BONIZZONI, PAOLA
BONIZZONI, PAOLA
DIPARTIMENTO DI INFORMATICA, SISTEMISTICA E COMUNICAZIONE
Differential analysis of alternative splicing events in gene regions using residual neural networks
2025 Ciccolella, S; Denti, L; Avila Cartes, J; Della Vedova, G; Pirola, Y; Rizzi, R; Bonizzoni, P
Identification of Chimeric RNAs: A Novel Machine Learning Perspective
2025 Bonizzoni, P; De Felice, C; Pirola, Y; Rizzi, R; Zaccagnino, R; Zizza, R
On recognizing graphs representing persistent perfect phylogenies
2025 Bonizzoni, P; Della Vedova, G; Soto Gomez, M; Trucco, G
Pangenome Graph Indexing via the Multidollar-BWT
2025 Cozzi, D; Riccardi, B; Denti, L; Ciccolella, S; Sadakane, K; Bonizzoni, P
Phasing Data from Genotype Queries via the µ-PBWT
2025 Cozzi, D; Bonizzoni, P; Boucher, C; Langmead, B; Pirola, Y
Considerations in the search for epistasis
2024 Balvert, M; Cooper-Knock, J; Stamp, J; Byrne, R; Mourragui, S; Van Gils, J; Benonisdottir, S; Schlüter, J; Kenna, K; Abeln, S; Iacoangeli, A; Daub, J; Browning, B; Taş, G; Hu, J; Wang, Y; Alhathli, E; Harvey, C; Pianesi, L; Schulte, S; González-Domínguez, J; Garrisson, E; Pasanuic, B; Zhang, S; Vorbrugg, S; Van Bemmelen, J; Dandinasivara, R; Markowska, M; Koyuturk, M; Guarracino, A; Bonizzoni, P; Bolognini, D; Von Berg, J; Baaijens, J; Cartes, J; Al-Chalabi, A; Snyder, M; Schönhuth, A; Sng, L; Twine, N
Differential quantification of alternative splicing events on spliced pangenome graphs
2024 Ciccolella, S; Cozzi, D; Della Vedova, G; Kuria, S; Bonizzoni, P; Denti, L
Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development
2024 Mahadevaraju, S; Pal, S; Bhaskar, P; Mcdonald, B; Benner, L; Denti, L; Cozzi, D; Bonizzoni, P; Przytycka, T; Brian, O
PangeBlocks: customized construction of pangenome graphs via maximal blocks
2024 Avila Cartes, J; Bonizzoni, P; Ciccolella, S; Della Vedova, G; Denti, L
RecGraph: recombination-aware alignment of sequences to variation graphs
2024 Avila Cartes, J; Bonizzoni, P; Ciccolella, S; Della Vedova, G; Denti, L; Didelot, X; Monti, D; Pirola, Y
Solving the Minimal Positional Substring Cover Problem in Sublinear Space
2024 Bonizzoni, P; Boucher, C; Cozzi, D; Gagie, T; Pirola, Y
Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property
2024 Bonizzoni, P; De Felice, C; Riccardi, B; Zaccagnino, R; Zizza, R
Accurate and fast clade assignment via deep learning and frequency chaos game representation
2023 Avila Cartes, J; Anand, S; Ciccolella, S; Bonizzoni, P; Della Vedova, G
Data Structures for SMEM-Finding in the PBWT
2023 Bonizzoni, P; Boucher, C; Cozzi, D; Gagie, T; Köppl, D; Rossi, M
ESGq: Alternative Splicing events quantification across conditions based on Event Splicing Graphs
2023 Cozzi, D; Bonizzoni, P; Denti, L
Identification of Chimeric RNAs: a novel machine learning perspective
2023 Bonizzoni, P; De Felice, C; Pirola, Y; Rizzi, R; Zaccagnino, R; Zizza, R
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT
2023 Bonizzoni, P; Della Vedova, G; Pirola, Y; Rizzi, R; Sgrò, M
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads
2023 Denti, L; Khorsand, P; Bonizzoni, P; Hormozdiari, F; Chikhi, R
μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data
2023 Cozzi, D; Rossi, M; Rubinacci, S; Gagie, T; Köppl, D; Boucher, C; Bonizzoni, P
Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?
2022 Bonizzoni, P; De Felice, C; Pirola, Y; Rizzi, R; Zaccagnino, R; Zizza, R