Publications

Journal Papers

2012 - Badaloni S, Di Camillo B, Sambo F. Qualitative Reasoning for Biological Network Inference from Systematic Perturbation Experiments. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Accepted.

2012 - Sambo F, Montes de Oca M A, Di Camillo B, Toffolo G and Stützle T. MORE: Mixed Optimization for Reverse Engineering. An application to modeling biological networks response via sparse systems of nonlinear differential equations. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Accepted. doi.

2012 - Di Camillo B, Sanavia T, Martini M, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C. Effect of size and heterogeneity of samples on biomarker discovery: synthetic and real data assessment. PLoS ONE 7(3): e32200. doi.

Conference Proceedings Full Papers

2012 - Badaloni S, Sambo F, Venco F. On Hybridizing Complete Bayesian Network Structure Search With Independence Tests. In: Mancini, T. and Oddi, A. (eds.) Proc. of the 19th RCRA International Workshop on Experimental Evaluation of Algorithms for solving problems with combinatorial explosion. CEUR-WS.org, in press.

2012 - Sambo F, Di Camillo B. Minimizing Time when Applying Bootstrap to Contingency Tables Analysis of Genome-Wide Data. In: Hamadi, Y., Schoenauer, M. (eds.) Learning and Intelligent Optimization. Lecture Notes in Computer Science. Springer Berlin / Heidelberg, in press.
A preliminary version is available as pdf file.

2011 - Badaloni S, Falda M, Massignan P, Sambo F. Redefinition of Mutual Information in the Fuzzy Sets framework for Computational Genomics. In: Madani, K., Dourado, A., Rosa, A. and Filipe, J. (eds.) Computational Intelligence. Studies in Computational Intelligence, vol. 343, pp. 73-83. Springer Berlin / Heidelberg.

2011 - Sambo F, Di Camillo B. Qualitative Reasoning on systematic gene perturbation experiments. In: Rizzo, R., Lisboa, P. J. G. (eds.) Computational Intelligence Methods for Bioinformatics and Biostatistics. Lecture Notes in Bioinformatics, vol. 6685, pp. 135-146. Springer Berlin / Heidelberg.
A preliminary version is available as pdf file.

2010 - Sambo F, Montes de Oca M A, Di Camillo B and Stützle T. On the difficulty of inferring gene regulatory networks: A study of the fitness landscape generated by relative squared error. In: Collet, P., Monmarché, N., Legrand, P., Schoenauer, M., Lutton, E. (eds.) Artificial Evolution, Lecture Notes in Computer Science, vol. 5975, pp. 74-85. Springer Berlin / Heidelberg
A preliminary version is available as a technical report.

2008 - Badaloni S, Falda M, Sambo F.,Zanini L. Addressing temporally constrained Delivery Problems with the Swarm Intelligence approach. In: W. Burgard, R. Dillmann, C. Plagemann, and N. Vahrenkamp (eds.) Intelligent Autonomous Systems 10. Baden-Baden, Germany: IOS Press, 2008, pp. 264-271.
A preliminary version is available as pdf file.

Book Chapters

2011 - Di Camillo B, Castiglioni I, Sambo F, Gilardi M C, Toffolo G M. Methods for discovery and integration of genetic and neuroimaging biomarkers. In: Fato M M, Gilardi M C, Schenone A. Neuroinformatica. vol. 30, BOLOGNA: Patron

Conference Proceedings Short Papers and Abstracts

2011 - Sambo F, Trifoglio E, Di Camillo B, Toffolo G, Cobelli C. Bag of Naïve Bayes: biomarker selection and classification from Genome-Wide SNP data. In: Clinical Bioinformatics. 11th Workshop on Network Tools and Applications in Biology NETTAB2011. Pavia, Italy. Oct 12-14, 2011.
A preliminary version is available as pdf file.

2011 - Sambo F, Di Camillo B, Toffolo G, Vella A, Cobelli C. Potential Role of GLP1R in the Pathogenesis of Type 2 Diabetes Identified Using Bayesian Networks. In: Special Issue: Abstracts of the 4th International Congress on Prediabetes and the Metabolic Syndrome, 6-9 April 2011, Madrid, Spain. Journal of Diabetes, 3 (s1), pp. 42-281

2011 - Sambo F, Di Camillo B, Toffolo G, Vella A, Cobelli C. Type 2 Diabetes: Bayesian Network Modelling of Genetic and Phenotypic Traits. In: Proceedings of the 4th International Conference on Advanced Technologies and Treatments for Diabetes. London, UK, February 16-19, 2011. Diabetes Technology and Therapeutics, 13 (2), pp. 173-293

2010 - Sanavia T, Sambo F, Grassi A, Di Camillo B, Toffolo G. Gene Network inference by significance analysis on genotype/phenotype data. In: Proceedings of the 2010 Joint Conference on Systems Biology, Regulatory Genomics, and Reverse Engineering Challenges. New York City, Nov 16 - 20. Honourable Mention for Best Performer (fourth place) in the DREAM5 challenge: Systems Genetics Challenge.

2010 - Di Camillo B, Martini M, Sanavia T, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C. Effect of size and heterogeneity of samples on biomarker discovery: synthetic and real data assessment. In: Proceedings of the 9th European Conference on Computational Biology ECCB10. Ghent, Belgium. Sep 26-29 2010.

2009 - Sambo F, Di Camillo B, Falda M, Toffolo G, Badaloni S. CNET: an algorithm for the inference of gene regulatory interactions from gene expression time series. In: Proceedings of the 14th Workshop on Intelligent Data Analysis in medicine and Pharmacology IDAMAP09, pp. 23-28.
IDAMAP09 Lecture Notes are available here.

2009 - Badaloni S, Falda M, Massignan P, Sambo F. Fuzzy Mutual Information for Reverse Engineering of Gene Regulatory Networks. In: Proceedings of the International Conference on Fuzzy Computation ICFC09. Madeira, Portugal, Oct. 5-7 2009. pp. 25-30.

2008 - Sambo F., Di Camillo B, Toffolo G. CNET: an algorithm for Reverse Engineering of Causal Gene Networks. In: Bioinformatics Methods for Biomedical Complex Systems Applications. 8th Workshop on Network Tools and Applications in Biology NETTAB2008. Varenna, Italy. May 19-21 2008, pp. 134-136.
A preliminary version is available as pdf file.

2008 - Sambo F, Di Camillo B, Falda M,Toffolo G, Badaloni S. Evaluation of local reliability of gene networks inferred from time series expression data. In: RECOMB Satellite on Regulatory Genomics and Systems Biology. Boston, MA. Oct 29 - Nov 2 2008. Abstract Book, p. 121.
The complete abstract book is available here.

2008 - Sambo F., Di Camillo B, ToffoloG. Role of network structure and experimental design on the performance of two Reverse Engineering methods. In: Proceedings of the 7th European Conference on Computational Biology ECCB2008. Cagliari, Italy. September 2008.
A preliminary version is available as pdf file.

2008 - Badaloni S, Falda M, Sambo F. Scale-free structure and topological properties in Reverse Engineering of Gene Regulatory Networks. In: Workshop Italiano di Vita Artificiale e Computazione Evolutiva WIVACE2008. Venezia, Italy. September 2008.
A preliminary version is available as pdf file.

Doctoral symposia and consortia

2009 - Sambo F. Stochastic Local Search Strategies for Reverse Engineering of Gene Regulatory Networks. In: LS-DS 2009: Doctoral Symposium on Engineering Stochastic Local Search Algorithms. Technical Report TR/IRIDIA/2009-024, IRIDIA, Université Libre de Bruxelles, Brussels, Belgium, August 2009. (pp. 61-65).
The complete Symposium Working Notes are available as a technical report.

2007 - Sambo F. Advanced algorithms for genomic data analysis. In: 11th Conference on Artificial Intelligence in Medicine AIME 2007 - Doctoral Consortium Working Notes. Amsterdam, The Netherlands, July 7-11, 2007.