Raffaella Rizzi

According to our database, Raffaella Rizzi authored at least 36 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò

Proceedings of the Bioinformatics and Biomedical Engineering, 2023

2022

Computational graph pangenomics: a tutorial on data structures and their applications.

Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén

Nat. Comput., 2022

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.

Paola Bonizzoni, Matteo Costantini, Clelia de Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza

Inf. Sci., 2022

KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints.

Paola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza

Proceedings of the Bioinformatics and Biomedical Engineering, 2022

Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?

Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza

Proceedings of the Developments in Language Theory - 26th International Conference, 2022

2021

Computing the multi-string BWT and LCP array in external memory.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

Theor. Comput. Sci., 2021

Shark: fishing relevant reads in an RNA-Seq sample.

Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni

Bioinform., 2021

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning.

Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza

Proceedings of the Algorithms for Computational Biology - 8th International Conference, 2021

2019

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era.

Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni

Quant. Biol., 2019

Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

J. Comput. Biol., 2019

2018

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.

Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni

BMC Bioinform., 2018

Divide and Conquer Computation of the Multi-string BWT and LCP Array.

Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Yuri Pirola, Marco Previtali, Raffaella Rizzi

Proceedings of the Sailing Routes in the World of Computation, 2018

2017

A colored graph approach to perfect phylogeny with persistent characters.

Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco

Theor. Comput. Sci., 2017

FSG: Fast String Graph Construction for De Novo Assembly.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

J. Comput. Biol., 2017

Species-Driven Persistent Phylogeny.

Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco

Fundam. Informaticae, 2017

Computing the BWT and LCP array of a Set of Strings in External Memory.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

CoRR, 2017

An External-Memory Algorithm for String Graph Construction.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

Algorithmica, 2017

Character-Based Phylogeny Construction and Its Application to Tumor Evolution.

Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez

Proceedings of the Unveiling Dynamics and Complexity, 2017

Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext.

Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi

Proceedings of the Algorithms for Computational Biology, 2017

2016

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

J. Comput. Biol., 2016

A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings.

Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi

CoRR, 2016

FSG: Fast String Graph Construction for De Novo Assembly of Reads Data.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

2014

Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs.

Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi

J. Comput. Biol., 2014

Constructing String Graphs in External Memory.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2012

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.

Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni

BMC Bioinform., 2012

Reconstructing isoform graphs from RNA-Seq data.

Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.

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

Nucleic Acids Res., 2011

Predicting Variants of Alternative Splicing from NGS data without the Genome

Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi

CoRR, 2011

PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text.

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2009

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach.

Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi

J. Comput. Biol., 2009

Minimum Factorization Agreement of Spliced ESTs.

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

2008

ASPicDB: A database resource for alternative splicing analysis.

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

Bioinform., 2008

2007

Exemplar Longest Common Subsequence.

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

2006

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, Graziano Pesole

Nucleic Acids Res., 2006

2005

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole

BMC Bioinform., 2005

2003

A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence.

Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003