Yuri Pirola

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 24

Top Topics

Machine Learning Approaches

Independence Relations

External Memory

Top Venues

J. Comput. Biol.

Publications

Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola
Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM (2024)
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)
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
MALVIRUS: an integrated application for viral variant analysis. BMC Bioinform. (15) (2021)
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)
Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali
MALVIRUS: an integrated application for viral variant analysis. BMC Bioinform. (15) (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)
Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinform. 36 (5) (2020)
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)
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)
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, 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, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. J. Comput. Biol. 23 (9) (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)
Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni
HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinform. 32 (11) (2016)
Carlo Batini, Paola Bonizzoni, Marco Comerio, Riccardo Dondi, Yuri Pirola, Francesco Salandra
A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas. J. Comput. Sci. Technol. 30 (1) (2015)
Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem. CPM (2015)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58 (7) (2015)
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)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. LATA (2014)
Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability. Algorithms 6 (1) (2013)
Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. BCB (2013)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
Parameterized complexity of k-anonymity: hardness and tractability. J. Comb. Optim. 26 (1) (2013)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. CoRR (2013)
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
A Fast and Practical Approach to Genotype Phasing and Imputation on a Pedigree with Erroneous and Incomplete Information. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (6) (2012)
Yuri Pirola, Paola Bonizzoni, Tao Jiang
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (1) (2012)
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information. ICCABS (2012)
Leonardo Vanneschi, Yuri Pirola, Giancarlo Mauri, Marco Tomassini, Philippe Collard, Sébastien Vérel
A study of the neutrality of Boolean function landscapes in genetic programming. Theor. Comput. Sci. 425 (2012)
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)
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni
Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers CoRR (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)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
Pure Parsimony Xor Haplotyping. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (4) (2010)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
Variants of constrained longest common subsequence. Inf. Process. Lett. 110 (20) (2010)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
-Anonymity: Hardness and Tractability. IWOCA (2010)
Yuri Pirola, Paola Bonizzoni, Tao Jiang
Haplotype Inference on Pedigrees with Recombinations and Mutations. WABI (2010)
Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang
Beyond evolutionary trees. Nat. Comput. 9 (2) (2010)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
Pure Parsimony Xor Haplotyping CoRR (2010)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
Pure Parsimony Xor Haplotyping. ISBRA (2009)
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)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
Variants of Constrained Longest Common Subsequence CoRR (2009)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
Parameterized Complexity of the k-anonymity Problem CoRR (2009)
Leonardo Vanneschi, Marco Tomassini, Philippe Collard, Sébastien Vérel, Yuri Pirola, Giancarlo Mauri
A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds. EuroGP (2007)
Leonardo Vanneschi, Yuri Pirola, Philippe Collard
A quantitative study of neutrality in GP boolean landscapes. GECCO (2006)