Yuri Pirola

60 papers A 1B 3C 7Journal 37Unranked 11
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
2025 — conf
Phasing Data from Genotype Queries via the μ-PBWT.
The Expanding World of Compressed Data
Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, Yuri Pirola
2024 J jnl
RecGraph: recombination-aware alignment of sequences to variation graphs.
Bioinform.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
2024 B conf
Solving the Minimal Positional Substring Cover Problem in Sublinear Space.
CPM
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola
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
MALVIRUS: an integrated application for viral variant analysis.
BMC Bioinform.
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
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
2020 J jnl
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites.
Bioinform.
Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini
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 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
An External-Memory Algorithm for String Graph Construction.
Algorithmica
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
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
2016 — ch.
Beyond Evolutionary Trees.
Encyclopedia of Algorithms
Riccardo Dondi, Yuri Pirola
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
HapCol: accurate and memory-efficient haplotype assembly from long reads.
Bioinform.
Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni
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
2016 J jnl
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.
J. Comput. Biol.
Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
2015 J jnl
A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas.
J. Comput. Sci. Technol.
Carlo Batini, Paola Bonizzoni, Marco Comerio, Riccardo Dondi, Yuri Pirola, Francesco Salandra
2015 J jnl
Covering Pairs in Directed Acyclic Graphs.
Comput. J.
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2015 B conf
On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem.
CPM
Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
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 C conf
Covering Pairs in Directed Acyclic Graphs.
LATA
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
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
2013 J jnl
Covering Pairs in Directed Acyclic Graphs.
CoRR
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2013 — conf
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes.
BCB
Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini
2013 J jnl
Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability.
Algorithms
Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
2013 J jnl
Parameterized complexity of k-anonymity: hardness and tractability.
J. Comb. Optim.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
2012 J jnl
A Fast and Practical Approach to Genotype Phasing and Imputation on a Pedigree with Erroneous and Incomplete Information.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
2012 — conf
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
ICCABS
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
2012 J jnl
A study of the neutrality of Boolean function landscapes in genetic programming.
Theor. Comput. Sci.
Leonardo Vanneschi, Yuri Pirola, Giancarlo Mauri, Marco Tomassini, Philippe Collard, Sébastien Vérel
2012 J jnl
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yuri Pirola, Paola Bonizzoni, Tao Jiang
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
2011 J jnl
Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers
CoRR
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
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
2010 J jnl
Beyond evolutionary trees.
Nat. Comput.
Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang
2010 C conf
Haplotype Inference on Pedigrees with Recombinations and Mutations.
WABI
Yuri Pirola, Paola Bonizzoni, Tao Jiang
2010 C conf
Parameterized Complexity of
IWOCA
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
2010 J jnl
Pure Parsimony Xor Haplotyping
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
2010 J jnl
Pure Parsimony Xor Haplotyping.
IEEE ACM Trans. Comput. Biol. Bioinform.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
2010 J jnl
Variants of constrained longest common subsequence.
Inf. Process. Lett.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
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
2009 J jnl
Parameterized Complexity of the k-anonymity Problem
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
2009 — conf
Pure Parsimony Xor Haplotyping.
ISBRA
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
2009 J jnl
Variants of Constrained Longest Common Subsequence
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
2007 B conf
A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds.
EuroGP
Leonardo Vanneschi, Marco Tomassini, Philippe Collard, Sébastien Vérel, Yuri Pirola, Giancarlo Mauri
2006 A conf
A quantitative study of neutrality in GP boolean landscapes.
GECCO
Leonardo Vanneschi, Yuri Pirola, Philippe Collard