GIULIO PAVESI - PUBLICATIONS My Pubmed list My DBLP list (check these first - both likely to be more up-to-date than the following lists) JOURNAL PAPERS: BIOINFORMATICS G. Pavesi, G. Mauri, G. Pesole. An algorithm for finding signals of unknown length in DNA sequences, Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Bioinformatics, 17: S207-S214, 2001. G. Pavesi, G. Mauri, G. Pesole. Methods for pattern discovery in unaligned biological sequences, Briefings in Bioinformatics, 2(4):417-430, 2001. G.Pavesi G.Mauri C.Gissi F.Iannelli G.Pesole. GeneSyn: a tool for detecting conserved gene order across genomes. Bioinformatics, 20(9):1472-1474, 2004. G.Pavesi, G.Mauri, M.Stefani, G.Pesole. RNAprofile: An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Research, 32(10):3258-3269, 2004. G.Pavesi, P.Mereghetti, G.Mauri, G.Pesole. Weeder Web: discovery of transcription factor binding sites in DNA sequences from related genes. Nucleic Acids Research 32(Web Server Issue):W199-W203, 2004 G.Pavesi, G.Mauri, G.Pesole. In silico representation and discovery of transcription factor binding sites. Briefings in Bioinformatics, 5(3):217-236, 2004. M. Tompa, N. Li, T. L. Bailey , G. M. Church , B. De Moor, E. Eskin, A. V. Favorov, M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Régnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1):137-144, 2005. The FANTOM Consortium (quorum ego). The transcriptional landscape of the mammalian genome. Science, 309(5740):1559-1563, 2005. G. Pavesi, P. Mereghetti, F. Zambelli, M. Stefani, G. Mauri, G. Pesole. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Research, 34(Web Server Issue), W566-570, 2006. G. Pavesi, Zambelli F, G.Pesole. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics, 8:46, 2007. M. Ceribelli, D. Dolfini, D. Merico, R. Gatta, A. Viganò, G. Pavesi, R. Mantovani. The histone like NF-Y is a bifunctional transcription factor. Mol Cell Biol. 28(6):2047-2058, 2008. T.Castrignanò, M.D'Antonio, A.Anselmo, D.Carrabino, DM.D'Onorio, A.D'Erchia, F.Licciulli, M.Mangiulli, F. Mignone, G.Pavesi, E.Picardi, A.Riva, R.Rizzi, P.Bonizzoni, G.Pesole. ASPicDB: A database resource for alternative splicing analysis. Bioinformatics, 24(10):1300-1304, 2008. G. Pavesi, F.Zambelli, C.Caggese, G.Pesole. Exalign: a new method for comparative analysis of exon-intron gene structures Nucleic Acids Research May; 36(8): e47, 2008. J.Intra, G.Pavesi, D.Horner. Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family. BMC Evolutionary Biology, 2008, 8:214 (22 July 2008). M.Ré, G. Pavesi. Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns. Artif Intell Med. 2009;45(2-3):117-23. F.Zambelli, G.Pesole, G.Pavesi. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res. 2009 37(Web Server issue):W247-52. DS. Horner, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings in Bioinformatics, 2009 Oct 27. [Epub ahead of print] G. Grillo Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010 Jan;38(Database issue):D75-80. Epub 2009 Oct 30. JOURNAL PAPERS: More BIO than INFORMATICS J. Intra, ME Perotti, G Pavesi, D Horner. Comparative and phylogenetic analysis of alpha-l-fucosidase genes. Gene 392:34-46, 2007. Epub 2006 Nov 11. Galbiati, L. Simoni, G. Pavesi, E. Cominelli, P. Francia, A. Vavasseur, M. Bevan, C. Tonelli. Gene trap lines identify Arabidopsis genes expressed in guard cells. Plant Journal 53(5):750-62, 2008. Epub 2007 Nov 23. M.Menges, G.Pavesi, P.Morandini, L. Bögre and J.A.H. Murray. Genomic organization and evolutionary conservation of plant D-type cyclins. Plant Physiol. 145(4):1558-76, 2007. G.Pavesi, A.Siccardi, G.Viale, C.Grazioli, T.Calciolari, M.L. Tenchini, P.Plevani. Humans, hedgehogs, and high school science. EMBO Reports, 9(3), 208-211, 2008. J.Intra, F.Cenni, G.Pavesi, M.E. Perotti. Interspecific analysis of the glycosidases of the sperm plasma membrane in Drosophila. Mol. Reprod. Devel. , 2008 May 16. [Epub ahead of print] DOI 10.1002/mrd.20932 M.E. Pasini, J.Intra, G. Pavesi Expression study of an alpha-l-fucosidase gene in the Drosophilidae family. Gene, 420(1):23-33, 2008. Epub 2008 May 15. S.Pozzi, Zambelli F, Merico D, Pavesi G, Robert A, Maltère P, Gidrol X, Mantovani R, Vigano MA. Transcriptional network of p63 in human keratinocytes. PLoS One. 2009;4(3):e5008. D.Dolfini Zambelli F, Pavesi G, Mantovani R. A perspective of promoter architecture from the CCAAT box. Cell Cycle. 2009 Dec 15;8(24):4127-37. JOURNAL PAPERS: Less BIO than INFORMATICS G. Mauri, G. Pavesi. A parallel algorithm for pattern discovery in biological sequences, Future generation Computer Systems, 18 (6): 849-854, 2002. G.Pavesi, G.Mauri, G.Pesole. An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. J.of Computer Science and Technology, 19(1): 2-12, 2004. G.Mauri, G.Pavesi. Algorithms for pattern matching and discovery in RNA secondary structure. Theoretical Computer Science, 335(1): 29-51, 2005. S. Inenaga, H. Hoshino, A. Shinohara, M. Takeda, S. Arikawa, G. Mauri, G. Pavesi. On-line construction of compact directed acyclic word graphs, Discrete and Applied Mathematics, 146(2): 156-179, 2005. G. Pavesi, G. Valentini. Classification of co-expressed genes from DNA regulatory regions. Information Fusion 10(3), pp. 233-241, 2009 JOURNAL PAPERS: OTHER STUFF S. Bandini, G. Mauri, G. Pavesi, C. Simone. Parallel simulation of reaction diffusion phenomena in percolation processes: a model based on cellular automata, Future Generation Computer Systems, 17 (6): 679-688, 2001. S. Bandini, G. Pavesi. Controlled generation of two -dimensional patterns based on stochastic cellular automata, Future Generation Computer Systems, 18 (7): 973-981, 2002. REFEREED CONFERENCE PROCEEDINGS 1. G. Mauri, G. Pavesi, A. Piccolboni. Approximation Algorithms for Protein Folding Prediction, in Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA '99), pp. 945-946, Baltimore, 1999. 2. S. Bandini, G. Mauri, G. Pavesi, C. Simone. A Parallel Model Based on Cellular Automata for the Simulation of Pesticide Percolation in the Soil, Proc. of the 5th Int’l Conference on Parallel Computing and Technologies (PACT 1999), Lecture Notes in Computer Science 1662, pp.383-394, 1999. 3. G. Mauri, G. Pavesi. Approximation Algorithms for String Folding Problems, in J. van Leeuwen et al. (Eds.) IFIP TCS 2000, Lecture Notes in Computer Science 1872, pp. 45-58. 4. S. Inenaga, H. Hoshino, A. Shinohara, M. Takeda, S. Arikawa, G. Mauri, G. Pavesi. On -Line Construction of Compact Directed Acyclic Word Graphs, Proceedings CPM 2001 Lecture Notes in Computer Science 2089, pp.169-179, 2001. 5. G. Mauri, G. Pavesi. Parallel Algorithms for the Analysis of Biological Sequences, Proceedings of the 6th International Conference on Parallel Computing and Technologies (PACT 2001), Lecture Notes in Computer Science 2127, pp. 456-466, 2001. 6. S. Bandini, G. Mauri, G. Pavesi. Parallel Generation of Percolation Beds Based on Stochastic Cellular Automata, Proceedings of the 6th International Conference on Parallel Computing and Technologies (PACT 2001), Lecture Notes in Computer Science 2127, pp. 391-397, 2001. 7. S. Bandini, S. Manzoni, G. Pavesi, C. Simone. L*MASS: a Language for Situated Multi -Agent Systems, VII Congresso dell'Associazione Italiana per l'Intelligenza Artificiale, Bari, Settembre 2001, Lecture Notes in Computer Science 2175, pp. 249-259, 2001. 8. S. Bandini, G. Pavesi, Simulation of Pesticide Percolation in the Soil Based on Cellular Automata, Proceedings of Integrated Assessment and Decision Support (IEMSS 2002), 2002. 9. S. Bandini, G. Pavesi. Simulation of Vegetable Populations Dynamics Based on Cellular Automata, Proceedings of ACRI 2002, Lecture Notes in Computer Science 2493, pp. 202-210, 2002. 10. G. Mauri, G. Pavesi. Pattern Discovery in RNA Secondary Structure Using Affix Trees, Proceedings of the 14th Symposium on Combinatorial Pattern Matching (CPM 2003), Lecture Notes in Computer Science 2676, pp. 278-294, 2003. 11. G. Pavesi, G. Mauri, G. Pesole. Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences, Proceedings of the 15th IEEE Int’l Conference on Tools with Artificial Intelligence (ICTAI 2003), pp. 10-18, 2003. 12. G. Mauri, R. Mosca, G. Pavesi: A GA Approach to the Definition of Regulatory Signals in Genomic Sequences. Proceedings of Genetic and Evolutionary Computation Conference (GECCO) 2004. Lecture Notes in Computer Science 3102, pp. 380-391, 2004. 13. S. Bandini, G. Pavesi. A Model Based on Cellular Automata for the Simulation of the Dynamics of Plant Populations. Proceedings of Integrated Assessment and Decision Support (IEMSS 2004), 2004. 14. S.Bandini, S.Manzoni, A.Namizada, G.Pavesi. A CA Approach to Study Complex Dynamics In Asset Markets. Proceedings of ACRI 2004, Lecture Notes in Computer Science 3305, pp. 591-600, 2004. 15. S.Bandini, G.Mauri, G.Pavesi, C.Simone. Computing with a Distributed Reaction-Diffusion Model. Proceedings of Machines, Computations, and Universality, 4th International Conference, MCU 2004, Lecture Notes in Computer Science 3354, pp 93-103. 16. M. Re, G. Pavesi. Signal Processing in Comparative Genomics. Proceedings of Applications of Fuzzy Sets Theory, 7th International Workshop on Fuzzy Logic and Applications (WILF 2007), Lecture Notes in Computer Science 4578, pp. 544-550, 2007. 17. G.Pavesi, F.Zambelli. Prediction of Over Represented Transcription Factor Binding Sites in Co-Regulated Genes Using Whole Genome Matching Statistics. . Proceedings of Applications of Fuzzy Sets Theory, 7th International Workshop on Fuzzy Logic and Applications (WILF 2007), Lecture Notes in Computer Science 4578, pp. 651-658, 2007. 18. F. Zambelli, M.Rè, G. Pavesi The Beacon Tools for the Analysis of Gene Expression and Its Regulation. Proceedings of ECTI-CARD 2009.

GIULIO PAVESI - PUBLICATIONS

My Pubmed list

My DBLP list

(check these first - both likely to be more up-to-date than the following lists)

JOURNAL PAPERS: BIOINFORMATICS

1.G. Pavesi, G. Mauri, G. Pesole. An algorithm for finding signals of unknown length in DNA sequences, Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Bioinformatics, 17: S207-S214, 2001.
2.G. Pavesi, G. Mauri, G. Pesole. Methods for pattern discovery in unaligned biological sequences, Briefings in Bioinformatics, 2(4):417-430, 2001.
3.G.Pavesi G.Mauri C.Gissi F.Iannelli G.Pesole. GeneSyn: a tool for detecting conserved gene order across genomes. Bioinformatics, 20(9):1472-1474, 2004.
4.G.Pavesi, G.Mauri, M.Stefani, G.Pesole. RNAprofile: An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Research, 32(10):3258-3269, 2004.
5.G.Pavesi, P.Mereghetti, G.Mauri, G.Pesole. Weeder Web: discovery of transcription factor binding sites in DNA sequences from related genes. Nucleic Acids Research 32(Web Server Issue):W199-W203, 2004
6.G.Pavesi, G.Mauri, G.Pesole. In silico representation and discovery of transcription factor binding sites. Briefings in Bioinformatics, 5(3):217-236, 2004.
7.M. Tompa, N. Li, T. L. Bailey , G. M. Church , B. De Moor, E. Eskin, A. V. Favorov, M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Régnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1):137-144, 2005.
8.The FANTOM Consortium (quorum ego). The transcriptional landscape of the mammalian genome. Science, 309(5740):1559-1563, 2005.
9.G. Pavesi, P. Mereghetti, F. Zambelli, M. Stefani, G. Mauri, G. Pesole. MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. Nucleic Acids Research, 34(Web Server Issue), W566-570, 2006.
10.G. Pavesi, Zambelli F, G.Pesole. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics, 8:46, 2007.
11.M. Ceribelli, D. Dolfini, D. Merico, R. Gatta, A. Viganò, G. Pavesi, R. Mantovani. The histone like NF-Y is a bifunctional transcription factor. Mol Cell Biol. 28(6):2047-2058, 2008.
12.T.Castrignanò, M.D'Antonio, A.Anselmo, D.Carrabino, DM.D'Onorio, A.D'Erchia, F.Licciulli, M.Mangiulli, F. Mignone, G.Pavesi, E.Picardi, A.Riva, R.Rizzi, P.Bonizzoni, G.Pesole. ASPicDB: A database resource for alternative splicing analysis. Bioinformatics, 24(10):1300-1304, 2008.
13.G. Pavesi, F.Zambelli, C.Caggese, G.Pesole. Exalign: a new method for comparative analysis of exon-intron gene structures Nucleic Acids Research May; 36(8): e47, 2008.
14.J.Intra, G.Pavesi, D.Horner. Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family. BMC Evolutionary Biology, 2008, 8:214 (22 July 2008).
15.M.Ré, G. Pavesi. Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns. Artif Intell Med. 2009;45(2-3):117-23.
16.F.Zambelli, G.Pesole, G.Pavesi. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res. 2009 37(Web Server issue):W247-52.
17.DS. Horner, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Briefings in Bioinformatics, 2009 Oct 27. [Epub ahead of print]
18.G. Grillo Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010 Jan;38(Database issue):D75-80. Epub 2009 Oct 30.

JOURNAL PAPERS: More BIO than INFORMATICS

1.J. Intra, ME Perotti, G Pavesi, D Horner. Comparative and phylogenetic analysis of alpha-l-fucosidase genes. Gene 392:34-46, 2007. Epub 2006 Nov 11.
1.Galbiati, L. Simoni, G. Pavesi, E. Cominelli, P. Francia, A. Vavasseur, M. Bevan, C. Tonelli. Gene trap lines identify Arabidopsis genes expressed in guard cells. Plant Journal 53(5):750-62, 2008. Epub 2007 Nov 23.
2.M.Menges, G.Pavesi, P.Morandini, L. Bögre and J.A.H. Murray. Genomic organization and evolutionary conservation of plant D-type cyclins. Plant Physiol. 145(4):1558-76, 2007.
3.G.Pavesi, A.Siccardi, G.Viale, C.Grazioli, T.Calciolari, M.L. Tenchini, P.Plevani. Humans, hedgehogs, and high school science. EMBO Reports, 9(3), 208-211, 2008.
4.J.Intra, F.Cenni, G.Pavesi, M.E. Perotti. Interspecific analysis of the glycosidases of the sperm plasma membrane in Drosophila. Mol. Reprod. Devel. , 2008 May 16. [Epub ahead of print] DOI 10.1002/mrd.20932
5.M.E. Pasini, J.Intra, G. Pavesi Expression study of an alpha-l-fucosidase gene in the Drosophilidae family. Gene, 420(1):23-33, 2008. Epub 2008 May 15.
6.S.Pozzi, Zambelli F, Merico D, Pavesi G, Robert A, Maltère P, Gidrol X, Mantovani R, Vigano MA. Transcriptional network of p63 in human keratinocytes. PLoS One. 2009;4(3):e5008.
7.D.Dolfini Zambelli F, Pavesi G, Mantovani R. A perspective of promoter architecture from the CCAAT box. Cell Cycle. 2009 Dec 15;8(24):4127-37.

JOURNAL PAPERS: Less BIO than INFORMATICS

1.G. Mauri, G. Pavesi. A parallel algorithm for pattern discovery in biological sequences, Future generation Computer Systems, 18 (6): 849-854, 2002.
2.G.Pavesi, G.Mauri, G.Pesole. An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. J.of Computer Science and Technology, 19(1): 2-12, 2004.
3.G.Mauri, G.Pavesi. Algorithms for pattern matching and discovery in RNA secondary structure. Theoretical Computer Science, 335(1): 29-51, 2005.
4.S. Inenaga, H. Hoshino, A. Shinohara, M. Takeda, S. Arikawa, G. Mauri, G. Pavesi. On-line construction of compact directed acyclic word graphs, Discrete and Applied Mathematics, 146(2): 156-179, 2005.
5.G. Pavesi, G. Valentini. Classification of co-expressed genes from DNA regulatory regions. Information Fusion 10(3), pp. 233-241, 2009

JOURNAL PAPERS: OTHER STUFF

1.S. Bandini, G. Mauri, G. Pavesi, C. Simone. Parallel simulation of reaction diffusion phenomena in percolation processes: a model based on cellular automata, Future Generation Computer Systems, 17 (6): 679-688, 2001.
2.S. Bandini, G. Pavesi. Controlled generation of two -dimensional patterns based on stochastic cellular automata, Future Generation Computer Systems, 18 (7): 973-981, 2002.

REFEREED CONFERENCE PROCEEDINGS

1. G. Mauri, G. Pavesi, A. Piccolboni. Approximation Algorithms for Protein Folding Prediction, in Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA '99), pp. 945-946, Baltimore, 1999.

2. S. Bandini, G. Mauri, G. Pavesi, C. Simone. A Parallel Model Based on Cellular Automata for the Simulation of Pesticide Percolation in the Soil, Proc. of the 5th Int’l Conference on Parallel Computing and Technologies (PACT 1999), Lecture Notes in Computer Science 1662, pp.383-394, 1999.

3. G. Mauri, G. Pavesi. Approximation Algorithms for String Folding Problems, in J. van Leeuwen et al. (Eds.) IFIP TCS 2000, Lecture Notes in Computer Science 1872, pp. 45-58.

4. S. Inenaga, H. Hoshino, A. Shinohara, M. Takeda, S. Arikawa, G. Mauri, G. Pavesi. On -Line Construction of Compact Directed Acyclic Word Graphs, Proceedings CPM 2001 Lecture Notes in Computer Science 2089, pp.169-179, 2001.

5. G. Mauri, G. Pavesi. Parallel Algorithms for the Analysis of Biological Sequences, Proceedings of the 6th International Conference on Parallel Computing and Technologies (PACT 2001), Lecture Notes in Computer Science 2127, pp. 456-466, 2001.

6. S. Bandini, G. Mauri, G. Pavesi. Parallel Generation of Percolation Beds Based on Stochastic Cellular Automata, Proceedings of the 6th International Conference on Parallel Computing and Technologies (PACT 2001), Lecture Notes in Computer Science 2127, pp. 391-397, 2001.

7. S. Bandini, S. Manzoni, G. Pavesi, C. Simone. L*MASS: a Language for Situated Multi -Agent Systems, VII Congresso dell'Associazione Italiana per l'Intelligenza Artificiale, Bari, Settembre 2001, Lecture Notes in Computer Science 2175, pp. 249-259, 2001.

8. S. Bandini, G. Pavesi, Simulation of Pesticide Percolation in the Soil Based on Cellular Automata, Proceedings of Integrated Assessment and Decision Support (IEMSS 2002), 2002.

9. S. Bandini, G. Pavesi. Simulation of Vegetable Populations Dynamics Based on Cellular Automata, Proceedings of ACRI 2002, Lecture Notes in Computer Science 2493, pp. 202-210, 2002.

10. G. Mauri, G. Pavesi. Pattern Discovery in RNA Secondary Structure Using Affix Trees, Proceedings of the 14th Symposium on Combinatorial Pattern Matching (CPM 2003), Lecture Notes in Computer Science 2676, pp. 278-294, 2003.

11. G. Pavesi, G. Mauri, G. Pesole. Predicting Conserved Hairpin Motifs in Unaligned RNA Sequences, Proceedings of the 15th IEEE Int’l Conference on Tools with Artificial Intelligence (ICTAI 2003), pp. 10-18, 2003.

12. G. Mauri, R. Mosca, G. Pavesi: A GA Approach to the Definition of Regulatory Signals in Genomic Sequences. Proceedings of Genetic and Evolutionary Computation Conference (GECCO) 2004. Lecture Notes in Computer Science 3102, pp. 380-391, 2004.

13. S. Bandini, G. Pavesi. A Model Based on Cellular Automata for the Simulation of the Dynamics of Plant Populations. Proceedings of Integrated Assessment and Decision Support (IEMSS 2004), 2004.

14. S.Bandini, S.Manzoni, A.Namizada, G.Pavesi. A CA Approach to Study Complex Dynamics In Asset Markets. Proceedings of ACRI 2004, Lecture Notes in Computer Science 3305, pp. 591-600, 2004.

15. S.Bandini, G.Mauri, G.Pavesi, C.Simone. Computing with a Distributed Reaction-Diffusion Model. Proceedings of Machines, Computations, and Universality, 4th International Conference, MCU 2004, Lecture Notes in Computer Science 3354, pp 93-103.

16. M. Re, G. Pavesi. Signal Processing in Comparative Genomics. Proceedings of Applications of Fuzzy Sets Theory, 7th International Workshop on Fuzzy Logic and Applications (WILF 2007), Lecture Notes in Computer Science 4578, pp. 544-550, 2007.

17. G.Pavesi, F.Zambelli. Prediction of Over Represented Transcription Factor Binding Sites in Co-Regulated Genes Using Whole Genome Matching Statistics. . Proceedings of Applications of Fuzzy Sets Theory, 7th International Workshop on Fuzzy Logic and Applications (WILF 2007), Lecture Notes in Computer Science 4578, pp. 651-658, 2007.

18. F. Zambelli, M.Rè, G. Pavesi The Beacon Tools for the Analysis of Gene Expression and Its Regulation. Proceedings of ECTI-CARD 2009.