Paolo Fontana

Paolo Fontana was graduated in Biology at the Padua University in 1999, working on a project of EST sequencing and clustering of human skeletal muscle. From 2000 to 2001 he worked as bioinformatician with a Telethon fellowship at CRIBI (Centro Ricerche Interdipartimentale Biotecnologie Innovative) of Padua University on a project of gene prediction on the human genome. From 2001 to 2002 he worked with a fellowship of the University of Trento on the development of a biological ontology based on first order logic to be used with a semantic reasoner. From 2002 to 2004 he obtained a fellowship of the Fondazione Edmund Mach working on clustering and functional annotation of Vitis vinifera ESTs. Since 2004 he has a permanent position as research fellow at FEM. He was involved in the sequencing projects of grape and apple genomes and in the development of software tools for genome functional annotation. Now he is head of High Performance Computing group and is working on functional prediction tools based on Gene Ontology and pathway annotation strategies for grape and apple.

 Top ten publication:

  1. Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SC (2005). The SSEA server for protein secondary structure alignment. Bioinformatics 2005 Feb 1; 21(3):393-5.
  2. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. Plos One Dec 19; 2(12):e1326.
  3. Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S (2009). Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology. PlosOne Feb 4(2):e4619.
  4. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, et al. (2010). The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics 42:833–839.
  5. Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S (2012). Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Briefings in Bioinformatics; doi:10.1093/bib/bbr063 .
  6. Falda M, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P (2012). Argot 2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. BMC Bioinformatics 13(Suppl 4):S14.
  7. De Filippo C, Ramazzotti M, Fontana P, Cavalieri D. Bioinformatic approaches for pathway reconstruction from metagenomics data (2012). Briefings in Bioinformatics 13(6)
  8. P. Radivojac, W. Clark, T.B. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J.M. Yunes, A.S. Talwakar, S. Repo, M.L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Toronen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D.W. Buchan, K. Bryson, D.T. Jones, B. Limaye, H. Inamdar, A. Datta, S.K. Manjari, R. Joshi, M. Chitale, D. Kihara, A.M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A.E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kassner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Bohm, T. Braun, M. Hecht, M. Heron, P. Honigschmid, T. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bjorne, T. Salakoski, A. Wong, H. Shatkay, M.N. Wass, M.J.E. Sternberg, N. Skunca, F. Supek, M. Bosnjak, P. Panov, S. Dzeroski, T. Smuc, Y.A.I. Kourmpetis, A.D.J. van Dijk, C.J.F. ter Braak, Y. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B.D. Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P.C. Babbitt, S.E. Brenner, C. Orengo, B. Rost, S.D. Mooney, I. Friedberg (2013). A Large-Scale Evaluation of Computational Protein Function Prediction. Nature Methods doi:10.1038/nmeth.2340 .
  9. Ometto L , Cestaro A, Ramasamy S, Grassi A, Revadi S, Siozios S, Moretto M, Fontana P, Varotto C, Pisani D, Dekker T, Wrobele N, Viola R, Pertot I, Cavalieri D, Blaxter M, Anfora G, Rota-Stabelli O (2013). Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest. Genome Biology and Evolution doi:10.1093/gbe/evt034 .
  10. Beltrame L, Bianco L, Fontana P, Cavalieri D (2013). Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data. Bioinformatics; doi:10.1093/bioinformatics/btt292 .