| 2013 | IJCNN | A neural network based algorithm for gene expression prediction from chromatin structure. | Marco Frasca, Giulio Pavesi |
| 2004 | GECCO | A GA Approach to the Definition of Regulatory Signals in Genomic Sequences. | Giancarlo Mauri, Roberto Mosca, Giulio Pavesi |
| 2004 | MCU | Computing with a Distributed Reaction-Diffusion Model. | Stefania Bandini, Giancarlo Mauri, Giulio Pavesi, Carla Simone |
| 2003 | CPM | Pattern Discovery in RNA Secondary Structure Using Affix Trees. | Giancarlo Mauri, Giulio Pavesi |
| 2003 | ICTAI | Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences. | Giulio Pavesi, Giancarlo Mauri, Graziano Pesole |
| 2001 | CPM | On-Line Construction of Compact Directed Acyclic Word Graphs. | Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi |
| 2001 | ISMB | An algorithm for finding signals of unknown length in DNA sequences. | Giulio Pavesi, Giancarlo Mauri, Graziano Pesole |
| 2001 | PACT | Parallel Generation of Percolation Beds Based on Stochastic Cellular Automata. | Stefania Bandini, Giancarlo Mauri, Giulio Pavesi |
| 2001 | PACT | Parallel Algorithms for the Analysis of Biological Sequences. | Giancarlo Mauri, Giulio Pavesi |
| 1999 | PACT | A Parallel Model Based on Cellular Automata for the Simulation of Pesticide Percolation in the Soil. | Stefania Bandini, Giancarlo Mauri, Giulio Pavesi, Carla Simone |
| 1999 | SODA | Approximation Algorithms for Protein Folding Prediction. | Giancarlo Mauri, Giulio Pavesi, Antonio Piccolboni |