Paola Bonizzoni

ORCID

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 60

Top Venues

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, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, Rosalba Zizza
Unveiling the connection between the Lyndon factorization and the Canonical Inverse Lyndon factorization via a border property. CoRR (2024)
Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, Rosalba Zizza
Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. MFCS (2024)
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
From the Lyndon factorization to the Canonical Inverse Lyndon factorization: back and forth. CoRR (2024)
Davide Cozzi, Paola Bonizzoni, Luca Denti
ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs. ITAT (2023)
Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. 39 (9) (2023)
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. IWBBIO (1) (2023)
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi
Data Structures for SMEM-Finding in the PBWT. SPIRE (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)
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29 (2) (2022)
Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova
Effective Clustering for Single Cell Sequencing Cancer Data. IEEE J. Biomed. Health Informatics 25 (11) (2021)
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinform. 37 (3) (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, 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)
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
On the longest common prefix of suffixes in an inverse Lyndon factorization and other properties. Theor. Comput. Sci. 862 (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)
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
Incomplete Directed Perfect Phylogeny in Linear Time. WADS (2021)
Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg
Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday. Theor. Comput. Sci. 894 (2021)
Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. Bioinform. 37 (2) (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, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
Unavoidable Sets, Prefix Graphs and Regularity of Circular Splicing Languages. Fundam. Informaticae 171 (1-4) (2020)
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
Lyndon Words versus Inverse Lyndon Words: Queries on Suffixes and Bordered Words. LATA (2020)
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
On Two Measures of Distance between Fully-Labelled Trees. CoRR (2020)
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
On Two Measures of Distance Between Fully-Labelled Trees. CPM (2020)
Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinform. (1) (2020)
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
Incomplete Directed Perfect Phylogeny in Linear Time. CoRR (2020)
Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova
Effective Clustering for Single Cell Sequencing Cancer Data. BCB (2019)
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
A rearrangement distance for fully-labelled trees. CoRR (2019)
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
Lyndon words versus inverse Lyndon words: queries on suffixes and bordered words. CoRR (2019)
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)
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
A Rearrangement Distance for Fully-Labelled Trees. CPM (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, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
Inverse Lyndon words and inverse Lyndon factorizations of words. Adv. Appl. Math. 101 (2018)
Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC Bioinform. 19 (1) (2018)
Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. ICCABS (2018)
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinform. 19 (1) (2018)
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, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
Inverse Lyndon words and Inverse Lyndon factorizations of words. CoRR (2017)
Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi
Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. AlCoB (2017)
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
Species-Driven Persistent Phylogeny. Fundam. Informaticae 154 (1-4) (2017)
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. BCB (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, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco
A colored graph approach to perfect phylogeny with persistent characters. Theor. Comput. Sci. 658 (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, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings. CoRR (2016)
Vasco Brattka, Paola Bonizzoni, Olivier Bournez, Elvira Mayordomo
Editorial. Comput. 5 (1) (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)
Paola Bonizzoni, Gianluca Della Vedova, Gabriella Trucco
Solving the Persistent Phylogeny Problem in polynomial time. CoRR (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, Natasa Jonoska
Existence of constants in regular splicing languages. Inf. Comput. 242 (2015)
Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza
Splicing Systems from Past to Future: Old and New Challenges. CoRR (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)
Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis
Restricted and Swap Common Superstring: A Multivariate Algorithmic Perspective. Algorithmica 72 (4) (2015)
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58 (7) (2015)
Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza
Splicing Systems from Past to Future: Old and New Challenges. Discrete Mathematics and Computer Science (2014)
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinform. 30 (1) (2014)
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco
Algorithms for the Constrained Perfect Phylogeny with Persistent Characters. CoRR (2014)
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)
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora
Complexity insights of the Minimum Duplication problem. Theor. Comput. Sci. 530 (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)
Paola Bonizzoni
The Holy Grail: Finding the Genetic Bases of Phenotypic Characters. UCNC (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. 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)
Paola Bonizzoni, Peter J. Cameron, Gianluca Della Vedova, Alberto Leporati, Giancarlo Mauri
A Unifying Framework to Characterize the Power of a Language to Express Relations CoRR (2012)
Vasco Brattka, Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Elvira Mayordomo
Editorial. Comput. 1 (1) (2012)
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora
Complexity Insights of the Minimum Duplication Problem. SOFSEM (2012)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
A randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters. Theor. Comput. Sci. 429 (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)
Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis
Restricted and Swap Common Superstring: A Parameterized View. IPEC (2012)
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Florian Sikora
On the parameterized complexity of the repetition free longest common subsequence problem. Inf. Process. Lett. 112 (7) (2012)
Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova
Reconstructing isoform graphs from RNA-Seq data. BIBM (2012)
Paola Bonizzoni, Chiara Braghin, Riccardo Dondi, Gabriella Trucco
The binary perfect phylogeny with persistent characters. Theor. Comput. Sci. 454 (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, Riccardo Dondi
Anonymizing binary and small tables is hard to approximate. J. Comb. Optim. 22 (1) (2011)
Paola Bonizzoni
Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model. ICCABS (2011)
Chiara Braghin, Riccardo Dondi, Gabriella Trucco, Paola Bonizzoni
The Binary Perfect Phylogeny with Persistent characters CoRR (2011)
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
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 39 (Database-Issue) (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, Claudio Ferretti, Anthonath Roslin Sagaya Mary, Giancarlo Mauri
Picture Languages Generated by Assembling Tiles. Fundam. Informaticae 110 (1-4) (2011)
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi
Predicting Variants of Alternative Splicing from NGS data without the Genome CoRR (2011)
Paola Bonizzoni, Natasha Jonoska
Regular Splicing Languages Must Have a Constant. Developments in Language Theory (2011)

Paola Bonizzoni.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Paola Bonizzoni