Giulio Pavesi

Federico Zambelli, Graziano Pesole, Giulio Pavesi: Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. Briefings in Bioinformatics 14(2): 225-237 (2013)

Matteo Giulietti, Francesco Piva, Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Tiziana Castrignanò, Anna Maria D'Erchia, Ernesto Picardi, Federico Zambelli, Giovanni Principato, Giulio Pavesi, Graziano Pesole: SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Research 41(Database-Issue): 125-131 (2013)

Paolo D'Onorio De Meo, Mattia D'Antonio, Francesca Griggio, Renato Lupi, Massimiliano Borsani, Giulio Pavesi, Tiziana Castrignanò, Graziano Pesole, Carmela Gissi: MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. Nucleic Acids Research 40(Database-Issue): 1168-1172 (2012)

Federico Zambelli, Gian Marco Prazzoli, Graziano Pesole, Giulio Pavesi: Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. Nucleic Acids Research 40(Web-Server-Issue): 510-515 (2012)

Pier Luigi Martelli, Mattia D'Antonio, Paola Bonizzoni, Tiziana Castrignanò, Anna Maria D'Erchia, Paolo D'Onorio De Meo, Piero Fariselli, Michele Finelli, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole: ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Research 39(Database-Issue): 80-85 (2011)

David Stephen Horner, Giulio Pavesi, Tiziana Castrignanò, Paolo D'Onorio De Meo, Sabino Liuni, Michael Sammeth, Ernesto Picardi, Graziano Pesole: Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings in Bioinformatics 11(2): 181-197 (2010)

Giorgio Grillo, Antonio Turi, Flavio Licciulli, Flavio Mignone, Sabino Liuni, Sandro Banfi, Vincenzo Alessandro Gennarino, David Stephen Horner, Giulio Pavesi, Ernesto Picardi, Graziano Pesole: UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Research 38(Database-Issue): 75-80 (2010)

Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang: Beyond evolutionary trees. Natural Computing 9(2): 421-435 (2010)

Matteo Ré, Giulio Pavesi: Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns. Artificial Intelligence in Medicine 45(2-3): 117-123 (2009)

Giulio Pavesi, Giorgio Valentini: Classification of co-expressed genes from DNA regulatory regions. Information Fusion 10(3): 233-241 (2009)

Federico Zambelli, Graziano Pesole, Giulio Pavesi: Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Research 37(Web-Server-Issue): 247-252 (2009)

Tiziana Castrignanò, Mattia D'Antonio, Anna Anselmo, Danilo Carrabino, A. D'Onorio De Meo, Anna Maria D'Erchia, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, A. Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole: ASPicDB: A database resource for alternative splicing analysis. Bioinformatics 24(10): 1300-1304 (2008)

Giulio Pavesi, Federico Zambelli, Graziano Pesole: WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 8 (2007)

Matteo Ré, Giulio Pavesi: Signal Processing in Comparative Genomics. WILF 2007: 544-550

Giulio Pavesi, Federico Zambelli: Prediction of over Represented Transcription Factor Binding Sites in Co-regulated Genes Using Whole Genome Matching Statistics. WILF 2007: 651-658

Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano Pesole: MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Research 34(Web-Server-Issue): 566-570 (2006)

Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi: On-line construction of compact directed acyclic word graphs. Discrete Applied Mathematics 146(2): 156-179 (2005)

Giancarlo Mauri, Giulio Pavesi: Algorithms for pattern matching and discovery in RNA secondary structure. Theor. Comput. Sci. 335(1): 29-51 (2005)

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole: In silico representation and discovery of transcription factor binding sites. Briefings in Bioinformatics 5(3): 217-236 (2004)

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole: An Algorithm for Finding Conserved Secondary Structure Motifs in Unaligned RNA Sequences. J. Comput. Sci. Technol. 19(1): 2-12 (2004)

Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole: Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research 32(Web-Server-Issue): 199-203 (2004)

Stefania Bandini, Sara Manzoni, Ahmad Naimzada, Giulio Pavesi: A CA Approach to Study Complex Dynamics in Asset Markets. ACRI 2004: 591-600

Giancarlo Mauri, Roberto Mosca, Giulio Pavesi: A GA Approach to the Definition of Regulatory Signals in Genomic Sequences. GECCO (1) 2004: 380-391

Stefania Bandini, Giancarlo Mauri, Giulio Pavesi, Carla Simone: Computing with a Distributed Reaction-Diffusion Model. MCU 2004: 93-103

Giancarlo Mauri, Giulio Pavesi: Pattern Discovery in RNA Secondary Structure Using Affix Trees. CPM 2003: 278-294

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole: Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences. ICTAI 2003: 10-17

Giancarlo Mauri, Giulio Pavesi: A parallel algorithm for pattern discovery in biological sequences. Future Generation Comp. Syst. 18(6): 849-854 (2002)

Stefania Bandini, Giulio Pavesi: Controlled generation of two-dimensional patterns based on Stochastic Cellular Automata. Future Generation Comp. Syst. 18(7): 973-981 (2002)

Stefania Bandini, Giulio Pavesi: Simulation of Vegetable Populations Dynamics Based on Cellular Automata. ACRI 2002: 202-209

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole: Methods for Pattern Discovery in Unaligned Biological Sequences. Briefings in Bioinformatics 2(4): 417 (2001)

Stefania Bandini, Giancarlo Mauri, Giulio Pavesi, Carla Simone: Parallel simulation of reaction-diffusion phenomena in percolation processes : A model based on cellular automata. Future Generation Comp. Syst. 17(6): 679-688 (2001)

Stefania Bandini, Sara Manzoni, Giulio Pavesi, Carla Simone: L*MASS: A Language for Situated Multi-agent Systems. AI*IA 2001: 249-254

Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi: On-Line Construction of Compact Directed Acyclic Word Graphs. CPM 2001: 169-180

Giulio Pavesi, Giancarlo Mauri, Graziano Pesole: An algorithm for finding signals of unknown length in DNA sequences. ISMB (Supplement of Bioinformatics) 2001: 207-214

Stefania Bandini, Giancarlo Mauri, Giulio Pavesi: Parallel Generation of Percolation Beds Based on Stochastic Cellular Automata. PaCT 2001: 391-400

Giancarlo Mauri, Giulio Pavesi: Parallel Algorithms for the Analysis of Biological Sequences. PaCT 2001: 456-468

Giancarlo Mauri, Giulio Pavesi: Approximation Algorithms for String Folding Problems. IFIP TCS 2000: 45-58

Stefania Bandini, Giancarlo Mauri, Giulio Pavesi, Carla Simone: A Parallel Model Based on Cellular Automata for the Simulation of Pesticide Percolation in the Soil. PaCT 1999: 383-394

Giancarlo Mauri, Giulio Pavesi, Antonio Piccolboni: Approximation Algorithms for Protein Folding Prediction. SODA 1999: 945-946