Publications by authors named "Simone Ciccolella"

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Differential quantification of alternative splicing events on spliced pangenome graphs.
Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni

PLoS Comput Biol· December 2024

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PangeBlocks: customized construction of pangenome graphs via maximal blocks.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti

BMC Bioinformatics· November 2024

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RecGraph: recombination-aware alignment of sequences to variation graphs.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti

Bioinformatics· May 2024

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Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data.
Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson

J Comput Biol· April 2023

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Accurate and fast clade assignment via deep learning and frequency chaos game representation.
Jorge Avila Cartes, Santosh Anand, Simone Ciccolella, Paola Bonizzoni, Gianluca Della Vedova

Gigascience· December 2022

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MALVIRUS: an integrated application for viral variant analysis.
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola

BMC Bioinformatics· April 2022

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Effective Clustering for Single Cell Sequencing Cancer Data.
Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova

IEEE J Biomed Health Inform· November 2021

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Simpler and Faster Development of Tumor Phylogeny Pipelines.
Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson

J Comput Biol· November 2021

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Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.
Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali

Bioinformatics· April 2021

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Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush

Bioinformatics· April 2021

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gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.
Simone Ciccolella, Mauricio Soto Gomez, Murray D Patterson, Gianluca Della Vedova, Iman Hajirasouliha

BMC Bioinformatics· December 2020

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Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach.
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto

IEEE/ACM Trans Comput Biol Bioinform· March 2020

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PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
Salem Malikic, Farid Rashidi Mehrabadi, Simone Ciccolella, Md Khaledur Rahman, Camir Ricketts

Genome Res· November 2019

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