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
2021 — conf
Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data.
ICCABS
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson
2021 J jnl
Effective Clustering for Single Cell Sequencing Cancer Data.
IEEE J. Biomed. Health Informatics
Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova
2021 J jnl
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.
Bioinform.
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
2021 J jnl
MALVIRUS: an integrated application for viral variant analysis.
BMC Bioinform.
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
2021 J jnl
Simpler and Faster Development of Tumor Phylogeny Pipelines.
J. Comput. Biol.
Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson
2021 J jnl
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.
Bioinform.
Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
2020 J jnl
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.
BMC Bioinform.
Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
2019 J jnl
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez
2019 — conf
Effective Clustering for Single Cell Sequencing Cancer Data.
BCB
Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova
2018 — conf
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.
ICCABS
Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
2017 — conf
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP.
BCB
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez