Paola Bonizzoni

179 papers A* 1B 15C 18Misc 3Journal 114Unranked 25
YearRankTypeTitle / Venue / Authors
2026 J jnl
Optimal-Time Mapping in Run-Length Compressed PBWT.
CoRR
Paola Bonizzoni, Davide Cozzi, Younan Gao
2025 B ed.
36th Annual Symposium on Combinatorial Pattern Matching, CPM 2025, Milan, Italy, June 17-19, 2025
CPM
Paola Bonizzoni, Veli Mäkinen
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 J jnl
Generalized marked systems.
Nat. Comput.
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
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 J jnl
On recognizing graphs representing Persistent Perfect Phylogenies.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez, Gabriella Trucco
2025 J jnl
On recognizing graphs representing persistent perfect phylogenies.
Nat. Comput.
Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez, Gabriella Trucco
2025 B conf
Pangenome Graph Indexing via the Multidollar-BWT.
SEA
Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, Paola Bonizzoni
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
Differential quantification of alternative splicing events on spliced pangenome graphs.
PLoS Comput. Biol.
Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti
2024 J jnl
From the Lyndon factorization to the Canonical Inverse Lyndon factorization: back and forth.
CoRR
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
2024 J jnl
PangeBlocks: customized construction of pangenome graphs via maximal blocks.
BMC Bioinform.
Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
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
2024 B conf
Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property.
MFCS
Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, Rosalba Zizza
2024 J jnl
Unveiling the connection between the Lyndon factorization and the Canonical Inverse Lyndon factorization via a border property.
CoRR
Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, Rosalba Zizza
2023 C conf
Data Structures for SMEM-Finding in the PBWT.
SPIRE
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi
2023 — conf
ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs.
ITAT
Davide Cozzi, Paola Bonizzoni, Luca Denti
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
2023 J jnl
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.
Bioinform.
Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
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 J jnl
Finding Maximal Exact Matches Using the r-Index.
J. Comput. Biol.
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
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 J jnl
Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday.
Theor. Comput. Sci.
Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg
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
Effective Clustering for Single Cell Sequencing Cancer Data.
IEEE J. Biomed. Health Informatics
Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova
2021 B conf
Incomplete Directed Perfect Phylogeny in Linear Time.
WADS
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
2021 J jnl
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.
Bioinform.
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
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
On the longest common prefix of suffixes in an inverse Lyndon factorization and other properties.
Theor. Comput. Sci.
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
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
2021 J jnl
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels.
Bioinform.
Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
2020 J jnl
Incomplete Directed Perfect Phylogeny in Linear Time.
CoRR
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
2020 C conf
Lyndon Words versus Inverse Lyndon Words: Queries on Suffixes and Bordered Words.
LATA
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
2020 B conf
On Two Measures of Distance Between Fully-Labelled Trees.
CPM
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
2020 J jnl
On Two Measures of Distance between Fully-Labelled Trees.
CoRR
Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski
2020 J jnl
Unavoidable Sets, Prefix Graphs and Regularity of Circular Splicing Languages.
Fundam. Informaticae
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
2020 J jnl
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.
BMC Bioinform.
Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, 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 B conf
A Rearrangement Distance for Fully-Labelled Trees.
CPM
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
2019 J jnl
A rearrangement distance for fully-labelled trees.
CoRR
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson
2019 J jnl
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez
2019 — conf
Effective Clustering for Single Cell Sequencing Cancer Data.
BCB
Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova
2019 J jnl
Lyndon words versus inverse Lyndon words: queries on suffixes and bordered words.
CoRR
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
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
2018 J jnl
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.
BMC Bioinform.
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni
2018 J jnl
Inverse Lyndon words and inverse Lyndon factorizations of words.
Adv. Appl. Math.
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
2018 — conf
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data.
ICCABS
Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni
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 — conf
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP.
BCB
Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, 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 J jnl
Inverse Lyndon words and Inverse Lyndon factorizations of words.
CoRR
Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza
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 J jnl
Editorial.
Comput.
Vasco Brattka, Paola Bonizzoni, Olivier Bournez, Elvira Mayordomo
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
2016 J jnl
Solving the Persistent Phylogeny Problem in polynomial time.
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Gabriella Trucco
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 J jnl
Existence of constants in regular splicing languages.
Inf. Comput.
Paola Bonizzoni, Natasa Jonoska
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
2015 J jnl
Restricted and Swap Common Superstring: A Multivariate Algorithmic Perspective.
Algorithmica
Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis
2015 J jnl
Splicing Systems from Past to Future: Old and New Challenges.
CoRR
Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza
2014 J jnl
Algorithms for the Constrained Perfect Phylogeny with Persistent Characters.
CoRR
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco
2014 J jnl
Complexity insights of the Minimum Duplication problem.
Theor. Comput. Sci.
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora
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
Further Steps in TANGO: improved taxonomic assignment in metagenomics.
Bioinform.
Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente
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
2014 — conf
Splicing Systems from Past to Future: Old and New Challenges.
Discrete Mathematics and Computer Science
Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza
2014 — ch.
When and How the Perfect Phylogeny Model Explains Evolution.
Discrete and Topological Models in Molecular Biology
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi, Teresa M. Przytycka
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
2013 C ed.
The Nature of Computation. Logic, Algorithms, Applications - 9th Conference on Computability in Europe, CiE 2013, Milan, Italy, July 1-5, 2013. Proceedings
CiE
Paola Bonizzoni, Vasco Brattka, Benedikt Löwe
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 J jnl
A Unifying Framework to Characterize the Power of a Language to Express Relations
CoRR
Paola Bonizzoni, Peter J. Cameron, Gianluca Della Vedova, Alberto Leporati, Giancarlo Mauri
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 randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters.
Theor. Comput. Sci.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
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 B conf
Complexity Insights of the Minimum Duplication Problem.
SOFSEM
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora
2012 J jnl
Editorial.
Comput.
Vasco Brattka, Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Elvira Mayordomo
2012 J jnl
On the parameterized complexity of the repetition free longest common subsequence problem.
Inf. Process. Lett.
Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Florian Sikora
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
2012 B conf
Restricted and Swap Common Superstring: A Parameterized View.
IPEC
Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis
2012 — conf
The Holy Grail: Finding the Genetic Bases of Phenotypic Characters.
UCNC
Paola Bonizzoni
2012 J jnl
The binary perfect phylogeny with persistent characters.
Theor. Comput. Sci.
Paola Bonizzoni, Chiara Braghin, Riccardo Dondi, Gabriella Trucco
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 J jnl
Anonymizing binary and small tables is hard to approximate.
J. Comb. Optim.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
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
Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model.
ICCABS
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
2011 J jnl
Picture Languages Generated by Assembling Tiles.
Fundam. Informaticae
Paola Bonizzoni, Claudio Ferretti, Anthonath Roslin Sagaya Mary, Giancarlo Mauri
2011 J jnl
Predicting Variants of Alternative Splicing from NGS data without the Genome
CoRR
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi
2011 C conf
Regular Splicing Languages Must Have a Constant.
Developments in Language Theory
Paola Bonizzoni, Natasha Jonoska
2011 J jnl
The Binary Perfect Phylogeny with Persistent characters
CoRR
Chiara Braghin, Riccardo Dondi, Gabriella Trucco, Paola Bonizzoni
2010 J jnl
A characterization of (regular) circular languages generated by monotone complete splicing systems.
Theor. Comput. Sci.
Paola Bonizzoni, Clelia De Felice, Rosalba Zizza
2010 J jnl
Constants and label-equivalence: A decision procedure for reflexive regular splicing languages.
Theor. Comput. Sci.
Paola Bonizzoni
2010 J jnl
Fingerprint Clustering with Bounded Number of Missing Values.
Algorithmica
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri
2010 C conf
Haplotype Inference on Pedigrees with Recombinations and Mutations.
WABI
Yuri Pirola, Paola Bonizzoni, Tao Jiang
2010 J jnl
On the regularity of circular splicing languages: a survey and new developments.
Nat. Comput.
Paola Bonizzoni, Clelia De Felice, Gabriele Fici, Rosalba Zizza
2010 C conf
Parameterized Complexity of
IWOCA
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
2010 J jnl
Preface.
Nat. Comput.
Paola Bonizzoni, Gheorghe Paun, Grzegorz Rozenberg, Claudio Zandron
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
A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2009 — conf
A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters.
ICTCS
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2009 — conf
Circular Languages Generated by Complete Splicing Systems and Pure Unitary Languages
DCM
Paola Bonizzoni, Clelia De Felice, Rosalba Zizza
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 — conf
Finite Splicing: Generative Capacity, New Models and Complexity Aspects.
Algorithmic Bioprocesses
Paola Bonizzoni, Remco Loos
2009 J jnl
Foreword.
Theor. Comput. Sci.
Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Andrea Sorbi
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 C conf
Picture Languages Generated by Assembling Tiles.
LATA
Paola Bonizzoni, Claudio Ferretti, Anthonath Roslin Sagaya Mary, Giancarlo Mauri
2009 — conf
Pure Parsimony Xor Haplotyping.
ISBRA
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi
2009 B conf
The
FCT
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2009 J jnl
Variants of Constrained Longest Common Subsequence
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola
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
2008 J jnl
On the Approximation of Correlation Clustering and Consensus Clustering.
J. Comput. Syst. Sci.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang
2007 J jnl
A Linear-Time Algorithm for the Perfect Phylogeny Haplotype Problem.
Algorithmica
Paola Bonizzoni
2007 J jnl
Anonymizing Binary Tables is APX-hard
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
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 C conf
A Decision Procedure for Reflexive Regular Splicing Languages.
Developments in Language Theory
Paola Bonizzoni, Giancarlo Mauri
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
2006 Misc conf
Exemplar Longest Common Subsequence.
International Conference on Computational Science (2)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
2006 B conf
Fingerprint Clustering with Bounded Number of Missing Values.
CPM
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri
2006 J jnl
Linear splicing and syntactic monoid.
Discret. Appl. Math.
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
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
2005 J jnl
Approximating Clustering of Fingerprint Vectors with Missing Values
CoRR
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2005 B conf
Correlation Clustering and Consensus Clustering.
ISAAC
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang
2005 Misc conf
Experimental Analysis of a New Algorithm for Partial Haplotype Completion.
International Conference on Computational Science (2)
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani
2005 J jnl
Experimental analysis of a new algorithm for partial haplotype completion.
Int. J. Bioinform. Res. Appl.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani
2005 J jnl
On the power of circular splicing.
Discret. Appl. Math.
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
2005 C conf
Recombinant DNA , Gene Splicing as Generative Devices of Formal Languages.
CiE
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri
2005 J jnl
Reconciling a gene tree to a species tree under the duplication cost model.
Theor. Comput. Sci.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2005 J jnl
Regular splicing languages and subclasses.
Theor. Comput. Sci.
Paola Bonizzoni, Giancarlo Mauri
2005 J jnl
The structure of reflexive regular splicing languages via Schützenberger constants.
Theor. Comput. Sci.
Paola Bonizzoni, Clelia De Felice, Rosalba Zizza
2004 J jnl
Circular splicing and regularity.
RAIRO Theor. Informatics Appl.
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
2004 J jnl
Foreword - Special Issue on Bioinformatics.
J. Comput. Sci. Technol.
Paola Bonizzoni, Gianluca Della Vedova, Tao Jiang
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
2003 C conf
Reconciling Gene Trees to a Species Tree.
CIAC
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
2003 C conf
Regular Languages Generated by Reflexive Finite Splicing Systems.
Developments in Language Theory
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
2003 J jnl
The Haplotyping Problem: An Overview of Computational Models and Solutions.
J. Comput. Sci. Technol.
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li
2002 C conf
Decision Problems for Linear and Circular Splicing Systems.
Developments in Language Theory
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
2001 Misc conf
An approximation algorithm for the shortest common supersequence problem: an experimental analysis.
SAC
Paolo Barone, Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
2001 J jnl
Experimenting an approximation algorithm for the LCS.
Discret. Appl. Math.
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
2001 J jnl
Nesting of prime substructures in k-ary relations.
Theor. Comput. Sci.
Paola Bonizzoni, Ross M. McConnell
2001 J jnl
Separating some splicing models.
Inf. Process. Lett.
Paola Bonizzoni, Claudio Ferretti, Giancarlo Mauri, Rosalba Zizza
2001 — conf
Splicing systems using merge and separate operations.
Where Mathematics, Computer Science, Linguistics and Biology Meet
Claudio Zandron, Giancarlo Mauri, Claudio Ferretti, Paola Bonizzoni
2001 J jnl
The complexity of multiple sequence alignment with SP-score that is a metric.
Theor. Comput. Sci.
Paola Bonizzoni, Gianluca Della Vedova
2000 B conf
Approximating the Maximum Isomorphic Agreement Subtree Is Hard.
CPM
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
2000 J jnl
Approximating the Maximum Isomorphic Agreement Subtree is Hard.
Int. J. Found. Comput. Sci.
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
2000 — conf
DNA and Circular Splicing.
DNA Computing
Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri, Rosalba Zizza
1999 J jnl
An Algorithm for the Modular Decomposition of Hypergraphs.
J. Algorithms
Paola Bonizzoni, Gianluca Della Vedova
1995 B conf
Modular Decomposition of Hypergraphs.
WG
Paola Bonizzoni, Gianluca Della Vedova
1994 A* conf
A Tight Lower Bound for Primitivity in k-Structures.
ICALP
Paola Bonizzoni
1994 J jnl
Primitive 2-structures with the (n-2)-Property.
Theor. Comput. Sci.
Paola Bonizzoni
1992 — ch.
Automata on infinite trees and rational control.
Tree Automata and Languages
Ahmed Saoudi, Paola Bonizzoni
1992 J jnl
On Automata on Infinite Trees.
Theor. Comput. Sci.
Paola Bonizzoni, Giancarlo Mauri
1992 — ch.
Recognizing sets of labelled acyclic graphs.
Tree Automata and Languages
Paola Bonizzoni, Giancarlo Mauri, Giovanni Pighizzini, Nicoletta Sabadini