Most recent papers:

P. Bonizzoni  G. Della Vedova   R. Dondi  T. Jiang  On the Approximation of Consensus Claustering and Correlation Clustering,  Journal of Computer  and System Sciences, in press, 2007.

P. Bonizzoni  A Linear-Time algorithm for the Perfect Phylogeny Haplotype Problem , Algorithmica, 48: 3, 2007.

P. Bonizzoni, G. Mauri. A decision procedure for reflexive splicing languages,  International Conference Developments in  Language Theory  DLT 06,    LNCS  4036, 315-326, 2006.

P. Bonizzoni,  G. Della Vedova,  R. Dondi,   G. Mauri  Fingerprint Clustering with Bounded Number of Missing Values, 17th Annual Symposium on Combinatorial Pattern Matching  CPM 2006 .

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Fertin, S. Vialette, Exemplar Longest Common Subsequence,   IWBRA 06,   LNCS   3992, 2006.

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.

P. Bonizzoni, R. Rizzi   G. Pesole. Computational Methods for Alternative Splicing Prediction.   Briefings In Functional Genomics And Proteomics , Oxford Journals,   5,   46-51, 2006.

P. Bonizzoni,  C. De Felice, G. Mauri   R. Zizza Linear splicing and syntactic monoid. Discrete Applied Mathematics,   154:3,   452-470, 2006

P. Bonizzoni, G. Della Vedova, R. Dondi   G. Mauri  A PTAS for the Maximum Consensus Clustering,  1st FIMA International Conference on Models and Methods for Human Genomics , Val D'Aosta,  2006


P. 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

P. Bonizzoni, G. Della Vedova,  R. Dondi   L. Mariani  Experimental Analysis of a New Algorithm for Partial Haplotype Completion.   International
Journal of Bioinformatics Research and Applications , 1:4, 461-473, 2005


P. Bonizzoni  G. Della Vedova   R. Dondi Reconciling a gene tree to a species tree Theoretical Computer Science  2005

P. Bonizzoni  G. Della Vedova   R. Dondi  L. Mariani Experimental Analysis of a New Algorithm for Partial Haplotype Completion. IWBRA 05

P. Bonizzoni  G. Della Vedova   R. Dondi  T. Jiang  Consensus Claustering and Correlation Clustering  ISSAC 2005

P. Bonizzoni   Recombinant DNA, gene splicing as generative devices of formal languages (invited talk) CIE 2005

P. Bonizzoni  G.Mauri  Regular splicing languages and subclasses   Theoretical Computer Science  340:1, 349-363 2005

P. Bonizzoni C. De Felice R. Zizza The structure of  regular splicing languages via Schützenberger constants  Theoretical Computer Science 334:1-3, 71-98 2005

P. Bonizzoni C. De Felice G.Mauri R. Zizza On the power of  circular splicing Discrete Applied Mathematics  2005




 P. Bonizzoni, G. Della Vedova, R. Dondi, L. Jing The haplotyping problem: a view of computational models and solutions.  International Journal of Computers and Science Technology, Vol. 18, N.6 pag. 675-688, 2003.

P.Bonizzoni, G. Pesole e R. Rizzi. A Method to detect alternative splicing sites  by agreeing ESTs to a genomic sequence.  Workshop on Algorithms in Computational Biology, WABI 2003.

P. Bonizzoni, G. Della Vedova e R. Dondi. Reconciling gene trees to a species tree,  Proc. Italian Conference on Algorithms and Complexity (CIAC2003)},  LNCS 2653, 120-131  Rome (Italy), 2003.

P. Bonizzoni e G. Della Vedova. The complexity of Multiple sequence alignment with  SP-score that is a metric. Theoretical Computer Science 259:1, 63-79 2001.

P. Bonizzoni, G. Della Vedova e G.Mauri. Experimenting an Approximation Algorithm for the LCS.  Discrete Applied Mathematics 110:1, 13-24, 2001.

P. Bonizzoni,  G. Della Vedova e G.Mauri Approximating the Maximum Isomorphic Subtree is Hard.  International Journal on the Foundations of Computer Science 11:4,   579-590, 2000.

P. Bonizzoni, M. D'Alessandro, G. Della Vedova e G. Mauri. Experimenting and Approximation algorithm for the LCS. In R. Battiti e A. Bertossi editors,  Proceedings of the International workshop on Algorithms and Experiments, ALEX 98  pages pages 96-102, 1998.

P. Bonizzoni, G. Della Vedova e  G. Mauri. An Approximation Algorithm for the Shortest Common Supersequence Problem: An Experimental Analysis,  Proceedings of the th ACM Symposium on Applied Computing (SAC2001)}, ACM, 55-60, 2001.

 P. Bonizzoni, G. Della Vedova e G.Mauri. Approximating the Maximum Isomorphic Agreement Subtree is Hard, In, D. Sankoff and R. Giancarlo editors,  Proceedings of the 11th Symposium on Combinatorial Pattern Matching (CPM2000)}, LNCS 1848, 119-128, 2001.

 P. Bonizzoni,  A. Eherenfeucht. Approximation of the Shortest Common Supersequence with ratio less than the alphabet size. Technical Report 149-95, Dipartimento di Scienze dell' Informazione, 1995.




P. Bonizzoni,   C. De Felice , G. Mauri e R. Zizza Circular splicing and regularity . Theoretical Informatics and Applications, RAIRO vol. 38 pag.189-228, 2004.

P. Bonizzoni,   C. De Felice,  G. Mauri e R. Zizza On the power of circular splicing.   submitted.

P. Bonizzoni,   C. De Felice,  G. Mauri e R. Zizza On linear splicing and the synctatic monoid.   submitted.

P. Bonizzoni,  C. Ferretti , G. Mauri e R. Zizza. Separating some splicing models.  Information Processing Letters  76:6,  255-259, 2001.

P. Bonizzoni, C. De Felice, G. Mauri, R.Zizza.  DNA and circular splicing, In A. Condon, G. Rozenberg editors, Proc. of International Meeting on DNA6, LNCS 2054, 117-129, 2001.

P. Bonizzoni, C. De Felice, G. Mauri, R.Zizza. Regular languages generated by reflexive finite splicing systems, Proc. th International Conference on Developments in Language Theory, DLT02, LNCS 2710,   134-145 Szeged (Hungary), July 7-11, 2003.

P. Bonizzoni, C. De Felice, G. Mauri, R.Zizza. Decision problems for linear and circular splicing systems, Proc. th  International Conference on Developments in Language Theory, DLT03,  LNCS 2450,  78-92 Kyoto, September 2002.

P. Bonizzoni, C. Ferretti e G. Mauri. Splicing systems with marked rules.  Romanian Journal of Information Science and Technology,1:4, 1999 (a preliminary version was
presented to MFCS 98).

 P. Bonizzoni, C. De Felice, G. Mauri, R.Zizza Linear and Circular Splicing,     WORDS99, Rouen, France 1999 .

 P. Bonizzoni, C. Ferretti, G. Mauri, R.Zizza. Separating some splicing models,  Proc. of  International Workshop on   GRAMMAR SYSTEMS2000, Austria, 2000.

P. Bonizzoni, C. De Felice, G. Mauri, R.Zizza.   Developments on Circular Splicing, WORDS01, Palermo 2001.




  P. Bonizzoni e   R. McConnell. Nesting of Indecomposable Substructures in k-ary Relational Structures. Theoretical Computer Science, 259:1, 341-357,  2001.

  P. Bonizzoni e G. Della Vedova. An algorithm for the modular decomposition of hypergraphs.  Journal of Algorithms, volume 32, 2:65-86, 1999..

  P. Bonizzoni. A tight lower bound for Primitivity in k-structures. In  Proceedings of the 21th International Colloquium on  automata, Languages and Programming, (ICALP94)}, LNCS volume 820, pages 556-567. Springer-Verlag, Berlin, 1994.

  P. Bonizzoni. Primitive  2-structures with the (n-2)-property.  Theoretical Computer Science,132:151-178,1994.

 P. Bonizzoni e A. Eherenfeucht. Minimal Indecomposable graphs. In  Proceedings of the 14th British Combinatorial Conference, Keele University, 1995.

  P. Bonizzoni e G. Della Vedova. Modular Decomposition of Hypergraphs. In  Proceedings of the Workshop on Graph-Theoretic Concepts in Computer Science, (WG95)}, LNCS volume 1017, pages 303-317. Springer-Verlag, Berlin, 1995.

P. Bonizzoni. The (n - 2) property of primitive 2-structures. In M. Venturini Zilli, A. M. Marchetti Spaccamela, P. Mentrasti, editors,  Proceedings of the Fourth Italian Conference on Theoretical Computer Science, pages 96-109. World Scientific, London, 1992.





P. Bonizzoni, G. Mauri. On automata on infinite trees.  Theoretical Computer Science, 93:227-244,1992.

A. Saoudi, P. Bonizzoni.  Automata on infinite trees and Rational Control. In A. Podelski, M. Nivat,  Tree Automata and Languages, pages 189-199, North Holland, 1992.

P. Bonizzoni,  G.Mauri,  G. Pighizzini e N. Sabadini.  Recognizing Sets of Labelled Acyclic Graphs. In A. Podelski, M. Nivat,  Tree Automata and Languages, pages 201-224, North Holland, 1992.

P. Bonizzoni, G.Mauri e G. Pighizzini. About infinite traces. In  Proceedings of the Workshop on Free Partially Commutative Monoids, Munchen, (V. Diekert editor) pages 146-153, 1990.