Raffaella Rizzi

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 24

Top Topics

Machine Learning

Alternative Splicing

External Memory

Graph Construction

Top Venues

J. Comput. Biol.

Publications

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. IWBBIO (1) (2023)
Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. 21 (1) (2022)
Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes? DLT (2022)
Paola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints. IWBBIO (2) (2022)
Paola Bonizzoni, Matteo Costantini, Clelia de Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. Inf. Sci. 607 (2022)
Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. CoRR (2022)
Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. AlCoB (2021)
Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
Shark: fishing relevant reads in an RNA-Seq sample. Bioinform. 37 (4) (2021)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Computing the multi-string BWT and LCP array in external memory. Theor. Comput. Sci. 862 (2021)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array. J. Comput. Biol. 26 (9) (2019)
Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Quant. Biol. 7 (4) (2019)
Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC Bioinform. 19 (1) (2018)
Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Divide and Conquer Computation of the Multi-string BWT and LCP Array. CiE (2018)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
FSG: Fast String Graph Construction for De Novo Assembly. J. Comput. Biol. 24 (10) (2017)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
An External-Memory Algorithm for String Graph Construction. Algorithmica 78 (2) (2017)
Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez
Character-Based Phylogeny Construction and Its Application to Tumor Evolution. CiE (2017)
Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi
Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. AlCoB (2017)
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
Species-Driven Persistent Phylogeny. Fundam. Informaticae 154 (1-4) (2017)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Computing the BWT and LCP array of a Set of Strings in External Memory. CoRR (2017)
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
A colored graph approach to perfect phylogeny with persistent characters. Theor. Comput. Sci. 658 (2017)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. J. Comput. Biol. 23 (3) (2016)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. ISBRA (2016)
Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings. CoRR (2016)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. CoRR (2016)
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. J. Comput. Biol. 21 (1) (2014)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Constructing String Graphs in External Memory. CoRR (2014)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Constructing String Graphs in External Memory. WABI (2014)
Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC Bioinform. 13 (S-5) (2012)
Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova
Reconstructing isoform graphs from RNA-Seq data. BIBM (2012)
Pier Luigi Martelli, Mattia D'Antonio, Paola Bonizzoni, Tiziana Castrignanò, Anna Maria D'Erchia, Paolo D'Onorio De Meo, Piero Fariselli, Michele Finelli, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 39 (Database-Issue) (2011)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text. ICCABS (2011)
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi
Predicting Variants of Alternative Splicing from NGS data without the Genome CoRR (2011)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi
Minimum Factorization Agreement of Spliced ESTs. WABI (2009)
Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. J. Comput. Biol. 16 (1) (2009)
Tiziana Castrignanò, Mattia D'Antonio, Anna Anselmo, Danilo Carrabino, A. D'Onorio De Meo, Anna Maria D'Erchia, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Alberto Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole
ASPicDB: A database resource for alternative splicing analysis. Bioinform. 24 (10) (2008)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette
Exemplar Longest Common Subsequence. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (4) (2007)
Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, Graziano Pesole
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinform. 6 (2005)
Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi
A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence. WABI (2003)