From BIMIB

Publications

Articles

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola & Romeo Rizzi. Pure Parsimony Xor Haplotyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics (to appear, 2010).

Ramakrishnan, N, Tadepalli, S, Watson, LT, Helm, RF, Antoniotti, M & Mishra, B . Reverse Engineering Dynamic Temporal Models of Biological Processes and their Relationships. PNAS (June, 2010) Volume published online before print:. [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 (Jan, 2009) Volume 16: pp. 43-66. [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 (2009) Volume 24: pp. 205-224.

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 (2009) Volume 6: pp. 47-62. [url]

Besozzi,Daniela, Busi,Nadia, Cazzaniga,Paolo, Ferretti,Claudio, Leporati,Alberto, Mauri,Giancarlo, Pescini,Dario & Zandron,Claudio. (Tissue) P systems with cell polarity. Mathematical Structures in Computer Science (2009) Volume 19: pp. 1141-1160. [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 (June, 2008) Volume 2: pp. 49-66.

Besozzi, Daniela, Cazzaniga, Paolo, Pescini, Dario & Mauri, Giancarlo. Modelling metapopulations with stochastic membrane systems. Biosystems (2008) Volume 91: pp. 499 - 514. [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 (2007) Volume 3: pp. e12.

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

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

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) (2005) Volume 102: pp. 6245-6250.

P. Bonizzoni, G. Della Vedova & R. Dondi. Reconciling a gene tree to a species tree under the duplication cost model.. Theoretical Computer Science (2005) Volume 1-2: pp. 36-53.

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. (October, 2009) Volume VI:.

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

P. Bonizzoni, G. Della Vedova, R. Dondi & J. 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. (2007) pp. 151-181.

In Proceedings

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. (in press, 2010) Volume 6293: pp. 148-161. [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).

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. (Sep, 2009) Volume 5724: pp. 1-12. [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. (May, 2009) Volume 5542: pp. 186-197. [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. (2009) pp. 116-127.

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. (2009) Volume 5957: pp. 210-226.

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).

L. Vanneschi, M. Tomassini, P. Collard, S. Verel, Y. Pirola & G. Mauri. A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds. In Proceedings of the 10th European Conference on Genetic Programming. Marc Ebner et al. (Ed.). Springer. (2007) Volume 4445: pp. 241-250. [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. (2006) pp. 106-116.

P. Bonizzoni, G. Della Vedova, R. Dondi, G. Fertin & S. Vialette. Exemplar Longest Common Subsequence.. In Proceeding of the 6th International Conference of Computational Science . (2006) pp. 622-629.

L. Vanneschi, Y. Pirola & P. Collard. A quantitative study of neutrality in GP boolean landscapes. In GECCO '06: Proceedings of the 8th annual conference on Genetic and evolutionary computation. ACM Press. (2006) pp. 895-902. [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. (2006) Volume 4361: pp. 298-313.

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]