| Protein Kinase A Activation Promotes Cancer Cell Resistance to Glucose Starvation and Anoikis R Palorini, G Votta, Y Pirola, H De Vitto, S De Palma, C Airoldi, M Vasso, ... PLoS genetics 12 (3), e1005931, 2016 | 88 | 2016 |
| ASPicDB: a database resource for alternative splicing analysis T Castrignanò, M D’Antonio, A Anselmo, D Carrabino, A D’Onorio De Meo, ... Bioinformatics 24 (10), 1300-1304, 2008 | 60 | 2008 |
| ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences P Bonizzoni, R Rizzi, G Pesole BMC bioinformatics 6, 1-16, 2005 | 51 | 2005 |
| ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing PL Martelli, M D’Antonio, P Bonizzoni, T Castrignano, AM D’Erchia, ... Nucleic acids research 39 (suppl_1), D80-D85, 2010 | 49 | 2010 |
| Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era R Rizzi, S Beretta, M Patterson, Y Pirola, M Previtali, G Della Vedova, ... Quantitative Biology 7, 278-292, 2019 | 47 | 2019 |
| Computational graph pangenomics: a tutorial on data structures and their applications JA Baaijens, P Bonizzoni, C Boucher, G Della Vedova, Y Pirola, R Rizzi, ... Natural Computing 21 (1), 81-108, 2022 | 45 | 2022 |
| 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, 1-21, 2018 | 44 | 2018 |
| Exemplar longest common subsequence P Bonizzoni, G Della Vedova, R Dondi, G Fertin, R Rizzi, S Vialette IEEE/ACM Transactions on Computational Biology and Bioinformatics 4 (4), 535-543, 2007 | 43 | 2007 |
| ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization T Castrignano, R Rizzi, IG Talamo, PDO De Meo, A Anselmo, P Bonizzoni, ... Nucleic Acids Research 34 (suppl_2), W440-W443, 2006 | 41 | 2006 |
| Computational methods for alternative splicing prediction. P Bonizzoni, R Rizzi, G Pesole Briefings in functional genomics & proteomics 5 (1), 2006 | 31 | 2006 |
| Modeling alternative splicing variants from RNA-Seq data with isoform graphs S Beretta, P Bonizzoni, GD Vedova, Y Pirola, R Rizzi Journal of Computational Biology 21 (1), 16-40, 2014 | 22 | 2014 |
| Detecting alternative gene structures from spliced ESTs: a computational approach P Bonizzoni, G Mauri, G Pesole, E Picardi, Y Pirola, R Rizzi Journal of computational biology 16 (1), 43-66, 2009 | 22 | 2009 |
| FSG: fast string graph construction for de novo assembly P Bonizzoni, GD Vedova, Y Pirola, M Previtali, R Rizzi Journal of computational biology 24 (10), 953-968, 2017 | 21 | 2017 |
| Multithread multistring Burrows–Wheeler transform and longest common prefix array P Bonizzoni, G Della Vedova, Y Pirola, M Previtali, R Rizzi Journal of computational biology 26 (9), 948-961, 2019 | 18 | 2019 |
| LSG: an external-memory tool to compute string graphs for next-generation sequencing data assembly P Bonizzoni, GD Vedova, Y Pirola, M Previtali, R Rizzi Journal of Computational Biology 23 (3), 137-149, 2016 | 18 | 2016 |
| An external-memory algorithm for string graph construction P Bonizzoni, G Della Vedova, Y Pirola, M Previtali, R Rizzi Algorithmica 78 (2), 394-424, 2017 | 14 | 2017 |
| A colored graph approach to perfect phylogeny with persistent characters P Bonizzoni, AP Carrieri, G Della Vedova, R Rizzi, G Trucco Theoretical Computer Science 658, 60-73, 2017 | 13 | 2017 |
| 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 Algorithms for Computational Biology: 4th International Conference, AlCoB …, 2017 | 12 | 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 |
| Constructing string graphs in external memory P Bonizzoni, G Della Vedova, Y Pirola, M Previtali, R Rizzi Algorithms in Bioinformatics: 14th International Workshop, WABI 2014 …, 2014 | 10 | 2014 |
