Recognizing sets of labelled acyclic graphs. - Paola Bonizzoni; Giancarlo Mauri; Giovanni Pighizzini; Nicoletta Sabadini (Tree Automata and Languages, 1992)

Automata on infinite trees and rational control. - Ahmed Saoudi; Paola Bonizzoni (Tree Automata and Languages, 1992)

On Automata on Infinite Trees. - Paola Bonizzoni; Giancarlo Mauri (Theor. Comput. Sci., 1992)

A Tight Lower Bound for Primitivity in k-Structures. - Paola Bonizzoni (ICALP, 1994)

Primitive 2-structures with the (n-2)-Property. - Paola Bonizzoni (Theor. Comput. Sci., 1994)

Modular Decomposition of Hypergraphs. - Paola Bonizzoni; Gianluca Della Vedova (WG, 1995)

An Algorithm for the Modular Decomposition of Hypergraphs. - Paola Bonizzoni; Gianluca Della Vedova (J. Algorithms, 1999)

DNA and Circular Splicing. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (DNA Computing, 2000)

Approximating the Maximum Isomorphic Agreement Subtree is Hard. - Paola Bonizzoni; Gianluca Della Vedova; Giancarlo Mauri (Int. J. Found. Comput. Sci., 2000)

Splicing systems using merge and separate operations. - Claudio Zandron; Giancarlo Mauri; Claudio Ferretti; Paola Bonizzoni (Where Mathematics, Computer Science, Linguistics and Biology Meet, 2001)

An approximation algorithm for the shortest common supersequence problem: an experimental analysis. - Paolo Barone; Paola Bonizzoni; Gianluca Della Vedova; Giancarlo Mauri (SAC, 2001)

Experimenting an approximation algorithm for the LCS. - Paola Bonizzoni; Gianluca Della Vedova; Giancarlo Mauri (Discret. Appl. Math., 2001)

Separating some splicing models. - Paola Bonizzoni; Claudio Ferretti; Giancarlo Mauri; Rosalba Zizza (Inf. Process. Lett., 2001)

Nesting of prime substructures in k-ary relations. - Paola Bonizzoni; Ross M. McConnell (Theor. Comput. Sci., 2001)

The complexity of multiple sequence alignment with SP-score that is a metric. - Paola Bonizzoni; Gianluca Della Vedova (Theor. Comput. Sci., 2001)

Decision Problems for Linear and Circular Splicing Systems. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (Developments in Language Theory, 2002)

Reconciling Gene Trees to a Species Tree. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (CIAC, 2003)

Regular Languages Generated by Reflexive Finite Splicing Systems. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (Developments in Language Theory, 2003)

A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence. - Paola Bonizzoni; Graziano Pesole; Raffaella Rizzi (WABI, 2003)

The Haplotyping Problem: An Overview of Computational Models and Solutions. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Jing Li 002 (J. Comput. Sci. Technol., 2003)

Circular splicing and regularity. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (RAIRO Theor. Informatics Appl., 2004)

Foreword - Special Issue on Bioinformatics. - Paola Bonizzoni; Gianluca Della Vedova; Tao Jiang 001 (J. Comput. Sci. Technol., 2004)

Recombinant DNA , Gene Splicing as Generative Devices of Formal Languages. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri (CiE, 2005)

Correlation Clustering and Consensus Clustering. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Tao Jiang 001 (ISAAC, 2005)

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. - Paola Bonizzoni; Raffaella Rizzi; Graziano Pesole (BMC Bioinform., 2005)

Approximating Clustering of Fingerprint Vectors with Missing Values - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (CoRR, 2005)

On the power of circular splicing. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (Discret. Appl. Math., 2005)

Experimental analysis of a new algorithm for partial haplotype completion. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Lorenzo Mariani (Int. J. Bioinform. Res. Appl., 2005)

The structure of reflexive regular splicing languages via Schützenberger constants. - Paola Bonizzoni; Clelia de Felice; Rosalba Zizza (Theor. Comput. Sci., 2005)

Regular splicing languages and subclasses. - Paola Bonizzoni; Giancarlo Mauri (Theor. Comput. Sci., 2005)

Reconciling a gene tree to a species tree under the duplication cost model. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (Theor. Comput. Sci., 2005)

A Decision Procedure for Reflexive Regular Splicing Languages. - Paola Bonizzoni; Giancarlo Mauri (Developments in Language Theory, 2006)

Exemplar Longest Common Subsequence. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Guillaume Fertin; Stéphane Vialette (International Conference on Computational Science (2), 2006)

Linear splicing and syntactic monoid. - Paola Bonizzoni; Clelia de Felice; Giancarlo Mauri; Rosalba Zizza (Discret. Appl. Math., 2006)

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. - Tiziana Castrignanò; Raffaella Rizzi; Ivano Giuseppe Talamo; Paolo D'Onorio De Meo; Anna Anselmo; Paola Bonizzoni; Graziano Pesole (Nucleic Acids Res., 2006)

A Linear-Time Algorithm for the Perfect Phylogeny Haplotype Problem. - Paola Bonizzoni (Algorithmica, 2007)

Anonymizing Binary Tables is APX-hard - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (CoRR, 2007)

Exemplar Longest Common Subsequence. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Guillaume Fertin; Raffaella Rizzi; Stéphane Vialette (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

ASPicDB: A database resource for alternative splicing analysis. - 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; et al. (Bioinform., 2008)

On the Approximation of Correlation Clustering and Consensus Clustering. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Tao Jiang 001 (J. Comput. Syst. Sci., 2008)

Finite Splicing: Generative Capacity, New Models and Complexity Aspects. - Paola Bonizzoni; Remco Loos (Algorithmic Bioprocesses, 2009)

The k-Anonymity Problem Is Hard. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (FCT, 2009)

A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (ICTCS, 2009)

Minimum Factorization Agreement of Spliced ESTs. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola; Raffaella Rizzi (WABI, 2009)

Parameterized Complexity of the k-anonymity Problem - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola (CoRR, 2009)

Circular Languages Generated by Complete Splicing Systems and Pure Unitary Languages - Paola Bonizzoni; Clelia de Felice; Rosalba Zizza (DCM, 2009)

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. - Paola Bonizzoni; Giancarlo Mauri; Graziano Pesole; Ernesto Picardi; Yuri Pirola; Raffaella Rizzi (J. Comput. Biol., 2009)

Foreword. - Paola Bonizzoni; S. Barry Cooper; Benedikt Löwe; Andrea Sorbi (Theor. Comput. Sci., 2009)

Parameterized Complexity of k-Anonymity: Hardness and Tractability. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola (IWOCA, 2010)

Haplotype Inference on Pedigrees with Recombinations and Mutations. - Yuri Pirola; Paola Bonizzoni; Tao Jiang 001 (WABI, 2010)

Fingerprint Clustering with Bounded Number of Missing Values. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Giancarlo Mauri (Algorithmica, 2010)

Variants of constrained longest common subsequence. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola (Inf. Process. Lett., 2010)

On the regularity of circular splicing languages: a survey and new developments. - Paola Bonizzoni; Clelia de Felice; Gabriele Fici; Rosalba Zizza (Nat. Comput., 2010)

Preface. - Paola Bonizzoni; Gheorghe Paun; Grzegorz Rozenberg; Claudio Zandron (Nat. Comput., 2010)

Pure Parsimony Xor Haplotyping. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola; Romeo Rizzi (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Constants and label-equivalence: A decision procedure for reflexive regular splicing languages. - Paola Bonizzoni (Theor. Comput. Sci., 2010)

A characterization of (regular) circular languages generated by monotone complete splicing systems. - Paola Bonizzoni; Clelia de Felice; Rosalba Zizza (Theor. Comput. Sci., 2010)

Regular Splicing Languages Must Have a Constant. - Paola Bonizzoni; Natasha Jonoska (Developments in Language Theory, 2011)

Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model. - Paola Bonizzoni (ICCABS, 2011)

PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi (ICCABS, 2011)

Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers - Yuri Pirola; Gianluca Della Vedova; Stefano Biffani; Alessandra Stella; Paola Bonizzoni (CoRR, 2011)

Predicting Variants of Alternative Splicing from NGS data without the Genome - Stefano Beretta 001; Paola Bonizzoni; Gianluca Della Vedova; Raffaella Rizzi (CoRR, 2011)

Picture Languages Generated by Assembling Tiles. - Paola Bonizzoni; Claudio Ferretti; Anthonath Roslin Sagaya Mary; Giancarlo Mauri (Fundam. Informaticae, 2011)

Anonymizing binary and small tables is hard to approximate. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (J. Comb. Optim., 2011)

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. - 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; et al. (Nucleic Acids Res., 2011)

Reconstructing isoform graphs from RNA-Seq data. - Stefano Beretta 001; Paola Bonizzoni; Raffaella Rizzi; Gianluca Della Vedova (BIBM, 2012)

Restricted and Swap Common Superstring: A Parameterized View. - Paola Bonizzoni; Riccardo Dondi; Giancarlo Mauri; Italo Zoppis (IPEC, 2012)

The Holy Grail: Finding the Genetic Bases of Phenotypic Characters. - Paola Bonizzoni (UCNC, 2012)

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. - Yuri Pirola; Raffaella Rizzi; Ernesto Picardi; Graziano Pesole; Gianluca Della Vedova; Paola Bonizzoni (BMC Bioinform., 2012)

Editorial. - Vasco Brattka; Paola Bonizzoni; S. Barry Cooper; Benedikt Löwe; Elvira Mayordomo (Comput., 2012)

A Unifying Framework to Characterize the Power of a Language to Express Relations - Paola Bonizzoni; Peter J. Cameron; Gianluca Della Vedova; Alberto Leporati; Giancarlo Mauri (CoRR, 2012)

On the parameterized complexity of the repetition free longest common subsequence problem. - Guillaume Blin; Paola Bonizzoni; Riccardo Dondi; Florian Sikora (Inf. Process. Lett., 2012)

An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. - Yuri Pirola; Paola Bonizzoni; Tao Jiang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A Fast and Practical Approach to Genotype Phasing and Imputation on a Pedigree with Erroneous and Incomplete Information. - Yuri Pirola; Gianluca Della Vedova; Stefano Biffani; Alessandra Stella; Paola Bonizzoni (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

The binary perfect phylogeny with persistent characters. - Paola Bonizzoni; Chiara Braghin; Riccardo Dondi; Gabriella Trucco (Theor. Comput. Sci., 2012)

A randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi (Theor. Comput. Sci., 2012)

Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. - Yuri Pirola; Gianluca Della Vedova; Paola Bonizzoni; Alessandra Stella; Filippo Biscarini (BCB, 2013)

Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability. - Paola Bonizzoni; Riccardo Dondi; Yuri Pirola (Algorithms, 2013)

Parameterized complexity of k-anonymity: hardness and tractability. - Paola Bonizzoni; Gianluca Della Vedova; Riccardo Dondi; Yuri Pirola (J. Comb. Optim., 2013)

Splicing Systems from Past to Future: Old and New Challenges. - Luc Boasson; Paola Bonizzoni; Clelia De Felice; Isabelle Fagnot; Gabriele Fici; Rocco Zaccagnino; Rosalba Zizza (Discrete Mathematics and Computer Science, 2014)

Constructing String Graphs in External Memory. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (WABI, 2014)

Further Steps in TANGO: improved taxonomic assignment in metagenomics. - Daniel Alonso-Alemany; Aurélien Barré; Stefano Beretta 001; Paola Bonizzoni; Macha Nikolski; Gabriel Valiente (Bioinform., 2014)

Algorithms for the Constrained Perfect Phylogeny with Persistent Characters. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Gabriella Trucco (CoRR, 2014)

Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. - Stefano Beretta 001; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi (J. Comput. Biol., 2014)

Complexity insights of the Minimum Duplication problem. - Guillaume Blin; Paola Bonizzoni; Riccardo Dondi; Romeo Rizzi; Florian Sikora (Theor. Comput. Sci., 2014)

When and How the Perfect Phylogeny Model Explains Evolution. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Riccardo Dondi; Teresa M. Przytycka (Discrete and Topological Models in Molecular Biology, 2014)

On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem. - Paola Bonizzoni; Riccardo Dondi; Gunnar W. Klau; Yuri Pirola; Nadia Pisanti; Simone Zaccaria (CPM, 2015)

Restricted and Swap Common Superstring: A Multivariate Algorithmic Perspective. - Paola Bonizzoni; Riccardo Dondi; Giancarlo Mauri; Italo Zoppis (Algorithmica, 2015)

Covering Pairs in Directed Acyclic Graphs. - Niko Beerenwinkel; Stefano Beretta 001; Paola Bonizzoni; Riccardo Dondi; Yuri Pirola (Comput. J., 2015)

Existence of constants in regular splicing languages. - Paola Bonizzoni; Natasa Jonoska (Inf. Comput., 2015)

A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas. - Carlo Batini; Paola Bonizzoni; Marco Comerio; Riccardo Dondi; Yuri Pirola; Francesco Salandra (J. Comput. Sci. Technol., 2015)

FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (ISBRA, 2016)

HapCol: accurate and memory-efficient haplotype assembly from long reads. - Yuri Pirola; Simone Zaccaria; Riccardo Dondi; Gunnar W. Klau; Nadia Pisanti; Paola Bonizzoni (Bioinform., 2016)

Editorial. - Vasco Brattka; Paola Bonizzoni; Olivier Bournez; Elvira Mayordomo (Comput., 2016)

A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings. - Paola Bonizzoni; Gianluca Della Vedova; Serena Nicosia; Marco Previtali; Raffaella Rizzi (CoRR, 2016)

Solving the Persistent Phylogeny Problem in polynomial time. - Paola Bonizzoni; Gianluca Della Vedova; Gabriella Trucco (CoRR, 2016)

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. - Paola Bonizzoni; Riccardo Dondi; Gunnar W. Klau; Yuri Pirola; Nadia Pisanti; Simone Zaccaria (J. Comput. Biol., 2016)

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (J. Comput. Biol., 2016)

Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext. - Stefano Beretta 001; Paola Bonizzoni; Luca Denti; Marco Previtali; Raffaella Rizzi (AlCoB, 2017)

Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (BCB, 2017)

An External-Memory Algorithm for String Graph Construction. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (Algorithmica, 2017)

Computing the BWT and LCP array of a Set of Strings in External Memory. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (CoRR, 2017)

Species-Driven Persistent Phylogeny. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Raffaella Rizzi; Gabriella Trucco (Fundam. Informaticae, 2017)

FSG: Fast String Graph Construction for De Novo Assembly. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (J. Comput. Biol., 2017)

A colored graph approach to perfect phylogeny with persistent characters. - Paola Bonizzoni; Anna Paola Carrieri; Gianluca Della Vedova; Raffaella Rizzi; Gabriella Trucco (Theor. Comput. Sci., 2017)

Divide and Conquer Computation of the Multi-string BWT and LCP Array. - Paola Bonizzoni; Gianluca Della Vedova; Serena Nicosia; Yuri Pirola; Marco Previtali; Raffaella Rizzi (CiE, 2018)

Inverse Lyndon words and inverse Lyndon factorizations of words. - Paola Bonizzoni; Clelia De Felice; Rocco Zaccagnino; Rosalba Zizza (Adv. Appl. Math., 2018)

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. - Stefano Beretta 001; Murray Patterson; Simone Zaccaria; Gianluca Della Vedova; Paola Bonizzoni (BMC Bioinform., 2018)

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. - Luca Denti; Raffaella Rizzi; Stefano Beretta 001; Gianluca Della Vedova; Marco Previtali; Paola Bonizzoni (BMC Bioinform., 2018)

A Rearrangement Distance for Fully-Labelled Trees. - Giulia Bernardini 001; Paola Bonizzoni; Gianluca Della Vedova; Murray Patterson (CPM, 2019)

Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (J. Comput. Biol., 2019)

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. - Raffaella Rizzi; Stefano Beretta 001; Murray Patterson; Yuri Pirola; Marco Previtali; Gianluca Della Vedova; Paola Bonizzoni (Quant. Biol., 2019)

Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. - Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Mauricio Soto Gomez (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

On Two Measures of Distance Between Fully-Labelled Trees. - Giulia Bernardini 001; Paola Bonizzoni; Pawel Gawrychowski (CPM, 2020)

Lyndon Words versus Inverse Lyndon Words: Queries on Suffixes and Bordered Words. - Paola Bonizzoni; Clelia De Felice; Rocco Zaccagnino; Rosalba Zizza (LATA, 2020)

γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. - Andrea Calabria; Stefano Beretta 001; Ivan Merelli; Giulio Spinozzi; Stefano Brasca; Yuri Pirola; Fabrizio Benedicenti; Erika Tenderini; Paola Bonizzoni; Luciano Milanesi; Eugenio Montini (Bioinform., 2020)

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. - Simone Ciccolella; Mauricio Soto Gomez; Murray D. Patterson; Gianluca Della Vedova; Iman Hajirasouliha; Paola Bonizzoni (BMC Bioinform., 2020)

Unavoidable Sets, Prefix Graphs and Regularity of Circular Splicing Languages. - Paola Bonizzoni; Clelia De Felice; Rocco Zaccagnino; Rosalba Zizza (Fundam. Informaticae, 2020)

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. - Paola Bonizzoni; Clelia De Felice; Alessia Petescia; Yuri Pirola; Raffaella Rizzi; Jens Stoye; Rocco Zaccagnino; Rosalba Zizza (AlCoB, 2021)

Incomplete Directed Perfect Phylogeny in Linear Time. - Giulia Bernardini 001; Paola Bonizzoni; Pawel Gawrychowski (WADS, 2021)

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. - Simone Ciccolella; Giulia Bernardini 001; Luca Denti; Paola Bonizzoni; Marco Previtali; Gianluca Della Vedova (Bioinform., 2021)

Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. - Simone Ciccolella; Camir Ricketts; Mauricio Soto Gomez; Murray Patterson; Dana Silverbush; Paola Bonizzoni; Iman Hajirasouliha; Gianluca Della Vedova (Bioinform., 2021)

Shark: fishing relevant reads in an RNA-Seq sample. - Luca Denti; Yuri Pirola; Marco Previtali; Tamara Ceccato; Gianluca Della Vedova; Raffaella Rizzi; Paola Bonizzoni (Bioinform., 2021)

On the longest common prefix of suffixes in an inverse Lyndon factorization and other properties. - Paola Bonizzoni; Clelia De Felice; Rocco Zaccagnino; Rosalba Zizza (Theor. Comput. Sci., 2021)

Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday. - Paola Bonizzoni; Lila Kari; Ion Petre; Grzegorz Rozenberg (Theor. Comput. Sci., 2021)

Computing the multi-string BWT and LCP array in external memory. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali; Raffaella Rizzi (Theor. Comput. Sci., 2021)

Effective Clustering for Single Cell Sequencing Cancer Data. - Simone Ciccolella; Murray Patterson; Paola Bonizzoni; Gianluca Della Vedova (IEEE J. Biomed. Health Informatics, 2021)

MALVIRUS: an integrated application for viral variant analysis. - Simone Ciccolella; Luca Denti; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali (BMC Bioinform., 2021)

Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes? - Paola Bonizzoni; Clelia De Felice; Yuri Pirola; Raffaella Rizzi; Rocco Zaccagnino; Rosalba Zizza (DLT, 2022)

KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints. - Paola Bonizzoni; Alessia Petescia; Yuri Pirola; Raffaella Rizzi; Rocco Zaccagnino; Rosalba Zizza (IWBBIO (2), 2022)

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. - Paola Bonizzoni; Matteo Costantini; Clelia de Felice; Alessia Petescia; Yuri Pirola; Marco Previtali; Raffaella Rizzi; Jens Stoye; Rocco Zaccagnino; Rosalba Zizza (Inf. Sci., 2022)

Finding Maximal Exact Matches Using the r-Index. - Massimiliano Rossi 001; Marco Oliva; Paola Bonizzoni; Ben Langmead; Travis Gagie; Christina Boucher 001 (J. Comput. Biol., 2022)

Computational graph pangenomics: a tutorial on data structures and their applications. - Jasmijn A. Baaijens; Paola Bonizzoni; Christina Boucher 001; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Jouni Sirén (Nat. Comput., 2022)

Identification of Chimeric RNAs: A Novel Machine Learning Perspective. - Paola Bonizzoni; Clelia De Felice; Yuri Pirola; Raffaella Rizzi; Rocco Zaccagnino; Rosalba Zizza (ICCABS, 2023)

ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs. - Davide Cozzi; Paola Bonizzoni; Luca Denti (ITAT, 2023)

Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. - Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Mattia Sgrò (IWBBIO (1), 2023)

Data Structures for SMEM-Finding in the PBWT. - Paola Bonizzoni; Christina Boucher 001; Davide Cozzi; Travis Gagie; Dominik Köppl; Massimiliano Rossi 001 (SPIRE, 2023)

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. - Davide Cozzi; Massimiliano Rossi 001; Simone Rubinacci; Travis Gagie; Dominik Köppl; Christina Boucher 001; Paola Bonizzoni (Bioinform., 2023)

Solving the Minimal Positional Substring Cover Problem in Sublinear Space. - Paola Bonizzoni; Christina Boucher 001; Davide Cozzi; Travis Gagie; Yuri Pirola (CPM, 2024)

Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. - Paola Bonizzoni; Clelia De Felice; Brian Riccardi; Rocco Zaccagnino; Rosalba Zizza (MFCS, 2024)

From the Lyndon factorization to the Canonical Inverse Lyndon factorization: back and forth. - Paola Bonizzoni; Clelia De Felice; Rocco Zaccagnino; Rosalba Zizza (CoRR, 2024)

Differential quantification of alternative splicing events on spliced pangenome graphs. - Simone Ciccolella; Davide Cozzi; Gianluca Della Vedova; Stephen Njuguna Kuria; Paola Bonizzoni; Luca Denti (PLoS Comput. Biol., 2024)

PangeBlocks: customized construction of pangenome graphs via maximal blocks. - Jorge Avila Cartes; Paola Bonizzoni; Simone Ciccolella; Gianluca Della Vedova; Luca Denti (BMC Bioinform., 2024)

Phasing Data from Genotype Queries via the μ-PBWT. - Davide Cozzi; Paola Bonizzoni; Christina Boucher 001; Ben Langmead; Yuri Pirola (The Expanding World of Compressed Data, 2025)

Pangenome Graph Indexing via the Multidollar-BWT. - Davide Cozzi; Brian Riccardi; Luca Denti; Simone Ciccolella; Kunihiko Sadakane; Paola Bonizzoni (SEA, 2025)

Differential analysis of alternative splicing events in gene regions using residual neural networks. - Simone Ciccolella; Luca Denti; Jorge Avila Cartes; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Paola Bonizzoni (Neural Comput. Appl., 2025)

On recognizing graphs representing Persistent Perfect Phylogenies. - Paola Bonizzoni; Gianluca Della Vedova; Mauricio Soto Gomez; Gabriella Trucco (CoRR, 2025)