Raffaella Rizzi

42 papers C 6Journal 27Unranked 9
YearRankTypeTitle / Venue / Authors
2025 J jnl
Differential analysis of alternative splicing events in gene regions using residual neural networks.
Neural Comput. Appl.
Simone Ciccolella, Luca Denti, Jorge Avila Cartes, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Paola Bonizzoni
2025 — conf
Minimizer Sketches of Lyndon-Fingerprints: A Novel Approach to Compute Overlaps Among Long Reads.
BIBM
Omar Masri, Yuri Pirola, Cristina Borghi, Paola Bonizzoni, Raffaella Rizzi
2023 — conf
Identification of Chimeric RNAs: A Novel Machine Learning Perspective.
ICCABS
Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
2023 — conf
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT.
IWBBIO (1)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò
2022 C conf
Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?
DLT
Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
2022 J jnl
Computational graph pangenomics: a tutorial on data structures and their applications.
Nat. Comput.
Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
2022 — conf
KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints.
IWBBIO (2)
Paola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
2022 J jnl
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.
CoRR
Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2022 J jnl
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.
Inf. Sci.
Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2021 — conf
Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning.
AlCoB
Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2021 J jnl
Computing the multi-string BWT and LCP array in external memory.
Theor. Comput. Sci.
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2021 J jnl
Shark: fishing relevant reads in an RNA-Seq sample.
Bioinform.
Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
2019 J jnl
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array.
J. Comput. Biol.
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2019 J jnl
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era.
Quant. Biol.
Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
2018 J jnl
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
BMC Bioinform.
Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
2018 C conf
Divide and Conquer Computation of the Multi-string BWT and LCP Array.
CiE
Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2017 J jnl
A colored graph approach to perfect phylogeny with persistent characters.
Theor. Comput. Sci.
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
2017 J jnl
An External-Memory Algorithm for String Graph Construction.
Algorithmica
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2017 C conf
Character-Based Phylogeny Construction and Its Application to Tumor Evolution.
CiE
Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez
2017 J jnl
Computing the BWT and LCP array of a Set of Strings in External Memory.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2017 J jnl
FSG: Fast String Graph Construction for De Novo Assembly.
J. Comput. Biol.
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2017 — conf
Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext.
AlCoB
Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi
2017 J jnl
Species-Driven Persistent Phylogeny.
Fundam. Informaticae
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
2016 J jnl
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi
2016 — conf
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data.
ISBRA
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2016 J jnl
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2016 J jnl
LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.
J. Comput. Biol.
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2014 C conf
Constructing String Graphs in External Memory.
WABI
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2014 J jnl
Constructing String Graphs in External Memory.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
2014 J jnl
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs.
J. Comput. Biol.
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
2012 J jnl
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.
BMC Bioinform.
Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni
2012 — conf
Reconstructing isoform graphs from RNA-Seq data.
BIBM
Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova
2011 J jnl
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res.
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
2011 — conf
PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text.
ICCABS
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi
2011 J jnl
Predicting Variants of Alternative Splicing from NGS data without the Genome
CoRR
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi
2009 J jnl
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach.
J. Comput. Biol.
Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi
2009 C conf
Minimum Factorization Agreement of Spliced ESTs.
WABI
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi
2008 J jnl
ASPicDB: A database resource for alternative splicing analysis.
Bioinform.
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
2007 J jnl
Exemplar Longest Common Subsequence.
IEEE ACM Trans. Comput. Biol. Bioinform.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette
2006 J jnl
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Nucleic Acids Res.
Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, Graziano Pesole
2005 J jnl
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.
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
2003 C conf
A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence.
WABI
Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi