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)

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

Probe selection algorithms with applications in the analysis of microbial communities. - James Borneman; Marek Chrobak; Gianluca Della Vedova; Andres Figueroa; Tao Jiang 001 (ISMB (Supplement of Bioinformatics), 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)

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

Approximating minimum quartet inconsistency (abstract). - Gianluca Della Vedova; Tao Jiang 001; Jing Li 002; Jianjun Wen (SODA, 2002)

Optimal algorithms for local vertex quartet cleaning. - Gianluca Della Vedova; Todd Wareham (Bioinform., 2002)

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

An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem. - Sergio Pozzi; Gianluca Della Vedova; Giancarlo Mauri (CMSB, 2004)

Multiple Sequence Alignment as a Facility-Location Problem. - Winfried Just; Gianluca Della Vedova (INFORMS J. Comput., 2004)

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

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

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

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

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

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)

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

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)

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

Beyond evolutionary trees. - Gianluca Della Vedova; Riccardo Dondi; Tao Jiang 001; Giulio Pavesi; Yuri Pirola; Lusheng Wang 001 (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)

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)

Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences. - Paul M. Ruegger; Gianluca Della Vedova; Tao Jiang 001; James Borneman (BMC Bioinform., 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)

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

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

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)

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)

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)

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

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

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)

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)

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)

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)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

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

Character-Based Phylogeny Construction and Its Application to Tumor Evolution. - Gianluca Della Vedova; Murray Patterson; Raffaella Rizzi; Mauricio Soto Gomez (CiE, 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)

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)

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)

Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 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)

Simpler and Faster Development of Tumor Phylogeny Pipelines. - Sarwan Ali; Simone Ciccolella; Lorenzo Lucarella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 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)

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)

Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. - Akshay Juyal; Zahra Tayebi; Alexander Zelikovsky; Mauricio Soto Gomez; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (ICCABS, 2023)

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

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. - Prakash Chourasia; Sarwan Ali; Simone Ciccolella; Gianluca Della Vedova; Murray Patterson (J. Comput. Biol., 2023)

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. - Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipovic; Mauricio Soto Gomez (Algorithms, 2023)

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)

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)

Cancer progression inference using a finite-state model to allow recurrences and losses of mutations. - Simone Ciccolella; Murray Patterson; Iman Hajirasouliha; Gianluca Della Vedova (Neural Comput. Appl., 2025)