| 2009 | WABI | On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices. | Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio |
| 2008 | ISMB | Predicting protein thermostability changes from sequence upon multiple mutations. | Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio |
| 2007 | ISPA | High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment. | Maria Mirto, Ivan Rossi, Italo Epicoco, Sandro Fiore, Piero Fariselli, Rita Casadio, Giovanni Aloisio |
| 2007 | PPAM | High Throughput Comparison of Prokaryotic Genomes. | Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio |
| 2007 | WABI | Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps. | Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio |
| 2006 | ISMB | BaCelLo: a balanced subcellular localization predictor. | Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio |
| 2005 | ECCB | Predicting protein stability changes from sequences using support vector machines. | Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio |
| 2004 | ISMB | A neural-network-based method for predicting protein stability changes upon single point mutations. | Emidio Capriotti, Piero Fariselli, Rita Casadio |
| 2003 | ISMB | An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. | Pier Luigi Martelli, Piero Fariselli, Rita Casadio |
| 2002 | ISMB | A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. | Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio |
| 2001 | ISMB | Improved prediction of the number of residue contacts in proteins by recurrent neural networks. | Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio |
| 2000 | ISMB | Prediction of the Number of Residue Contacts in Proteins. | Piero Fariselli, Rita Casadio |
| 1999 | ISMB | A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion. | Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli |
| 1997 | ISMB | Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins. | P. Arrigo, Piero Fariselli, Rita Casadio |
| 1996 | ISMB | Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming. | Burkhard Rost, Rita Casadio, Piero Fariselli |
| 1995 | ISMB | Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks. | Rita Casadio, Mario Compiani, Piero Fariselli, Francesco Vivarelli |