2008

• E. Capobianco, “Model validation for gene selection and regulation maps.,” Funct Integr Genomics, vol. 8, no. 2, pp. 87–99, 2008.
• B. Liu, A. de la Fuente, and I. Hoeschele, “Gene network inference via structural equation modeling in genetical genomics experiments.,” Genetics, vol. 178, pp. 1763-1776, 2008.
• E. Pieroni, S. de la Fuente van Bentem, G. Mancosu, E. Capobianco, H. Hirt, and A. de la Fuente, “Protein networking: insights into global functional organization of proteomes.,” Proteomics, vol. 8, no. 4, pp. 799–816, 2008.
• A. de la Fuente, G. Fotia, F. Maggio, G. Mancosu, and E. Pieroni, “Insights into biological information processing: Structural and dynamical analysis of a human protein signalling network,” Journal of Physics A: Mathematical and Theoretical, vol. 41, no. 224013, 2008.
  

2007

• A. Pandolfi, G. Fotia, and F. Manganiello, “Finite element simulations of laser refractive surgery.,” Engineering with Computers, 2008. in press - accepted in 2007.
• M. Fusco, L. Corona, T. Onni, E. Marras, C. Longheu, G. Idini, and S. Tola, “Development of a sensitive and specific enzyme-linked immunosorbent assay based on recombinant antigens for rapid detection of antibodies against mycoplasma agalactiae in sheep.,” Clin Vaccine Immunol, vol. 14, no. 4, pp. 420–425, 2007.
• E. Pavoni, D. Cacchiarelli, R. Tittarelli, M. Orsini, A. Galtieri, B. Giardina, and A. Brancaccio, “Duplication of the dystroglycan gene in most branches of teleost fish.,” BMC Mol Biol, vol. 8, p. 34, 2007.
• T. Castrignano, P. D. De Meo, D. Carrabino, M. Orsini, M. Floris, and A. Tramontano, “The meps server for identifying protein conformational epitopes.,” BMC Bioinformatics, vol. 8 Suppl 1, p. S6, 2007.
• M. L. Tress, P. L. Martelli, A. Frankish, G. A. Reeves, J. J. Wesselink, C. Yeats, P. L. Olason, M. Albrecht, H. Hegyi, A. Giorgetti, D. Raimondo, J. Lagarde, R. A. Laskowski, G. Lopez, M. I. Sadowski, J. D. Watson, P. Fariselli, I. Rossi, A. Nagy, W. Kai, Z. Storling, M. Orsini, Y. Assenov, H. Blankenburg, C. Huthmacher, F. Ramirez, A. Schlicker, F. Denoeud, P. Jones, S. Kerrien, S. Orchard, S. E. Antonarakis, A. Reymond, E. Birney, S. Brunak, R. Casadio, R. Guigo, J. Harrow, H. Hermjakob, D. T. Jones, T. Lengauer, C. A. Orengo, L. Patthy, J. M. Thornton, A. Tramontano, and A. Valencia, “The implications of alternative splicing in the encode protein complement.,” Proc Natl Acad Sci U S A, vol. 104, no. 13, pp. 5495–5500, 2007.
• D. Carrabino, P. D’Onorio De Meo, N. Sanna, T. Castrignano, M. Orsini, M. Floris, and A. Tramontano, “The mepsmap server. mapping epitopes on protein surface: mining annotated proteins.,” IEEE Trans Nanobioscience, vol. 6, no. 2, pp. 155–161, 2007.
• D. F. Veiga, F. F. da Rocha Vicente, M. Grivet, A. de la Fuente, and A. T. Vasconcelos, “Genome-wide partial correlation analysis of escherichia coli microarray data,” Genet Mol Res, vol. 6, no. 4, pp. 730–742, 2007.
  
  

2006

• S. Boccia, P. Laurenti, P. Borella, U. Moscato, G. Capalbo, A. Cambieri, R. Amore, G. Quaranta, F. Boninti, M. Orsini, G. Branca, G. Fadda, V. Romano-Spica, and G. Ricciardi, “Prospective 3-year surveillance for nosocomial and environmental legionella pneumophila: implications for infection control.,” Infect Control Hosp Epidemiol, vol. 27, no. 5, pp. 459–465, 2006.
• S. Rolla, C. Nicolo, S. Malinarich, M. Orsini, G. Forni, F. Cavallo, and F. Ria, “Distinct and non-overlapping t cell receptor repertoires expanded by dna vaccination in wild-type and her-2 transgenic balb/c mice.,” J Immunol, vol. 177, no. 11, pp. 7626–7633, 2006.
  
  

Conferences

2008

• M. Fanton, M. Floris, G. Frau, J. Masciocchi, M. Sturlese, P. Palla, F. Cedrati, P. Rodriguez-Tomé, and S. Moro, “Mmsinc: a new web-based large-scale chemoinformatics platform.,” in BIOTECHNO 2008 Proceedings, IEEE Computer Society Press, 2008.
• F. Reinier, M. Orsini, and E. Capobianco, “Mirware: a toolkit for mining micrornas targets coordination,” in Non-Coding RNAs: Computational Chal lenges and Applications. Antalya, Turkey, 28-30 April 2008.
  
• E. Marras and E. Capobianco, “Multiscale look in protein interactomics,” in Organization of Biological Networks, IMA Annual Program Year Workshop, Institute for Mathematics and its Applications (IMA), University of Minnesota, March 2008.
• E. Marras and E. Capobianco, “Multiscale tour in protein interactomics,” in Organization of Biological Networks, IMA Annual Program Year Workshop, Institute for Mathematics and its Applications (IMA), University of Minnesota, March 2008.

2007

• E. Marras and E. Capobianco, “Interactome inference by reducing dimensionality,” in 4th Integrative Bioinformatics Workshop, Un. of Gent (Belgium), 10-12 September 2007, September 2007.
• A. de la Fuente, “Exploring a web of genes: Structure and dynamics of a yeast gene network,” in STATPHYS23 – COMPLEX NETWORKS, from Biology to Information Technology – Pula (Italy), July 2-6, 2007, july 2007.
• E. Pieroni, G. Mancosu, and A. de la Fuente, “Growing a yeast gene network.,” in STATPHYS23 – COMPLEX NETWORKS, from Biology to Information Technology – Pula (Italy), July 2-6, 2007, july 2007.
• F. Maggio, E. Pieroni, G. Fotia, G. Mancosu, and A. de la Fuente, “Dynamics on ‘signed motifs’ in a yeast gene network,” in STATPHYS23 – COMPLEX NETWORKS, from Biology to Information Technology – Pula (Italy), July 2-6, 2007, july 2007.
• G. Mancosu, G. Fotia, E. Pieroni, F. Maggio, and A. de la Fuente, “A web of genes: Inference and structural analysis of a yeast gene network,” in TATPHYS23 – COMPLEX NETWORKS, from Biology to Information Technology – Pula (Italy), July 2-6, 2007, july 2007.
• E. Marras and E. Capobianco, “Interactome inference by reducing dimensionality.,” in Von Neumann Symposium on Sparse representation and high dimensional geometry, Snowbird, Utah, 8-12 July 2007, july 2007.
• M. Valentini, A. Giorgetti, D. Raimondo, and A. Tramontano, “Flexible protein-protein docking: Mtgase/g-csf,” in 3DSIG07 - Vienna, 18-20 July 2007, july 2007.
• M. Orsini, M. Floris, A. Tramontano, and T. A. Thanaraj, “Splivap: A data resource on splice-mediated changes in isoform protein sequences,” in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna (Austria), July 21-25, 2007, july 2007.
• M. Valentini, A. Giorgetti, D. Raimondo, and A. Tramontano, “Flexible protein-protein docking: Mtgase/g-csf,” in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna (Austria), July 21-25, 2007, july 2007.
• F. Maggio, G. Fotia, G. Mancosu, E. Pieroni, and A. de la Fuente, “Dynamics on ‘signed motifs’ in a yeast gene network,” in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna (Austria), July 21-25, 2007, july 2007.
• G. Mancosu, G. Fotia, E. Pieroni, F. Maggio, and A. de la Fuente, “Inference and structural analysis of a yeast gene network,” in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna (Austria), July 21-25, 2007, july 2007.
• G. Brunetti, S. Contrino, M. Floris, G. Frau, J. Masciocchi, and P. Rodriguez-Tomé, “Andhìra, a database for bioactive molecules of the sardinian endemic flora (ii),” in Future Trends in Phytochemistry - A Young Scientists Symposium - Gargnano, Italia, no. P30, June 2007.
• G. Mocci, M. C. Lancioni, M. Ballero, C. Sanna, and C. Foddis, “Andhìra, a database for bioactive molecules of the sardinian endemic flora (i),” in Future Trends in Phytochemistry - A Young Scientists Symposium - Gargnano, Italia, no. P28, June 2007.
• H. Rabeson, H. Ratiney, E. Capobianco, R. de Beer, D. D. van Ormondt, and D. Graveron Demilly, “Is spending extra scan time on measuring a macromolecule-only signal worthwhile? ,” in Joint Annual Meeting ISMRM-ESMRMB, Berlin, 19-25 May 2007, May 2007.
• O. Marullo, A. Soggiu, P. Roncada, P. Rodriguez-Tomé, and E. Capobianco, “2d gel electrophoresis image analysis,” in 42 International Symposium Analytical Technologies: Tools and Implementation Strategies in Animal Science - Porto Conte Ricerche, Alghero, 29 May, 2007, May 2007.
• M. Persico, R. Hoffmann, E. Marras, and E. Capobianco, “Evolutive constraints for "wiring" and characterizing human subproteomes,” in Italian Bioinformatics Society (BITS) Annual Meeting, Napoli, 26-28 April, 2007, no. ID: 221, April 2007.
• E. Capobianco, “Sieving genomic features by signal separation,” in SAMSI Biosystems Modeling Workshop, Statistical and Applied Mathematical Sciences Institute, Raleigh-Durham, NC, USA, 5-7 March 2007, march 2007.

2006

• M. Valentini, D. W. M. Hofmann, B. D’Aguanno, L. Pisani, and E. Pieroni, “Molecular dynamics study of composite nafion membranes,” in Fuel Cells Science & Technology Conference, Torino, 13-14 September, 2006, September 2006.
• E. Capobianco, “Statistical embedding in complex biosystems,” in Integrative Bioinformatics, International Workshop, Rothamsted Research, Harpenden, UK, 4-6 September, 2006, September 2006.
• E. Capobianco, “Entropic embedding and fluctuation analysis in biological manifolds,” in XVIII Congresso Nazionale della SIBPA, Società Italiana di Biofisica Pura e Applicata, Palermo, 17-21 September, 2006, September 2006.
• M. Valentini, D. W. M. Hofmann, B. D’Aguanno, L. Pisani, and E. Pieroni, “Molecular dynamics analysis of hydrated nafion membranes,” in 6th International Symposium on New Materials for Electrochemical Systems, Montreal, 9-12 July, 2006, july 2006.
• L. Pisani, M. Valentini, B. D’Aguanno, D. W. M. Hofmann, and E. Pieroni, “A simple analytical model for the conductivity of polymeric sulfonated membranes,” in 6th International Symposium on New Materials for Electrochemical Systems, Montreal, 9-12 July, 2006, july 2006.
• D. W. M. Hofmann, M. Valentini, B. D’Aguanno, L. Pisani, and E. Pieroni, “Simulation of composite nafion fuel cell membranes,” in 6th International Symposium on New Materials for Electrochemical Systems, Montreal, 9-12 July, 2006, july 2006.
• P. Rodriguez-Tomé, F. Reinier, J. Masciocchi, S. Carcangiu, and G. Brunetti, “Setting up a bioinformatics service center in a distributed environment,” in NETTAB’06 workshop, Pula, 10-13 July 2006, july 2006.
• S. Carcangiu and P. Rodriguez-Tomé, “Web services for bioinformatics applications in the python/zope platform,” in NETTAB’06 workshop, Pula, 10-13 july 2006, july 2006.
• T. Castrignanò, P. D’Onorio De Meo, D. Carrabino, M. Orsini, M. Floris, and A. Tramontano, “The meps server for identifying protein conformational epitopes,” in NETTAB’06 workshop, Pula, 10-13 July 2006, july 2006.
• H. Ratiney, M. Sdika, H. Rabeson, C. Cudalbu, S. Cavassila, E. Capobianco, R. de Beer, D. van Ormondt, and D. Graveron-Demilly, “Signal disentanglement in in vivo mr spectroscopy: by semi-parametric processing or by measurement? ,” in Data Processing for MR Spectroscopy and Imaging, International Society for Magnetic Resonance in Medicine. Warrenton, Virginia (USA), 11-13 November, 2006, 2006.
• E. Capobianco, “Learning latent dynamics in biological manifolds,” in Integrative Post-Genomics, Lyon’s international multidisciplinary meeting, Lyon (FR), 29, 30 November and 1 December, 2006, 2006.