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 Computing and Applications, 2025.

• doi: 10.1007/s00521-025-10992-2

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

• doi: 10.1186/s12859-024-05958-5

RecGraph: recombination-aware alignment of sequences to variation graphs. Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola. Bioinformatics, 2024.

• doi: 10.1093/bioinformatics/btae292 code

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

• doi: 10.3390/a16070333

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson. Journal of Computational Biology, 2023.

• doi: 10.1089/cmb.2022.0424

Accurate and fast clade assignment via deep learning and frequency chaos game representation. Jorge Avila Cartes, Santosh Anand, Simone Ciccolella, Paola Bonizzoni, Gianluca Della Vedova. GigaScience, 2022.

• doi: 10.1093/gigascience/giac119 code

Computational graph pangenomics: a tutorial on data structures and their applications. Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén. Natural Computing, 2022.

• doi: 10.1007/s11047-022-09882-6

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

• doi: 10.1186/s12859-022-04668-0 code

Simpler and Faster Development of Tumor Phylogeny Pipelines. Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson. Journal of Computational Biology, 2021.

• doi: 10.1089/cmb.2021.0271 code

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

• doi: 10.1093/bioinformatics/btaa779 code

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. Bioinformatics, 2021.

• doi: 10.1093/bioinformatics/btaa722 code

Computing the multi-string BWT and LCP array in external memory. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. Theoretical Computer Science, 2021.

• doi: 10.1016/j.tcs.2020.11.041

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

• doi: 10.1109/JBHI.2021.3081380

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

• doi: 10.1093/bioinformatics/btaa676 code

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} Bioinformatics, 2020.

• doi: 10.1186/s12859-020-03736-7 code

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. on Computational Biology and Bioinformatics, 2019.

• doi: 10.1109/TCBB.2018.2865729 code

Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. Journal of Computational Biology, 2019.

• doi: 10.1089/cmb.2018.0230 code

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni. Quantitative Biology, 2019.

• doi: 10.1007/s40484-019-0181-x

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni. {BMC} Bioinformatics, 2018.

• doi: 10.1186/s12859-018-2253-8 code

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

• doi: 10.1186/s12859-018-2436-3 code

PATRI, a Genomics Data Integration Tool for Biomarker Discovery.

1. Ukmar, G. E. M. Melloni, L. Raddrizzani, P. Rossi, S. Di Bella, M. R. Pirchio, M. Vescovi, A. Leone, M. Callari, M. Cesarini, A. Somaschini, Gianluca Della Vedova, M. G. Daidone, M. Pettenella, A. Isacchi, R. Bosotti.

BioMed Research International, 2018.

• doi: 10.1155/2018/2012078

A colored graph approach to perfect phylogeny with persistent characters. Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco. Theoretical Computer Science, 2017.

• doi: 10.1016/j.tcs.2016.08.015

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

• doi: 10.1007/s00453-016-0165-4 code

FSG: Fast String Graph Construction for De Novo Assembly. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. Journal of Computational Biology, 2017.

• doi: 10.1089/cmb.2017.0089 code

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

• doi: 10.3233/FI-2017-1552

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. Journal of Computational Biology, 2016.

• doi: 10.1089/cmb.2015.0172 code

Tools and data services registry: a community effort to document bioinformatics resources. Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen, Søren Brunak. Nucleic Acids Research, 2015.

• doi: 10.1093/nar/gkv1116

Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi. Journal of Computational Biology, 2014.

• doi: 10.1089/cmb.2013.0112

Effectiveness of oral bisphosphonates for primary prevention of osteoporotic fractures. Arianna Ghirardi, Mauro Di Bari, Antonella Zambon, Lorenza Scotti, Gianluca Della Vedova, Francesco Lapi, Francesco Cipriani, Achille P. Caputi, Alberto Vaccheri, Dario Gregori, Rosaria Gesuita, Annarita Vestri, Tommaso Staniscia, Giampiero Mazzaglia, Giovanni Corrao. European Journal of Clinical Pharmacology, 2014.

• doi: 10.1007/s00228-014-1708-8

Explaining evolution via constrained persistent perfect phylogeny. Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco. BMC Genomics, 2014.

• doi: 10.1186/1471-2164-15-S6-S10

Oral bisphosphonates do not increase the risk of severe upper gastrointestinal complications: A nested case-control study.

1. Ghirardi, L. Scotti, G. Della Vedova, L.C. D'Oro, F. Lapi, F. Cipriani, A.P. Caputi, A. Vaccheri, D. Gregori, R. Gesuita, A. Vestri, T. Staniscia, G. Mazzaglia, G. Corrao, E. Sessa, V. Arcoraci, A. Parodi, A. Zambon, N. Montanaro, C. Piccinni, C. Suzzi, A. Puccini, M. Sturkenboom, P. Geppetti, L. Sati, Bari Di, F. Forlan, F. Carle, A. Menna, M. Valenti.

BMC Gastroenterology, 2014.

• doi: 10.1186/1471-230X-14-5

User-only design to assess drug effectiveness in clinical practice: application to bisphosphonates and secondary prevention of fractures. Giovanni Corrao, Arianna Ghirardi, Giulia Segafredo, Antonella Zambon, Gianluca Della Vedova, Francesco Lapi, Francesco Cipriani, Achille Caputi, Alberto Vaccheri, Dario Gregori, Rosaria Gesuita, Annarita Vestri, Tommaso Staniscia, Giampiero Mazzaglia, Mauro Di Bari, {on behalf of the BEST investigators}. Pharmacoepidemiology and Drug Safety, 2014.

• doi: 10.1002/pds.3650

Parameterized complexity of k-anonymity: hardness and tractability. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola. Journal of Combinatorial Optimization, 2013.

• doi: 10.1007/s10878-011-9428-9

Risk of Severe Upper Gastrointestinal Complications among Oral Bisphosphonate Users. Arianna Ghirardi, Lorenza Scotti, Antonella Zambon, Gianluca Della Vedova, Luca Cavalieri D'oro, Francesco Lapi, Francesco Cipriani, Achille P. Caputi, Alberto Vaccheri, Dario Gregori, Rosaria Gesuita, Annarita Vestri, Tommaso Staniscia, Giampiero Mazzaglia, Giovanni Corrao, {on behalf of the BEST Investigators}. PLoS ONE, 2013.

• doi: 10.1371/journal.pone.0073159

A randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. Theoretical Computer Science, 2012.

• doi: 10.1016/j.tcs.2011.12.022

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. on Computational Biology and Bioinformatics, 2012.

• doi: 10.1109/TCBB.2012.100

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} Bioinformatics, 2012.

• doi: 10.1186/1471-2105-13-S5-S2 code

Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences. Paul M. Ruegger, Gianluca Della Vedova, Tao Jiang, James Borneman. {BMC} Bioinformatics, 2011.

• doi: 10.1186/1471-2105-12-394

Anonymizing binary and small tables is hard to approximate. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. Journal of Combinatorial Optimization, 2011.

• doi: 10.1007/s10878-009-9277-y

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

• doi: 10.1007/s00453-008-9265-0

Pure Parsimony Xor Haplotyping. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi. {IEEE} {ACM} Trans. on Computational Biology and Bioinformatics, 2010.

• doi: 10.1109/TCBB.2010.52

Variants of constrained longest common subsequence. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola. Information Processing Letters, 2010.

• doi: 10.1016/j.ipl.2010.07.015

Beyond evolutionary trees. Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang. Natural Computing, 2010.

• doi: 10.1007/s11047-009-9156-6

On the Approximation of Correlation Clustering and Consensus Clustering. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang. Journal of Computer and System Sciences, 2008.

• doi: 10.1016/j.jcss.2007.06.024

Exemplar Longest Common Subsequence. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stèphane Vialette. {IEEE} {ACM} Trans. on Computational Biology and Bioinformatics, 2007.

• doi: 10.1145/1322075.1322078

Reconciling a gene tree to a species tree under the duplication cost model. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. Theoretical Computer Science, 2005.

• doi: 10.1016/j.tcs.2005.05.016

Experimental analysis of a new algorithm for partial haplotype completion. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani. International Journal of Bioinformatics Research and Applications, 2005.

• doi: 10.1504/IJBRA.2005.008448

Towards a Theory of Conservative Computing.

1. Cattaneo, Gianluca Della Vedova, A. Leporati, R Leporini.

International Journal of Theoretical Physics, 2005.

• doi: 10.1007/s10773-005-7064-9

Multiple Sequence Alignment as a Facility-Location Problem. Winfried Just, Gianluca Della Vedova. {INFORMS} Journal on Computing, 2004.

• doi: 10.1287/ijoc.1040.0093

A library of efficient bioinformatics algorithms. Gianluca Della Vedova, Riccardo Dondi. Applied Bioinformatics, 2003.

The Haplotyping Problem: An Overview of Computational Models and Solutions. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li. Journal of Computer Science and Technology, 2003.

• doi: 10.1007/BF02945456

Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes.

1. Valinsky, G. Della Vedova, A. J. Scupham, S. Alvey, A. Figueroa, B. Yin, R. J. Hartin, M. Chrobak, D. E. Crowley, T. Jiang, J. Borneman.

Applied and Environmental Microbiology, 2002.

• doi: 10.1128/AEM.68.7.3243-3250.2002

Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition.

1. Valinsky, Gianluca Della Vedova, T. Jiang, J Borneman.

Applied and Environmental Microbiology, 2002.

• doi: 10.1128/Applied and Environmental Microbiology.68.12.5999-6004.2002

Optimal algorithms for local vertex quartet cleaning. Gianluca Della Vedova, Todd Wareham. Bioinformatics, 2002.

• doi: 10.1093/bioinformatics/18.10.1297

Probe selection Algorithms with applications in the analysis of microbial communities.

1. Borneman, M. Chrobak, Gianluca Della Vedova, A. Figueroa, T Jiang.

Bioinformatics, 2001.

• doi: 10.1093/bioinformatics/17.suppl_1.S39

An Algorithm for the Modular Decomposition of Hypergraphs. Paola Bonizzoni, Gianluca Della Vedova. Journal of Algorithms, 1999.

• doi: 10.1006/jagm.1999.1016

Approximating the Maximum Isomorphic Agreement Subtree is Hard. Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. International Journal on the Foundations of Computer Science, 2000.

• doi: 10.1142/S0129054100000363

Experimenting an approximation algorithm for the LCS. Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. Discrete Applied Mathematics, 2001.

• doi: 10.1016/S0166-218X(00)00300-0

The complexity of multiple sequence alignment with SP-score that is a metric. Paola Bonizzoni, Gianluca Della Vedova. Theoretical Computer Science, 2001.

• doi: 10.1016/S0304-3975(99)00324-2

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. In International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2025.

• doi: 10.1007/978-3-031-82768-6_8

Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò. In Bioinformatics and Biomedical Engineering (BIBE), 2023.

• doi: 10.1007/978-3-031-34953-9_5

Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson. In International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2022.

• doi: 10.1007/978-3-031-17531-2_11

Effective Clustering for Single Cell Sequencing Cancer Data. Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova. In ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2019.

• doi: 10.1145/3307339.3342149

A Rearrangement Distance for Fully-Labelled Trees. Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson. In 30th Annual Symposium on Combinatorial Pattern Matching, CPM 2019, June 18-20, 2019, Pisa, Italy, 2019.

• doi: 10.4230/LIPIcs.CPM.2019.28

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. In Sailing Routes in the World of Computation - 14th Conference on Computability in Europe, CiE 2018, Kiel, Germany, July 30 - August 3, 2018, Proceedings, 2018.

• doi: 10.1007/978-3-319-94418-0_11

gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni. In International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2018.

• doi: 10.1109/ICCABS.2018.8542058

Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez. In ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2017.

• doi: 10.1145/3107411.3107441

Character-Based Phylogeny Construction and Its Application to Tumor Evolution. Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez. In Unveiling Dynamics and Complexity - 13th Conference on Computability in Europe, CiE 2017, Turku, Finland, June 12-16, 2017, Proceedings, 2017.

• doi: 10.1007/978-3-319-58741-7_1

FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. In Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings, 2016.

• doi: 10.1007/978-3-319-38782-6_3

Constructing String Graphs in External Memory. Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. In Workshop on Algorithms in Bioinformatics (WABI), 2014.

• doi: 10.1007/978-3-662-44753-6_23

Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini. In ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2013.

• doi: 10.1145/2506583.2506592

Reconstructing isoform graphs from RNA-Seq data. Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2012.

• doi: 10.1109/BIBM.2012.6392734

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. In International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2012.

• doi: 10.1109/ICCABS.2012.6182643

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. In IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2011.

• doi: 10.1109/ICCABS.2011.5729935

Parameterized Complexity of emphk-Anonymity: Hardness and Tractability. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola. In International Workshop on Combinatorial Algorithms (IWOCA), 2010.

• doi: 10.1007/978-3-642-19222-7_25

The emphk-Anonymity Problem Is Hard. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. In Fundamentals of Computation Theory (ICT), 2009.

• doi: 10.1007/978-3-642-03409-1_4

A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. In Italian Conference on Theoretical Computer Science (ICTCS), 2009.

Pure Parsimony Xor Haplotyping. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi. In International Symposium on Bioinformatics Research and Applications (ISBRA), 2009.

• doi: 10.1007/978-3-642-01551-9_19

Minimum Factorization Agreement of Spliced ESTs. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi. In Workshop on Algorithms in Bioinformatics (WABI), 2009.

• doi: 10.1007/978-3-642-04241-6_1

Fingerprint Clustering with Bounded Number of Missing Values. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri. In Combinatorial Pattern Matching (CPM), 2006.

• doi: 10.1007/11780441_11

Exemplar Longest Common Subsequence. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, St{\'{e}}phane Vialette. In Computational Science (ICCS), 2006.

• doi: 10.1007/11758525_85

Experimental Analysis of a New Algorithm for Partial Haplotype Completion. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani. In Computational Science (ICCS), 2005.

• doi: 10.1007/11428848_121

Correlation Clustering and Consensus Clustering. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang. In Algorithms and Computation, International Symposium (ISAAC), 2005.

• doi: 10.1007/11602613_24

An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem. Sergio Pozzi, Gianluca Della Vedova, Giancarlo Mauri. In Computational Methods in Systems Biology (CMSB), 2004.

• doi: 10.1007/978-3-540-25974-9_1

Reconciling Gene Trees to a Species Tree. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. In Algorithms and Complexity, Italian Conference, (CIAC), 2003.

• doi: 10.1007/3-540-44849-7_18

Optimal algorithms for local vertex quartet cleaning. Gianluca Della Vedova, Todd Wareham. In Symposium on Applied Computing (SAC), 2002.

• doi: 10.1145/508791.508827

Approximating minimum quartet inconsistency (abstract). Gianluca Della Vedova, Tao Jiang, Jing Li, Jianjun Wen. In ACM-SIAM Symposium on Discrete Algorithms (SODA), 2002.

Probe selection algorithms with applications in the analysis of microbial communities. James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa, Tao Jiang. In Intelligent Systems for Molecular Biology (ISMB), 2001.

An approximation algorithm for the shortest common supersequence problem: an experimental analysis. Paolo Barone, Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. In ACM Symposium on Applied Computing (SAC), 2001.

• doi: 10.1145/372202.372275

Approximating the Maximum Isomorphic Agreement Subtree Is Hard. Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. In Combinatorial Pattern Matching (CPM), 2000.

• doi: 10.1007/3-540-45123-4_12

Multiple Sequence Alignment as a Facility Location Problem. Winfried Just, Gianluca Della Vedova. In Prague Stringology Club Workshop (PSCW), 2000.

Experimenting an Approximation Algorithm for the LCS. Paola Bonizzoni, Massimo D'Alessandro, Gianluca Della Vedova, Giancarlo Mauri. In Algorithms and Experiments (ALEX98), 1998.

Modular Decomposition of Hypergraphs. Paola Bonizzoni, Gianluca Della Vedova. In Graph-Theoretic Concepts in Computer Science (WG), 1995.

• doi: 10.1007/3-540-60618-1_84

Transcriptome Assembly and Alternative Splicing Analysis. Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi. In RNA Bioinformatics, 2015.

• doi: 10.1007/978-1-4939-2291-8₁1

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

• doi: 10.1007/978-3-642-40193-0_4

The Haplotyping Problem: An Overview of Computational Models and Solutions. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li. In Genome Sequencing technology and algorithms, 2008.

Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG). L Valinsky, AJ Scupham, Gianluca Della Vedova, Z Liu, A Figueroa, K Jampachaisri, B Yin, E Bent, R Mancini-Jones, J Press, others.

The Comparison of Phylogenetic Networks: Algorithms and Complexity. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri. In Bioinformatics Algorithms, 2007.

• doi: 10.1002/9780470253441.ch7

A tool for the comparison of transcript differential expression analysis pipelines. Stefano Beretta, Yuri Pirola, Valeria Ranzani, Grazisa Rossetti, Raoul Bonnal, Raffaella Rizzi, Gianluca Della Vedova, Massimiliano Pagani, Paola Bonizzoni.

• doi: 10.7287/peerj.preprints.2212v1