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ORCIDYuri Pirola
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- affiliation: University of Milano-Bicocca, Milan, Italy
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2020 – today
- 2024
[c19]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola:
Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM 2024: 12:1-12:16- 2023
- [c18]Paola Bonizzoni
, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò:
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. IWBBIO (1) 2023: 62-76 - 2022
- [j26]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: 458-476 (2022) - [j25]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): 81-108 (2022) - [c17]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: 3-12 - [c16]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: 436-449 - [i9]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 abs/2202.13884 (2022) - 2021
- [j24]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): 464-472 (2021) - [j23]Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali:
MALVIRUS: an integrated application for viral variant analysis. BMC Bioinform. 22-S(15): 625 (2021) - [j22]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: 42-58 (2021) - [c15]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: 16-28 - 2020
- [j21]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): 1622-1624 (2020)
2010 – 2019
- 2019
- [j20]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): 948-961 (2019) - [j19]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): 278-292 (2019) - 2018
- [c14]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: 107-117 - 2017
- [j18]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
An External-Memory Algorithm for String Graph Construction. Algorithmica 78(2): 394-424 (2017) - [j17]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): 953-968 (2017) - [i8]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 abs/1705.07756 (2017) - 2016
- [j16]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): 1610-1617 (2016) - [j15]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): 137-149 (2016) - [j14]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): 718-736 (2016) - [c13]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: 27-39 - [r1]Riccardo Dondi, Yuri Pirola:
Beyond Evolutionary Trees. Encyclopedia of Algorithms 2016: 183-189 - [i7]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. CoRR abs/1604.03587 (2016) - 2015
- [j13]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58(7): 1673-1686 (2015) - [j12]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): 214-224 (2015) - [c12]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: 100-113 - 2014
- [j11]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): 16-40 (2014) - [c11]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. LATA 2014: 126-137 - [c10]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. WABI 2014: 311-325 - [i6]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. CoRR abs/1405.7520 (2014) - 2013
- [j10]Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability. Algorithms 6(1): 1-11 (2013) - [j9]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized complexity of k-anonymity: hardness and tractability. J. Comb. Optim. 26(1): 19-43 (2013) - [c9]Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini:
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. BCB 2013: 33 - [i5]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. CoRR abs/1310.5037 (2013) - 2012
- [j8]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): S2 (2012) - [j7]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): 12-25 (2012) - [j6]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): 1582-1594 (2012) - [j5]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: 34-57 (2012) - [c8]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: 1-6 - 2011
- [c7]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: 33-39 - [i4]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 abs/1107.3724 (2011) - 2010
- [j4]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Variants of constrained longest common subsequence. Inf. Process. Lett. 110(20): 877-881 (2010) - [j3]Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang:
Beyond evolutionary trees. Nat. Comput. 9(2): 421-435 (2010) - [j2]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 598-610 (2010) - [c6]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized Complexity of k-Anonymity: Hardness and Tractability. IWOCA 2010: 242-255 - [c5]Yuri Pirola, Paola Bonizzoni, Tao Jiang:
Haplotype Inference on Pedigrees with Recombinations and Mutations. WABI 2010: 148-161 - [i3]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. CoRR abs/1001.1210 (2010)
2000 – 2009
- 2009
- [j1]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): 43-66 (2009) - [c4]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. ISBRA 2009: 186-197 - [c3]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi:
Minimum Factorization Agreement of Spliced ESTs. WABI 2009: 1-12 - [i2]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized Complexity of the k-anonymity Problem. CoRR abs/0910.3148 (2009) - [i1]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Variants of Constrained Longest Common Subsequence. CoRR abs/0912.0368 (2009) - 2007
- [c2]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: 241-250 - 2006
- [c1]Leonardo Vanneschi, Yuri Pirola, Philippe Collard:
A quantitative study of neutrality in GP boolean landscapes. GECCO 2006: 895-902
Coauthor Index
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