Riccardo Dondi

I am an Assistant Professor at the University of Bergamo. My research interests are

  • Algorithms
  • Computational Complexity
  • Approximation Complexity
  • Parameterized Complexity

In particular, I am interested in some problems in Computational Biology: Haplotyping, Clustering (Consensus Clustering, Fingerprint Clustering), Sequence Alignment, Phylogeny Reconstruction. I am also interested in some combinatorial problems in Privacy Preserving Data Publishing (K-Anonymity, L-Diversity)

Education

2005: Ph.D. Computer Science (Università di Milano-Bicocca)

1999: M.Sc. Computer Science (Università di Milano)

Pubblications

International Journal Papers

P. Bonizzoni, G. Della Vedova, R. Dondi, T. Jiang, On the Approximation of Correlation Clustering and Consensus Clustering. Journal of Computer and System Sciences, vol. 74(5), pp. 671-696, 2008.

R. Albert, B. DasGupta, R. Dondi, E. Sontag, Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs. Algorithmica, vol. 51, pp. 129-159, 2008.

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Fertin, R. Rizzi, S. Vialette, Exemplar Longest Common Subsequence. IEEE/ACM Transactions on Computational Biology and Binformatics, vol. 4, pp. 535-543, 2007.

R. Albert, B. DasGupta, R. Dondi, S. Kachalo, E. Sontag, A. Zelikovsky, K. Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. Journal of Computational Biology, vol. 14, pp. 927-949, 2007.

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 (IJBRA), 1(4), pp. 461-473, 2005

P. Bonizzoni, G. Della Vedova, R. Dondi, Reconciling a Gene Tree to a Species Tree Under the Duplication Cost Model. Theoretical Computer Science, vol. 1-2, pp. 36-53, 2005.

A. Agostini, R. Boselli, F. De Paoli, R. Dondi, Situation-Based Knowledge Presentation for Mobile Workers. International Journal of Information Technology 1 (1): 25-28, 2004.

P. Bonizzoni, G. Della Vedova, R. Dondi, J. Li, The Haplotyping Problem: An Overview of Computational Models and Solutions. Journal of Computer Science and Technology 18(6):675-688, 2003.

G. Della Vedova, R. Dondi, A library of efficient bioinformatics algorithms. Applied Bioinformatics, 2(2):117-121, 2003.

Book Chapters

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Mauri, The Comparison of Phylogenetic Networks: Algorithms and Complexity. In I. I. Mandoiu, A. Zelikovsky. Bioinformatics Algorithms: Techniques and Applications, pp. 143-173, John Wiley & Sons, 2008.

P. Bonizzoni, G. Della Vedova, R. Dondi, J. Li, The Haplotyping Problem: An Overview of Computational Models and Solutions. In S. Kim, H. Tang, E. R. Mardis. Genome Sequencing Technology and Algorithms, pp. 151-181, Artech House, 2008.

International Conferences

P. Bonizzoni, G. Della Vedova, R. Dondi, Y. Pirola, R. Rizzi, Minimum Factorization Agreement of Spliced ESTs. In S. Salzberg, T. Warnow, editors, Proceedings of WABI 2009, 9th International Workshop on Algorithms in Bioinformatics, volume 5724 of LNCS, pp. 1-12, 2009.

R. Dondi, The Longest Haplotype Reconstruction Problem Revisited. In M. Kutylowski, W. Charatonik, M. Gebala, editors, Proceedings of FCT 2009, 17th Annual Symposium on Fundamentals of Computation Theory, volume 5699 of LNCS, pp. 109-120, 2009.

P. Bonizzoni, G. Della Vedova, R. Dondi, The k-Anonymity Problem Is Hard. In M. Kutylowski, W. Charatonik, M. Gebala, editors, Proceedings of FCT 2009, 17th Annual Symposium on Fundamentals of Computation Theory, volume 5699 of LNCS, pp. 26-37, 2009.

R. Dondi, G. Fertin, S. Vialette, Maximum Motif Problem in Vertex-Colored Graphs. In G. Kucherov, E. Ukkonen, editors, Proceedings of CPM 2009, 20th Annual Symposium on Combinatorial Pattern Matching, volume 5577 of LNCS pp. 221-235, 2009.

P. Bonizzoni, G. Della Vedova, R. Dondi, Y. Pirola, R. Rizzi, Pure Parsimony Xor Haplotyping. In I. Mandoiu, G. Narasimhan, Y. Zhang, editors, Proceedings of ISBRA 2009, 5th International Symposium on Bioinformatics Research and Applications, volume 5542 of LNCS, pp. 186-197, 2009.

A. Mangiatordi, R. Dondi,W. Fornasa, Moving Assistive Technology on the Web: The Farfalla Experience. In M. Lytras, J. M. Carroll, E. Damiani, R. Tennyson, D. Avison, G. Vossen, P. Ord˜A3˜A ez de Pablos, editors, Proceedings of WSKS 2008, First World Summit on the Knowledge Society, volume 19 of CCIS, pp. 598-602, 2008.

R. Dondi, G. Fertin, S. Vialette, Weak pattern matching in colored graphs: Minimizing the number of connected components. In G. Italiano, E. Moggi, L. Laura, editors, Proceedings of ICTCS 2007, 10th Italian Conference on Theoretical Computer Science, pp. 27-38, 2007.

R. Albert, B. DasGupta, R. Dondi, S. Kachalo, E. Sontag, A. Zelikovsky, K. Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. In R. Giancarlo and S. Hannenhalli, editors, Proceedings of the WABI 2007, 7th International Workshop on Algorithms in Bioinformatics, volume 4645 of LNCS, pp. 407-419, 2007.

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Mauri, Fingerprint Clustering with Bounded Number of Missing Values. In M. Lewenstein and G. Valiente, editors, Proceedings of CPM 2006, 17th Annual Symposium on Combinatorial Pattern Matching, volume 4009 of LNCS, pp. 106-116, 2006.

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Fertin, S. Vialette, Exemplar Longest Common Subsequence. In V. N. Alexandrov, G. D. van Albada, P. M. A. Sloot and J. Dongarra, editors, Proceedings of ICCS 2006, 5th International Conference on Computational Science, volume 3992 of LNCS, pp. 622-629, 2006.

P. Bonizzoni, G. Della Vedova, R. Dondi, T. Jiang, Correlation Clustering and Consensus Clustering. In X. Deng and D. Du, Proceedings of ISAAC 2005, 16th Annual International Symposium on Algorithms and Computation, volume 3827 of LNCS pp. 226-235, 2005.

P. Bonizzoni, G. Della Vedova, R. Dondi, L. Mariani, Experimental Analysis of a New Algorithm for Partial Haplotype Completion. In V. S. Sunderam, G. D. van Albada, P. M. A. Sloot and J .Dongarra, editors, Proceedings of ICCS 2005, 5th International Conference on Computational Science, volume 3515 of LNCS, pp. 952-959, 2005.

A. Agostini, S. Albolino, R. Boselli, G. De Michelis, F. De Paoli, R. Dondi, Stimulating Knowledge Discovery and Sharing, In K. Schmidt, M. Pendergast, M. Tremaine and Carla Simone, editors, Proceedings of GROUP 2003, the ACM International Conference on Supporting Group Work, pp. 248-257, 2003.

R. Boselli, F. De Paoli, R. Dondi, Knowledge Organization and Retrieval in the MILK System. In Proceedings of SEKE 2003, the 15th International Conference Fifteenth International Conference on Software Engineering and Knowledge Engineering , pp. 372-376, 2003.

P. Bonizzoni, G. Della Vedova, R. Dondi. Reconciling Gene Trees to a Species Tree. In R. Petreschi, G. Persiano and R. Silvestri, editors, Algorithms and Complexity, Proceedings of the 5th Italian Conference (CIAC 2003), volume 2653 of LNCS, pp. 120-131, 2003.