Papers

Publications 2007-2013

Corteggiani Carpinelli E, Telatin A, Vitulo N, Forcato F, D’Angelo M, Schiavon R, Vezzi A, Giacometti G M, Morosinotto T, Valle G. Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Molecular Plant. 2013

Campagna D, Telatin A, Forcato C, Vitulo N, Valle G. PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics. 2013

Campanaro S, Pascale FD, Telatin A, Schiavon R, Bartlett DH, Valle G. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain. BMC Genomics. 2012

Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012

Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, Kubaláková M, Perrotta G, Facella P, Lopez L, Pietrella M, Gianese G, Doležel J, Giuliano G, Cattivelli L, Valle G, Stanca AM. First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One. 2011

Belgrano A, Rakicevic L, Mittempergher L, Campanaro S, Martinelli VC, Mouly V, Valle G, Kojic S, Faulkner G. Multi-tasking role of the mechanosensing protein Ankrd2 in the signaling network of striated muscle. PLoS One. 2011

Maccagnan A, Riva M, Feltrin E, Simionati B, Vardanega T, Valle G, Cannata N. Combining ontologies and workflows to design formal protocols for biological laboratories. Autom Exp. 2010

Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res. 2010

Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics. 2010

Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pè ME, Horner DS. High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics. 2009

Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010

Benna C, Peron S, Rizzo G, Faulkner G, Megighian A, Perini G, Tognon G, Valle G, Reggiani C, Costa R, Zordan MA. Post-transcriptional silencing of the Drosophila homolog of human ZASP: a molecular and functional analysis. Cell Tissue Res. 2009

Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G. PASS: a program to align short sequences. Bioinformatics. 2009

Feltrin E, Campanaro S, Diehl AD, Ehler E, Faulkner G, Fordham J, Gardin C, Harris M, Hill D, Knoell R, Laveder P, Mittempergher L, Nori A, Reggiani C, Sorrentino V, Volpe P, Zara I, Valle G, Deegan J. Muscle Research and Gene Ontology: New standards for improved data integration. BMC Med Genomics. 2009

von Nandelstadh P, Ismail M, Gardin C, Suila H, Zara I, Belgrano A, Valle G, Carpen O, Faulkner G. A class III PDZ binding motif in the myotilin and FATZ families binds enigma family proteins: a common link for Z-disc myopathies. Mol Cell Biol. 2009

Campanaro S, Treu L, Valle G. Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. BMC Evol Biol. 2008

Manavski SA, Valle G. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008

Todesco S, Campagna D, Levorin F, D’Angelo M, Schiavon R, Valle G, Vezzi A. PABS: an online platform to assist BAC-by-BAC sequencing projects. Biotechniques. 2008

Lauro FM, Tran K, Vezzi A, Vitulo N, Valle G, Bartlett DH. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure. J Bacteriol. 2008

Campanaro S, Picelli S, Torregrossa R, Colluto L, Ceol M, Del Prete D, D’Angelo A, Valle G, Anglani F. Genes involved in TGF beta1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map. BMC Genomics. 2007

Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, … Valle G,…; The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007

Vitulo N, Vezzi A, Romualdi C, Campanaro S, Valle G. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile. BMC Bioinformatics. 2007

Vitulo N, Vezzi A, Galla G, Citterio S, Marino G, Ruperti B, Zermiani M, Albertini E, Valle G, Barcaccia G. Characterization and evolution of the cell cycle-associated mob domain-containing proteins in eukaryotes. Evol Bioinform Online. 2007