April 26, 2017, Wednesday

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Publications

Articles

Graudenzi, A, Caravagna, G, De Matteis, G & Antoniotti, M. Investigating the Relation between Stochastic Differentiation, Homeostasis and Clonal Expansion in Intestinal Crypts via Multiscale Modeling. PLoS ONE Vol. 9 (5) (May, 2014).

Caravagna, G, D'Onofrio, A, Antoniotti, M & Mauri, G. Stochastic Hybrid Automata with non-istantaneous transitions to model biochemical systems with delays. Information and Computation (January, 2014).

Cava, C, Zoppis, I, Gariboldi, M, Castiglioni, I, Mauri, G & Antoniotti, M. Combined Analysis of Chromosomal Instabilities and Gene Expression for Colon Cancer Progression Inference. Journal of Clinical Bioinformatics Vol. 4 (2) (January, 2014).

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]

Antoniotti, M, Bader, G, Caravagna, G, Crippa, S, Graudenzi, A & Mauri, G. GESTODifferent: A Cytoscape plugin for the generation and the identification of Gene Regulatroy Networks describing a stochastic cell differentiation process. Bioinformatics (January, 2013).

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]

Alhazov, A, Antoniotti, M & Leporati, A. Characterizing the Computational Power of Energy-Based P-Systems. International Journal of Computer Mathematics Vol. 90 pp. 789-800 (April, 2013).

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]

De Matteis, Giovanni, Graudenzi, Alex & Antoniotti, Marco. Simulation of Multicellular Systems and Colonic Crypts: A Survey of Methods and a Perspective on Future Developments. To appear - already published online. Journal of Mathematical Biology (June, 2012).

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]

Leonardo Vanneschi, Yuri Pirola, Giancarlo Mauri, Marco Tomassini, Philippe Collard & Sebastien Verel. A study of the neutrality of Boolean function landscapes in genetic programming. Theoretical Computer Science Vol. 425 pp. 34-57 (2012). [url]

Zoppis, I, Gianazza, E, Borsani, M, Chinello, C, Maininin, V, Galbusera, C, Ferrarese, C, Galimberti, G, Sorbi, S, Borroni, B, Magni, F, Antoniotti, M & Mauri, G. Mutual Information Optimization for Mass Spectra Data Alignment. IEEE/ACM Transactions on Comutational Biology and Bioinformatics Vol. 99 (2011). [url]

Vanneschi, L, Farinaccio, A, Mauri, G, Antoniotti, M, Provero, P & Giacobini, M. A Comparison of Machine Learning Techniques for Survival Prdiction in Breast Cancer. BioData Mining Vol. 4 (11) (2011). [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]

Ramakrishnan, N, Tadepalli, S, Watson, LT, Helm, RF, Antoniotti, M & Mishra, B . Reverse Engineering Dynamic Temporal Models of Biological Processes and their Relationships. PNAS Vol. 107 (28) pp. 12511-12516 (July, 2010). [url]

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

Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola & Lusheng Wang. Beyond Evolutionary Trees. Natural Computing (Sep, 2009). [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]

Colombo, G, Merico, D, Boncoraglio, G, De Paoli, F, Ellul, J, Frisoni, G, Nagy, Z, van der Lugt, A, Vassanyi, I & Antoniotti, M. An Ontological Modelling Approach to Neurovascular Disease Study: the NEUROWEB Case. Journal of Biomedical Informatics (December, 2009). [url]

Colombo, G, Merico, D, Nagy, Z, De Paoli, F, Antoniotti, M & Mauri, G. Ontological modeling at a domain interface: bridging clinical and biomolecular knwoledge. The Knowledge Engineering Review Vol. 24 (3) pp. 205-224 (2009).

Antoniotti, M, Carreras, M, Farinaccio, A, Mauri, G, Merico, D & Zoppis, I. An Application of Kernel Methods to Gene Cluster Temporal Meta-Analysis. Computers & Operations Research (2009). [url]

Besozzi, Daniela, Cazzaniga, Paolo, Dugo, Matteo, Pescini, Dario & Mauri, Giancarlo. A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis. EPTCS Vol. 6 pp. 47-62 (2009). [url]

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

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

S. Ryu, S. Lin, N. Ugel, M. Antoniotti & B. Mishra. Mathematical Modeling of the formation of Apoptosome in Intrinsic Pathway of Apoptosis. Systems and Synthetic Biology Vol. 2 (1-2) pp. 49-66 (June, 2008).

Besozzi, Daniela, Cazzaniga, Paolo, Pescini, Dario & Mauri, Giancarlo. Modelling metapopulations with stochastic membrane systems. Biosystems Vol. 91 (3) pp. 499 - 514 (2008). [url]

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

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

Castrignano, Tiziana, D'Antonio, M, Anselmo, Anna, Carrabino, Danilo, D'Onorio De Meo, A, D'Erchia, A M, Licciculli, Flavio, Mangiulli, M, Mignone, Flavio, Pavesi, Giulio, Picardi, Ernesto, Riva, A, Rizzi, Raffaella, Bonizzoni, Paola & Pesole, Graziano. ASPicDB: A database resource for alternative splicing analysis. Bioinformatics Vol. 24 (10) pp. 1300-1304 (2008). [url]

J. P. Mathew, B. S. Taylor, G. D. Bader, S. Pyarajan, M. Antoniotti, A. M. Chinnaiyan, C. Sander, S. J. Burakoff & B. Mishra. From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Computational Biology Vol. 3 (2) pp. e12 (2007).

Besozzi, D, Cazzaniga, P, Pescini, D & Mauri, G. Seasonal variance in P system models for metapopulations. Prog. Nat. Sci. Vol. 17 (4) pp. 392-400 (2007).

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

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

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

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

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

P. E. Barbano, M. Antoniotti, J. Feng, M. Spivak & B. Mishra. A Coherent Framework for Multi-resolution Analysis of Biological Networks with Memory: RAS Pathway, Cell Cycle and Immune System. Proceedings of the National Academy of Science (PNAS) Vol. 102 (18) pp. 6245-6250 (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).

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

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

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

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

Bonizzoni, Paola, Rizzi, Raffaella & Pesole, Graziano. 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]

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

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

Bonizzoni, Paola & Della Vedova, Gianluca. 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]

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

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

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

In Book

Kleinberg, S, Antoniotti, M, Tadepalli, S, Ramakrishnan, N & Mishra, B. Systems Biology via Redescription and Ontologies (II): A Tool for Discovery in Complex Systems. In Special Issue on the Proceedings of the Sixth International Conference on Complex Systems. Minai, AA.;Braha, D;Bar-Dam, Y (Ed.). Spinger. Vol. VI (October, 2009).

Besozzi, Daniela, Cazzaniga, Paolo, Pescini, Dario & Mauri, Giancarlo. Algorithmic Bioprocesses. SpringerVerlag (Ed.). pp. 519-542 (2009).

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

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

Bonizzoni, Paola, Della Vedova,Gianluca, Dondi, Riccardo & Li, Jing. 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]

Caravagna, G, Graudenzi, A, Antoniotti, M, Mauri, G & D'Onofrio, A. Effects of delayed immune-response in tumor immune-system interplay. In First International Workshop on Hybrud Systems and Biology. (September, 2012).

Zoppis, I, Borsani, M, Gianazza, E, Chinello, C, Antoniotti, M, Deelder, AM, van der Burgt, YEM, Magni, F & Mauri, M. Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. In International Conference on Bioinformatics Models, Method and Algorithms (Bioinformatics 2012). (February, 2012).

Graudenzi, Alex, Caravagna, Giulio, De Matteis, Giovanni & Antoniotti, Marco. A multiscale model of intestinal crypt dynamics. In Proceedings of the Italian Workshop on Artificial Life and Evolutionary Computation. (February, 2012). [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]

Filisetti, A & Graudenzi, A. The influence of different kinetic rates on the dynamics of a simple model of catalytic reaction network. In Proceedings of the Italian Workshop on Artificial Life and Evolutionary Computation. (2012).

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]

L. Vanneschi, A. Farinaccio, M. Giacobini, M. Antoniotti, G. Mauri & P. Provero. Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. In Proceedings of the EvoBIO 2010 Conference. (April, 2010).

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]

Besozzi, Daniela, Cazzaniga, Paolo, Mauri, Giancarlo, Pescini, Dario & Vanneschi, Leonardo. A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems. In Proc. of EvoBIO. (5483) pp. 116-127 (2009).

Cazzaniga, Paolo, Mauri, Giancarlo, Milanesi, Luciano, Mosca, Ettore & Pescini, Dario. A novel variant of tissue P systems for the modelling of biochemical systems. In Proc. of the 10th International Workshop on Membrane Computing. G. Paun and M.J. Perez-Jimenez and A. Riscos-Nunez and G. Rozenberg and A. Salomaa (Ed.). LNCS. Vol. 5957 pp. 210-226 (2009).

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

Bonizzoni, Paola, Della Vedova, Gianluca & Dondi, Riccardo. 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).

Bonizzoni, Paola, Della Vedova, Gianluca & Dondi, Riccardo. 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]

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

G. Colombo, D. Merico, G. Frisoni, M. Antoniotti, F. De Paoli & G. Mauri. An ontological modeling approach to neurovascular disease studies: the NEUROWEB case. In Proceedings of the NETTAB Conference. (2007).

I. Zoppis, D. Merico, M. Antoniotti, B. Mishra & G. Mauri. Discovering Relations among GO-annotated Clusters by Graph Kernel Methods. In International Symposium on Bioinformatics Research and Applications (ISBRA). (2007).

Leonardo Vanneschi, Marco Tomassini, Philippe Collard, Sebastien Verel, Yuri Pirola & Giancarlo Mauri. A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds. In Genetic Programming, 10th European Conference, Proceedings. Marc Ebner et al. (Ed.). Springer. Vol. 4445 pp. 241-250 (2007). [url]

D. Merico, I. Zoppis, M. Antoniotti & G. Mauri. Evaluating Graph Kernels for Relation Discovery in GO-annotated Clusters. In Proocedings of the 11th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES2007). (2007).

S. Kleinberg, M. Antoniotti, S. Tadepalli, N. Ramakrishnan & B. Mishra. Remembrance of Experiments Past: A Redescription Based Tool for Discovery in Complex Systems. In Proceedings of the International Conference on Complex Systems. (June, 2006).

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).

Leonardo Vanneschi, Yuri Pirola & Philippe Collard. A quantitative study of neutrality in GP boolean landscapes. In Genetic and Evolutionary Computation, 8th Annual Conference, GECCO 2006, Proceedings. ACM Press. pp. 895-902 (2006). [Free official version]   [url]

Cazzaniga, P, Pescini, D, Besozzi, D & Mauri, G. Tau leaping stochastic simulation method in P systems. In Proc. of the 7th International Workshop on Membrane Computing. H. J. Hoogeboom and G. P\u{a}un and G. Rozenberg and A. Salomaa (Ed.). LNCS. Vol. 4361 pp. 298-313 (2006).

Bonizzoni, Paola, Della Vedova, Gianluca, Dondi, Riccardo, Fertin, Guillaume & Vialette, Stephane. 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]

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

Bonizzoni, Paola & Mauri, Giancarlo. 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]

Bonizzoni, Paola, Della Vedova, Gianluca, Dondi, Riccardo & Jiang, Tao. 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]

Bonizzoni, Paola, Della Vedova, Gianluca, Dondi, Riccardo & Mariani, Lorenzo. 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]

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

Barone, Paolo, Bonizzoni, Paola, Della Vedova, Gianluca & Mauri, Giancarlo. 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]

Bonizzoni, Paola, Della Vedova, Gianluca & Mauri, Giancarlo. 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]

Phd Thesis

Yuri Pirola. Combinatorial Problems in Studies of Genetic Variations: Haplotyping and Transcript Analysis. Univ. degli Studi di Milano-Bicocca, Milan, Italy. (2010). [url]