| ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events L Denti, R Rizzi, S Beretta, GD Vedova, M Previtali, P Bonizzoni BMC bioinformatics 19 (1), 444, 2018 | 57 | 2018 |
| MALVA: genotyping by Mapping-free ALlele detection of known VAriants L Denti, M Previtali, G Bernardini, A Schönhuth, P Bonizzoni Iscience 18, 20-27, 2019 | 38 | 2019 |
| SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads L Denti, P Khorsand, P Bonizzoni, F Hormozdiari, R Chikhi Nature Methods 20 (4), 550-558, 2023 | 36* | 2023 |
| Triplet-based similarity score for fully multilabeled trees with poly-occurring labels S Ciccolella, G Bernardini, L Denti, P Bonizzoni, M Previtali, ... Bioinformatics 37 (2), 178-184, 2021 | 30 | 2021 |
| Mapping RNA-seq data to a transcript graph via approximate pattern matching to a hypertext S Beretta, P Bonizzoni, L Denti, M Previtali, R Rizzi International Conference on Algorithms for Computational Biology, 49-61, 2017 | 13 | 2017 |
| Shark: fishing relevant reads in an RNA-Seq sample L Denti, Y Pirola, M Previtali, T Ceccato, G Della Vedova, R Rizzi, ... Bioinformatics 37 (4), 464-472, 2021 | 11* | 2021 |
| MALVIRUS: an integrated application for viral variant analysis S Ciccolella, L Denti, P Bonizzoni, G Della Vedova, Y Pirola, M Previtali BMC bioinformatics 22 (Suppl 15), 625, 2021 | 10* | 2021 |
| Comparative genome analysis using sample-specific string detection in accurate long reads P Khorsand, L Denti, Human Genome Structural Variant Consortium, ... Bioinformatics advances 1 (1), vbab005, 2021 | 10 | 2021 |
| RecGraph: recombination-aware alignment of sequences to variation graphs J Avila Cartes, P Bonizzoni, S Ciccolella, G Della Vedova, L Denti, ... Bioinformatics 40 (5), btae292, 2024 | 8* | 2024 |
| Graph theory and definitions S Beretta, L Denti, M Previtali Encyclopedia of bioinformatics and computational biology: ABC of …, 2019 | 6 | 2019 |
| Pangenome graph augmentation from unassembled long reads L Denti, P Bonizzoni, B Brejova, R Chikhi, T Krannich, T Vinar, ... bioRxiv, 2025.02. 07.637057, 2025 | 3 | 2025 |
| Differential quantification of alternative splicing events on spliced pangenome graphs S Ciccolella, D Cozzi, G Della Vedova, SN Kuria, P Bonizzoni, L Denti PLOS Computational Biology 20 (12), e1012665, 2024 | 3 | 2024 |
| PangeBlocks: customized construction of pangenome graphs via maximal blocks J Avila Cartes, P Bonizzoni, S Ciccolella, G Della Vedova, L Denti BMC bioinformatics 25 (1), 344, 2024 | 3 | 2024 |
| ESGq: Alternative Splicing events quantification across conditions based on Event Splicing Graphs D Cozzi, P Bonizzoni, L Denti bioRxiv, 2023.07. 05.547757, 2023 | 2 | 2023 |
| Network properties S Beretta, L Denti, M Previtali Encyclopedia of Bioinformatics and Computational Biology: ABC of …, 2019 | 2 | 2019 |
| Differential analysis of alternative splicing events in gene regions using residual neural networks S Ciccolella, L Denti, J Avila Cartes, G Della Vedova, Y Pirola, R Rizzi, ... Neural Computing and Applications 37 (9), 6819-6829, 2025 | 1 | 2025 |
| Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development S Mahadevaraju, S Pal, P Bhaskar, BD McDonald, L Benner, L Denti, ... bioRxiv, 2024 | 1 | 2024 |
| Alignment-Free Genotyping of Known Variations with MALVA G Bernardini, L Denti, M Previtali Variant Calling: Methods and Protocols, 247-256, 2022 | 1 | 2022 |
| Algorithms for analyzing genetic variability from Next-Generation Sequencing data L Denti Università degli Studi di Milano-Bicocca, 2020 | 1 | 2020 |
| Alignment-free detection of differences between sequencing datasets A Petescia, L Denti, A Gafurov, V Hodorová, J Nosek, B Brejová, T Vinař iScience 28 (11), 2025 | | 2025 |
