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

Approximation Algorithms for Protein Folding Prediction. - Giancarlo Mauri; Giulio Pavesi; Antonio Piccolboni (SODA, 1999)

Approximation Algorithms for String Folding Problems. - Giancarlo Mauri; Giulio Pavesi (IFIP TCS, 2000)

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

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

Parallel Generation of Percolation Beds Based on Stochastic Cellular Automata. - Stefania Bandini; Giancarlo Mauri; Giulio Pavesi (PaCT, 2001)

Parallel Algorithms for the Analysis of Biological Sequences. - Giancarlo Mauri; Giulio Pavesi (PaCT, 2001)

Methods for Pattern Discovery in Unaligned Biological Sequences. - Giulio Pavesi; Giancarlo Mauri; Graziano Pesole (Briefings Bioinform., 2001)

Parallel simulation of reaction-diffusion phenomena in percolation processes : A model based on cellular automata. - Stefania Bandini; Giancarlo Mauri; Giulio Pavesi; Carla Simone (Future Gener. Comput. Syst., 2001)

Simulation of Vegetable Populations Dynamics Based on Cellular Automata. - Stefania Bandini; Giulio Pavesi (ACRI, 2002)

Controlled generation of two-dimensional patterns based on Stochastic Cellular Automata. - Stefania Bandini; Giulio Pavesi (Future Gener. Comput. Syst., 2002)

A parallel algorithm for pattern discovery in biological sequences. - Giancarlo Mauri; Giulio Pavesi (Future Gener. Comput. Syst., 2002)

Pattern Discovery in RNA Secondary Structure Using Affix Trees. - Giancarlo Mauri; Giulio Pavesi (CPM, 2003)

Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences. - Giulio Pavesi; Giancarlo Mauri; Graziano Pesole (ICTAI, 2003)

String algorithms in computational biology. - Giulio Pavesi (2003)

A CA Approach to Study Complex Dynamics in Asset Markets. - Stefania Bandini; Sara Manzoni; Ahmad Naimzada; Giulio Pavesi (ACRI, 2004)

A GA Approach to the Definition of Regulatory Signals in Genomic Sequences. - Giancarlo Mauri; Roberto Mosca 002; Giulio Pavesi (GECCO (1), 2004)

Computing with a Distributed Reaction-Diffusion Model. - Stefania Bandini; Giancarlo Mauri; Giulio Pavesi; Carla Simone (MCU, 2004)

In silico representation and discovery of transcription factor binding sites. - Giulio Pavesi; Giancarlo Mauri; Graziano Pesole (Briefings Bioinform., 2004)

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

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

On-line construction of compact directed acyclic word graphs. - Shunsuke Inenaga; Hiromasa Hoshino; Ayumi Shinohara; Masayuki Takeda; Setsuo Arikawa; Giancarlo Mauri; Giulio Pavesi (Discret. Appl. Math., 2005)

Algorithms for pattern matching and discovery in RNA secondary structure. - Giancarlo Mauri; Giulio Pavesi (Theor. Comput. Sci., 2005)

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. - Giulio Pavesi; Paolo Mereghetti; Federico Zambelli; Marco Stefani; Giancarlo Mauri; Graziano Pesole (Nucleic Acids Res., 2006)

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

Signal Processing in Comparative Genomics. - Matteo Ré; Giulio Pavesi (WILF, 2007)

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

ASPicDB: A database resource for alternative splicing analysis. - 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; Alberto Riva; et al. (Bioinform., 2008)

Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns. - Matteo Ré; Giulio Pavesi (Artif. Intell. Medicine, 2009)

Classification of co-expressed genes from DNA regulatory regions. - Giulio Pavesi; Giorgio Valentini (Inf. Fusion, 2009)

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2009)

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

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

Beyond evolutionary trees. - Gianluca Della Vedova; Riccardo Dondi; Tao Jiang 001; Giulio Pavesi; Yuri Pirola; Lusheng Wang 001 (Nat. Comput., 2010)

A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data. - Federico Zambelli; Giulio Pavesi (CIBB, 2011)

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. - 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; et al. (Nucleic Acids Res., 2011)

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

Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. - Federico Zambelli; Gian Marco Prazzoli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2012)

A neural network based algorithm for gene expression prediction from chromatin structure. - Marco Frasca 001; Giulio Pavesi (IJCNN, 2013)

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Briefings Bioinform., 2013)

SpliceAid-F: a database of human splicing factors and their RNA-binding sites. - 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 (Nucleic Acids Res., 2013)

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. - Federico Zambelli; Graziano Pesole; Giulio Pavesi (Nucleic Acids Res., 2013)

On the NF-Y regulome as in ENCODE (2019). - Mirko Ronzio; Andrea Bernardini; Giulio Pavesi; Roberto Mantovani; Diletta Dolfini (PLoS Comput. Biol., 2020)

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. - Matteo Chiara; Anna Maria D'Erchia; Carmela Gissi; Caterina Manzari; Antonio Parisi; Nicoletta Resta; Federico Zambelli; Ernesto Picardi; Giulio Pavesi; David Stephen Horner; Graziano Pesole (Briefings Bioinform., 2021)

UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. - Claudio Lo Giudice; Federico Zambelli; Matteo Chiara; Giulio Pavesi; Marco Antonio Tangaro; Ernesto Picardi; Graziano Pesole (Nucleic Acids Res., 2023)