Papers

Journal Papers

  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi: Pure Parsimony Xor Haplotyping. IEEE/ACM Trans. Comput. Biology Bioinform. to appear.
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi: Anonymizing Binary and Small Tables is Hard to Approximate. Journal of Combinatorial Optimization, to appear.
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi: Approximating Clustering of Fingerprint Vectors with Missing Values. Algorithmica, to appear.
  • Paola Bonizzoni A Linear-Time algorithm for the Perfect Phylogeny Haplotype Problem, Algorithmica, 48: 3, 267-285, 2007.
  • Tiziana Castrignanò, M. D’Antonio, Anna Anselmo, Danilo Carrabino, A. D’Onorio De Meo, A. M. D’Erchia, Flavio Licciulli, M. Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, A. Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole, ASPicDB: A database resource for alternative splicing analysis. Bioinformatics 24(10): 1300-1304 (2008), Oxford Journals.
  • Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi. Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. Journal of Computational Biology, vol. 16, n.1, 2009.
  • Paola Bonizzoni, Clelia De Felice, Gabriele Fici, Rosalba Zizza. On regularity of circular splicing languages: a survey and new developments. Natural Computing, Published Online 2009, Springer.
  • Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Andrea Sorbi Foreword Theoretical Computer Science,410(4-5): 283-284, 2009.
  • Paola Bonizzoni, Gheorghe Paun Grzegorz Rozenberg, Claudio Zandron, Foreword Natural Computing, Published Online 2009.
  • Paola Bonizzoni, Constants and label-equivalence: A decision procedure for reflexive splicing languages. Theoretical Computer Science, Volume 411, Issue 6, 6 February 2010, Pages 865-877, Elsevier.
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang: On the Approximation of Correlation Clustering and Consensus Clustering. J. Comput. Syst. Sci. 74(5): 671-696 (2008). download by DOI
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette: Exemplar Longest Common Subsequence. IEEE/ACM Trans. Comput. Biology Bioinform. 4(4): 535-543 (2008). download by DOI
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani. Experimental Analysis of a New Algorithm for Partial Haplotype Completion. International Journal of Bioinformatics Research and Applications. 1(4): 461-473, (2006). download by DOI
  • T. Castrignanò, R. Rizzi, G. Talamo, P. De Meo, A. Anselmo, P. Bonizzoni G. Pesole ASPIC:a web resource for alternative splicing prediction and transcript isoforms characterization. Nucleic Acids Research, Oxford Journals, 2006.
  • Paola Bonizzoni, R. Rizzi G. Pesole. Computational Methods for Alternative Splicing Prediction. Briefings In Functional Genomics And Proteomics , Oxford Journals, 5, 46-51, 2006.
  • Paola Bonizzoni, C. De Felice, G. Mauri R. Zizza Linear splicing and syntactic monoid. Discrete Applied Mathematics, 154:3, 452-470, 2006
  • Paola Bonizzoni, R. Rizzi G. Pesole ASPIC: a Novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences BMC Bioinformatics 2005
  • Paola Bonizzoni G.Mauri Regular splicing languages and subclasses Theoretical Computer Science 340:1, 349-363 2005
  • Paola Bonizzoni C. De Felice R. Zizza The structure of regular splicing languages via Schützenberger constants Theoretical Computer Science 334:1-3, 71-98 2005
  • Paola Bonizzoni C. De Felice G.Mauri R. Zizza On the power of circular splicing Discrete Applied Mathematics 2005
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. Reconciling a Gene Tree to a Species Tree Under the Duplication Cost Model. Theoretical Computer Science. 347(1-2): 36-53, (2005). download by DOI
  • Paola Bonizzoni, Gianluca Della Vedova, Tao Jiang. Foreword – Special Issue on Bioinformatics. Journal of Computer Science and Technology. 19(1): 1-1, (2004).
  • Paola Bonizzoni, C. De Felice , G. Mauri e R. Zizza Circular splicing and regularity . Theoretical Informatics and Applications, RAIRO vol. 38 pag.189-228, 2004.
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li. The Haplotyping Problem: An Overview of Computational Models and Solutions. Journal of Computer Science and Technology. 18(6): 675-688, (2003).
  • Paola Bonizzoni, Gianluca Della Vedova. The Complexity of Multiple Sequence Alignment with SP-Score that is a Metric. Theoretical Computer Science. 259(1): 63-79, (2001).
  • Paola Bonizzoni, C. Ferretti , G. Mauri e R. Zizza. Separating some splicing models. Information Processing Letters 76:6, 255-259, 2001.
  • Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. Experimenting an Approximation Algorithm for the LCS. Discrete Applied Mathematics. 110(1): 13-24, (2001).
  • Paola Bonizzoni e R. McConnell. Nesting of Indecomposable Substructures in k-ary Relational Structures. Theoretical Computer Science, 259:1, 341-357, 2001.
  • Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. Approximating the Maximum Isomorphic Agreement Subtree is hard. International Journal on the Foundations of Computer Science. 11(4): 579-590, (2000).
  • Paola Bonizzoni, Gianluca Della Vedova. An Algorithm to Compute the Modular Decomposition of Hypergraphs. Journal of Algorithms. 32(2): 65-86, (1999).
  • Paola Bonizzoni. Primitive 2-structures with the (n-2)-property. Theoretical Computer Science,132:151-178,1994.
  • Paola Bonizzoni, G. Mauri. On automata on infinite trees. Theoretical Computer Science, 93:227-244,1992.

Conference Papers

  1. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi: Minimum Factorization Agreement of Spliced ESTs. Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009), 2009.
  2. Paola Bonizzoni, Claudio Ferretti, A. Roslin Sagaya Mary, Giancarlo Mauri, Picture languages generated by assembling tiles, International Conference on Language and Automata Theory and Applications (LATA 2009), vol. 5457 of LNCS, pp. 224-235, 2009.
  3. Paola Bonizzoni, Clelia de Felice and Rosalba Zizza. On circular semi-simple splicing systems, Automatha 2009 (Leige).
  4. Paola Bonizzoni, Clelia De Felice, Rosalba Zizza, Circular languages generated by complete splicing systems and pure unitary languages, S. Barry Cooper and Vincent Danos editors: Developments in Computational Models, DCM 09, EPTCS 9, pp. 22-31, doi:10.4204/EPTCS.9.3.
  5. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi: A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. Proceedings of the 11th Italian Conference on Theoretical Computer Science (ICTCS 2009), 2009.
  6. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi: The k-anonymity Problem is Hard. Proceedings of the 17th International Symposium on Fundamentals of Computation Theory (FCT 2009), 2009.
  7. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi: Pure Parsimony Xor Haplotyping. Proceedings of the 5th International Symposium on Bioinformatics Research and Applications, (ISBRA 2009), vol. 5542 of LNCS. pp. 186-197, 2009.
  8. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri. Fingerprint Clustering with Bounded Number of Missing Values. Proceedings of the 17th Symposium on Combinatorial Pattern Matching (CPM 2006). vol. 4009 of LNCS. pp. 106-116, 2006.
  9. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Exemplar Longest Common Subsequence. International Conference on Computational Science (2). vol. 3992 of LNCS. 622-629, 2006.
  10. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang. Correlation Clustering and Consensus Clustering. Algorithms and Computation, 16th International Symposium (ISAAC). vol. 3827 of LNCS. 226-235, 2005.
  11. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani. Experimental Analysis of a New Algorithm for Partial Haplotype Completion. International Conference on Computational Science (2). vol. 3515 of LNCS. 952-959, 2005.
  12. Paola Bonizzoni, C. De Felice, G. Mauri Recombinant DNA, Gene Splicing as Generative Devices of Formal Languages (Invited talk) CIE 2005, vol. 3526 of LNCS, 65-67, 2005.
  13. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi. Reconciling Gene Trees to a Species Tree. Algorithms and Complexity, Proceedings of the 5th Italian Conference (CIAC 2003). vol. 2653 of LNCS. 120-131, 2003.
  14. Paola Bonizzoni, C. De Felice, G. Mauri, R.Zizza. Regular languages generated by reflexive finite splicing systems, Proc. 7th International Conference on Developments in Language Theory, DLT03, vol. 2710 of LNCS, 134-145 Szeged (Hungary), July 7-11, 2003.
  15. Paola Bonizzoni, G. Pesole e R. Rizzi. A method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence, Proc. 3rd International Workshop on Algorithms in Bioinformatics (WABI2003), vol.2812 of LNBI, 62-77 Budapest (Hungary), 2003.
  16. Paola Bonizzoni, C. De Felice, G. Mauri, R.Zizza. Decision problems for linear and circular splicing systems, Proc. 6th International Conference on Developments in Language Theory, DLT02, vol. 2450 of LNCS, 78-92 Kyoto, September 2002.
  17. Paolo Barone, Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. An Approximation Algorithm for the Shortest Common Supersequence: An Experimental Analysis. Proceedings of the 16th ACM Symposium on Applied Computing (SAC 2001). 56-60, 2001.
  18. Paola Bonizzoni, C. De Felice, G. Mauri, R.Zizza. DNA and circular splicing, In A. Condon, G. Rozenberg editors, Proc. of International Meeting on DNA based Computers DNA6}, vol. 2054 of LNCS, 117-129, 2001.
  19. Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri. Approximating the Maximum Isomorphic Agreement Subtree is hard. Proceedings of the 11th Symposium on Combinatorial Pattern Matching (CPM 2000). vol. 1848 of LNCS. 119-128, 2000.
  20. Paola Bonizzoni, Massimo D’Alessandro, Gianluca Della Vedova, Giancarlo Mauri. Experimenting an Approximation Algorithm for the LCS. Algorithms and Experiments (ALEX 98). 96-102, 1998.
  21. Paola Bonizzoni, Gianluca Della Vedova. Modular Decomposition of Hypergraphs. Proceedings of the 21st Workshop on Graph-Theoretic Concepts in Computer Science (WG 95). vol. 1017 of LNCS. 303-317, 1995.
  22. Paola Bonizzoni. A tight lower bound for Primitivity in k-structures. Proceedings of the 21st International Colloquium on automata, Languages and Programming, (ICALP94), vol. 820 of LNCS, pag. 556-567, 1994.

Book Chapters

  1. Paola Bonizzoni, Remco Loss, Finite Splicing: Generative Capacity, New Models and Complexity Aspects. Springer In “Algorithmic Bioprocesses Series: Natural Computing Series” Condon, A.; Harel, D.; Kok, J.N.; Salomaa, A.; Winfree, E. Editors, 2009, pg. 313.
  2. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri. The Comparison of Phylogenetic Networks: Algorithms and Complexity, pp. 143-173. In “Bioinformatics Algorithms: Techniques and Applications”, Ion Mandoiu, Alexander Zelikovsky Editors. Wiley-Interscience Publisher, 2008.
  3. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li. The Haplotyping Problem: An Overview of Computational Models and Solutions, pp. 151-181. In “Genome Sequencing Technology and Algorithms”, Sun Kim, Haixu Tang, Elaine R. Mardis Editors. Artech House Publisher, 2007.
  4. A. Saoudi e P. Bonizzoni. Automata on infinite trees and Rational Control. In A. Podelski, M. Nivat, In “Tree Automata and Languages”, pag.189-199, North Holland, 1992.
  5. Paola Bonizzoni, G.Mauri, G. Pighizzini e N.Sabadini. Recognizing Sets of Labelled Acyclic Graphs. In A. Podelski, M. Nivat, In “Tree Automata and Languages”, pag. 201-224, North Holland, 1992.