July 24, 2017, Monday

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Bonizzoni Paola

Paola Bonizzoni
Paola Bonizzoni

Paola Bonizzoni is full professor in Computer Science at the Università di Milano-Bicocca.

Her research interests are mainly in the area of theoretical computer science, and include: formal languages and automata, graph theory, design and engineering of algorithms, computational complexity and bioinformatics. Recently, she was involved in a research in bioinformatics concerning sequence and phylogenetic analysis, obtaining results mainly on the computational complexity and solution of combinatorial problems on trees and sequences. Moreover, she got results on the computational power of formal systems for molecular computation based on the recombination of linear and circular DNA.


Contents

Education

1993 Ph. D. Computer Science at Università di Milano, my Advisor was Prof. A. Ehrenfeucht (University of Colorado at Boulder - USA) and my co-advisors Prof. G. Mauri (Università di Milano) Prof. G. Rozenberg (University of Leiden - Holland )


Associations


Events

Member of the Program Committee of


Projects

  • ASPIC-DB], alternative splicing prediction database
  • PPH, software for haplotype inference by perfect phylogeny
  • PIntron, intron prediction software
  • FIRB '08 Bioinformatics: genomics and proteomics


Address

Dipartimento di Informatica Sistemistica e Comunicazione
Università Degli Studi di Milano-Bicocca
Viale Sarca 336 Milano, 20126 (ITALY)
Email: bonizzoni at disco dot unimib dot it
Tel. (+39) 02-64487814, fax: (+39) 02-64487839


Publications

Articles

Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola & Raffaella Rizzi. Modeling alternative splicing variants from RNA-Seq data with isoform graphs. Journal of Computational Biology Vol. 21 (1) pp. 16-40 (Jan, 2014). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Yuri Pirola. Parameterized complexity of k-anonymity: hardness and tractability. Journal of Combinatorial Optimization Vol. 26 (1) pp. 19-43 (Jul, 2013). [url]

Paola Bonizzoni, Riccardo Dondi & Yuri Pirola. Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability. Algorithms Vol. 6 (1) pp. 1-11 (Jan, 2013). [url]

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella & Paola Bonizzoni. A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information. IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 9 (6) pp. 1582-1594 (Nov, 2012). [url]

Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova & Paola Bonizzoni. PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC Bioinformatics Vol. 13 (S5) (Apr, 2012). [url]

Yuri Pirola, Paola Bonizzoni & Tao Jiang. An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 9 (1) pp. 9-25 (2012). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Yuri Pirola. Variants of constrained longest common subsequence. Information Processing Letters Vol. 110 (20) pp. 877-881 (Sep, 2010). [arXiv version]   [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola & Romeo Rizzi. Pure Parsimony Xor Haplotyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 7 (4) pp. 598-610 (Oct-Dec, 2010). [arXiv version]   [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Giancarlo Mauri. Fingerprint Clustering with Bounded Number of Missing Values. ALGORITHMICA Vol. 58 pp. 282-303 (2010). [url]

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 (1) pp. 43-66 (Jan, 2009). [url]

Paola Bonizzoni. Constants and label-equivalence: A decision procedure for reflexive splicing languages. THEORETICAL COMPUTER SCIENCE Vol. 411 (6) pp. 865-877 (2009). [url]

Paola Bonizzoni, Clelia De Felice, Gabriele Fici & Rosalba Zizza. On the regularity of circular splicing languages: a survey and new developments. NATURAL COMPUTING (2009). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Tao Jiang. On the Approximation of Correlation Clustering and Consensus Clustering. JOURNAL OF COMPUTER AND SYSTEM SCIENCES Vol. 74 pp. 671-696 (2008).

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Giancarlo Mauri. Fingerprint clustering with bounded number of missing values. ALGORITHMICA (2008). [url]

Tiziana Castrignano, M D'Antonio, Anna Anselmo, Danilo Carrabino, A D'Onorio De Meo, A M D'Erchia, Flavio Licciculli, 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 Vol. 24 (10) pp. 1300-1304 (2008). [url]

Paola Bonizzoni. A Linear Time Algorithm for the Perfect Phylogeny Haplotype Problem. ALGORITHMICA Vol. 48 pp. 267-285 (2007).

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi & Stephane Vialette. Exemplar Longest Common Subsequence. IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 4 (4) pp. 535-543 (2007). [url]

Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri & Rosalba Zizza. Linear splicing and syntactic monoid. DISCRETE APPLIED MATHEMATICS Vol. 154:3 pp. 452-470 (2006).

Paola Bonizzoni, Raffaella Rizzi & Graziano Pesole. Computational Methods for Alternative Splicing Prediction. BRIEFINGS IN FUNCTIONAL GENOMICS \& PROTEOMICS Vol. 5 pp. 46-51 (2006).

Tiziana Castrignano, Raffaella Rizzi, G Talamo, A D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni & Graziano Pesole. ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. NUCLEIC ACIDS RESEARCH Vol. 34 pp. 440-443 (2006).

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).

Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri & Rosalba Zizza. On the power of circular splicing. DISCRETE APPLIED MATHEMATICS Vol. 150 pp. 51-56 (2005).

Paola Bonizzoni, Clelia De Felice & Rosalba Zizza. The structure of re?exive regular splicing languages via Schutzenberger constants. Theoretical Computer Science Vol. 334 (1-3) pp. 71-98 (2005). [url]

Paola Bonizzoni, Gianluca Della Vedova & Riccardo Dondi. Reconciling a Gene Tree to a Species Tree Under the duplication cost Model. THEORETICAL COMPUTER SCIENCE Vol. 347 pp. 36-53 (2005).

Paola Bonizzoni & Giancarlo Mauri. Regular splicing languages and subclasses. THEORETICAL COMPUTER SCIENCE Vol. 340 pp. 349-363 (2005).

Paola Bonizzoni, Raffaella Rizzi & Graziano 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 Vol. 6 pp. 244 (2005). [url]

Paola Bonizzoni, Clelia De Felice, Giancarlo Mauri & Rosalba Zizza. Circular splicing and regularity. RAIRO. INFORMATIQUE THEORIQUE ET APPLICATIONS Vol. 38 pp. 189-228 (2004). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Jing Li. The Haplotyping Problem: an Overview of Computational Problems and Solutions. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY Vol. 18 (6) pp. 675-688 (2003).

Paola Bonizzoni & Gianluca Della Vedova. The complexity of Multiple Sequence Alignment with a SP-score that is a metric. THEORETICAL COMPUTER SCIENCE Vol. 259 (1-2) pp. 63-79 (2001). [url]

Paola Bonizzoni, Gianluca Della Vedova & Giancarlo Mauri. Experimenting an Approximation Algorithm for the LCS. DISCRETE APPLIED MATHEMATICS Vol. 110 (1) pp. 13-24 (2001). [url]

Paola Bonizzoni, Gianluca Della Vedova & Giancarlo Mauri. Approximating the Maximum Isomorphic Agreement Subtree is Hard. INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE Vol. 11 pp. 579-590 (2000).

Paola Bonizzoni & Gianluca Della Vedova. An Algorithm for the Modular Decomposition of Hypergraphs. JOURNAL OF ALGORITHMS Vol. 32 (2) pp. 65-86 (1999).

In Book

Paola Bonizzoni & Remco Loos. Finite Splicing: Generative Capacity, New Models and Complexity Aspects. In Algorithmic Bioprocesses. Condon, Harel, Kok, Salomaa, and Winfree (Ed.). Springer. (2009). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Giancarlo Mauri. The Comparison of Phylogenetic Networks: Algorithms and Complexity. In Bioinformatics Algorithms: Techniques and Applications. Wiley-Interscience. pp. 143-173 (2008). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Jing Li. The Haplotyping Problem: An Overview of Computational Models and Solutions. In Genome Sequencing Technology and Algorithms. S. Kim, H. Tang, E. R. Mardis (Ed.). Norwood. pp. 151-181 (2007).

In Proceedings

Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi & Yuri Pirola. Covering pairs in directed acyclic graphs. In Language and Automata Theory and Applications, 8th Int. Conf., LATA 2014, Madrid, Spain, March 10-14, Proceedings. Springer. Vol. 8370 pp. 126-137 (2014). [url]

Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella & Filippo Biscarini. Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. In Bioinformatics, Computational Biology, and Biomedical Informatics, 4th ACM Int. Conf., ACM BCB 2013, Washington DC, USA, Sept. 22-25. ACM. pp. 33-41 (2013). [url]

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella & Paola Bonizzoni. A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information. In Computational Advances in Bio and medical Sciences, 2nd IEEE Int. Conference, ICCABS 2012, Las Vegas NV, USA, Feb. 23-25, Proceedings. IEEE. (2012). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Yuri Pirola. Parameterized Complexity of k-Anonymity: Hardness and Tractability. In Combinatorial Algorithms, 21st Int. Workshop, IWOCA 2010, London UK, Jul 26-28, Revised selected papers. C. Iliopoulos and W. Smyth (Ed.). Springer. Vol. 6460 pp. 242-255 (2011). [url]

Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola & Raffaella Rizzi. PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text. In Computational Advances in Bio and medical Sciences, 1st IEEE Int. Conference, ICCABS 2011, Orlando FL, USA, Feb 3-5, 2011. IEEE. pp. 33-39 (2011). [url]

Yuri Pirola, Paola Bonizzoni & Tao Jiang. Haplotype Inference on Pedigrees with Recombinations and Mutations. In Algorithms in Bioinformatics, 10th Int. Workshop, WABI 2010, Liverpool UK, Sep 6-8, 2010, Proceedings. V. Moulton and M. Singh (Ed.). Springer. Vol. 6293 pp. 148-161 (2010). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola & Raffaella Rizzi. Minimum Factorization Agreement of Spliced ESTs. In Algorithms in Bioinformatics, 9th Int. Workshop, WABI 2009, Philadelphia PA, USA, Sep 12-13, 2009, Proceedings. Springer. Vol. 5724 pp. 1-12 (Sep, 2009). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola & Romeo Rizzi. Pure Parsimony Xor Haplotyping. In Bioinformatics Research and Applications, 5th Int. Symposium, ISBRA 2009, Fort Lauderdale FL, USA, May 13-16, 2009, Proceedings. Ion I. Mandoiu and Giri Narasimhan and Yanqing Zhang (Ed.). Springer. Vol. 5542 pp. 186-197 (May, 2009). [url]

Paola Bonizzoni, Claudia De Felice & Rosalba Zizza. Circular languages generated by complete splicing systems and pure unitary languages. In Computational Models From Nature. EPTCS. pp. 23-31 (2009). [url]

Paola Bonizzoni, Gianluca Della Vedova & Riccardo Dondi. A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. In Proceedings of the 11th Italian Conference on Theoretical Computer Science (ICTCS 2009). (2009).

Paola Bonizzoni, Gianluca Della Vedova & Riccardo Dondi. The k-anonymity Problem is Hard. In PROCEEDINGS 17TH INTERNATIONAL SYMPOSIUM ON FUNDAMENTALS OF COMPUTATION THEORY (FCT 2009). Springer Verlag. Vol. 5699 pp. 26-37 (2009). [url]

Paola Bonizzoni, Claudio Ferretti, Sagaya Mary Anthonath Roslin & Giancarlo Mauri. Picture Languages Generated by Assembling Tiles. In LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS. Springer-Verlag. Vol. 5457 pp. 224-235 (2009). [url]

P. Bonizzoni, G. Della Vedova, R. Dondi & G. Mauri. Fingerprint Clustering with Bounded Number of Missing Values. In Proceeding of the 17th Annual Symposium on Combinatorial Pattern Matching. pp. 106-116 (2006).

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin & Stephane Vialette. Exemplar Longest Common Subsequence. In Computational Science - ICCS 2006, 6th International Conference, Reading, UK, May 28-31, 2006, Proceedings, Part II. Vassil N. Alexandrov and G. Dick van Albada and Peter M. A. Sloot and Jack Dongarra (Ed.). Springer. Vol. 3992 pp. 622-629 (2006). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Giancarlo Mauri. A PTAS for the Maximum Consensus Clustering. In Proceedings of the 1st FIMA International Conference Models and Methods for Human Genomics. (2006).

Paola Bonizzoni & Giancarlo Mauri. A decision procedure for reflexive splicing languages. In Developments in Language Theory, 10th International Conference, DLT 2006, Santa Barbara, CA, USA, June 26-29, 2006, Proceedings. Oscar H. Ibarra and Zhe Dang (Ed.). Springer. Vol. 4036 pp. 315-326 (2006). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Tao Jiang. Correlation Clustering and Consensus Clustering. In Algorithms and Computation, 16th International Symposium, ISAAC 2005, Sanya, Hainan, China, December 19-21, 2005, Proceedings. Xiaotie Deng and Ding-Zhu Du (Ed.). Springer. Vol. 3827 pp. 226-235 (2005). [url]

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi & Lorenzo Mariani. Experimental Analysis of a New Algorithm for Partial Haplotype Inference. In Computational Science - ICCS 2005, 5th International Conference, Atlanta, GA, USA, May 22-25, 2005, Proceedings, Part II. Vaidy S. Sunderam and G. Dick van Albada and Peter M. A. Sloot and Jack Dongarra (Ed.). Springer. Vol. 3515 pp. 952-959 (2005). [url]

Paola Bonizzoni, Gianluca Della Vedova & Riccardo Dondi. Reconciling Gene Trees to a Species Tree. Vol. LNCS 2653 pp. 120-131 (May 28-30, 2003).

Paolo Barone, Paola Bonizzoni, Gianluca Della Vedova & Giancarlo Mauri. An Approximation Algorithm for the Shortest Common Supersequence Problem: An Experimental Analysis. In Proceedings of the 2001 ACM Symposium on Applied Computing (SAC), March 11-14, 2001, Las Vegas, NV, USA. ACM. pp. 56-60 (2001). [url]

Paola Bonizzoni, Gianluca Della Vedova & Giancarlo Mauri. Approximating the Maximum Isomorphic Agreement Subtree Is Hard. In Combinatorial Pattern Matching, 11th Annual Symposium, CPM 2000, Montreal, Canada, June 21-23, 2000, Proceedings. Raffaele Giancarlo and David Sankoff (Ed.). Springer. Vol. 1848 pp. 119-128 (2000). [url]


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