IGA Publications

• rNA: a Fast and Accurate Short Reads Numerical Aligner.
  Vezzi F,Del Fabbro C,Tomescu AI, Policriti A.
  Briefings in Bioinformatics. 2011; Epub ahead of print
  doi: 10.1093/bioinformatics/btr617
• A 3000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.
  Rustenholz C, Choulet F, Laugier C, Šafář J, Šimková H, Doležel J, Magni F, Scalabrin S, Cattonaro F, Vautrin S, Bellec A, Bergès H, Feuillet C, Paux E.
  Plant Physiology. 2011; Epub ahead of print
  doi: 10.1104/pp.111.183921
• Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance.
  Di Gaspero G, Copetti D, Coleman C, Castellarin SD, Eibach R, Kozma P, Lacombe T, Gambetta G, Zvyagin A, Cindrić P, Kovács L, Morgante M, Testolin R..
  Theoretical and Applied Genetics. 2011; Epub ahead of print
  doi: 10.1007/s00122-011-1703-8
• Large scale detection of rare variants via pooled multiplexed next generation sequencing: towards next generation Ecotilling.
  Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, Cattonaro F, Morgante M.
  The Plant Journal. 2011; Epub ahead of print
  doi: 10.1111/j.1365-313X.2011.04627.x
• The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin.
  Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S, Frare E, Vignani R, Cresti M, Morgante M, Pezzotti M, Pe ME, Policriti A, Testolin R.
  Theoretical and Applied Genetics. 2010; 121:8
  doi: 10.1007/s00122-010-1411-9
• Enhanced reference guided assembly.
  Cattonaro F, Policriti A, Vezzi F.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2010
  doi: 10.1109/BIBM.2010.5706540
• Expansion and subfunctionalisation of flavonoid 3',5'-hydroxylases in the grapevine lineage.
  Falginella L, Castellarin SD, Testolin R, Gambetta GA, Morgante M, Di Gaspero G.
  BMC Genomics. 2010; 11:562
  doi: 10.1186/1471-2164-11-562
• Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.
  Cavallini A, Natali L, Zuccolo A, Giordani T, Jurman I, Ferrillo V, Vitacolonna N, Sarri V, Cattonaro F, Ceccarelli M, Cionini PG, Morgante M.
  Theoretical and Applied Genetics. 2010; 120:3
  doi: 10.1007/s00122-009-1170-7
• Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar.
  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.
  BMC Genomics. 2010; 26:11
  doi: 10.1186/1471-2164-11-204
• TEA: a Transposable Elements Annotator.
  Del Fabbro C, Policriti A, Morgante M, Vitacolonna N.
  Proceedings of The 2009 International Conference on Bioinformatics and Computational Biology. 2009; 2:528-535, ISBN 1-60132-095-7
• Automated FingerPrint Background removal: FPB.
  Scalabrin S, Policriti A, Morgante M.
  BMC Bioinformatics. 2009; 10:127
  doi: 10.1186/1471-2105-10-127
• The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines.
  Coleman C, Copetti D, Cipriani G, Hoffmann S, Kozma P, Kovács L, Morgante M, Testolin R, Di Gaspero G.
  BMC Genetics. 2009; 10:89
  doi: 10.1186/1471-2156-10-89
• GAM: Genomic Assemblies Merger. A Graph Based Method to Integrate Different Assemblies.
  Casagrande A, Del Fabbro C, Scalabrin S, Policriti A.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2009
  doi: 10.1109/BIBM.2009.28
• Annotating genomes with massive-scale RNA-sequencing.
  Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli S, Jaillon O, Artiguenave F.
  Genome Biology. 2008; 9:12
  doi: 10.1186/gb-2008-9-12-r175
• A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping.
  Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, Morgante M, Testolin R.
  BMC Plant Biology. 2008; 8:127
  doi: 10.1186/1471-2229-8-127
• Resistance to Erysiphe necator in the grapevine 'Kishmish vatkana' is controlled by a single locus through restriction of hyphal growth.
  Hoffmann S, Di Gaspero G, Kovács L, Howard S, Kiss E, Galbács Z, Testolin R, Kozma P.
  Theor Appl Genet. 2008; 116:3
  doi: 10.1007/s00122-007-0680-4
• High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.
  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.
  BMC Genomics. 2009; 10:558
  doi: 10.1186/1471-2164-10-558
• A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.
  Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF.
  BMC Plant Biology. 2008; 8:66
  doi: 10.1186/1471-2229-8-66
• The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
  Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner DS, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P.
  Nature. 2007; 449:7161
  doi: 10.1038/nature06148
• Structured Motifs Search.
  Morgante M, Policriti A, Vitacolonna N, Zuccolo A.
  Journal of Computational Biology. 2005; 12:8
  doi: 10.1145/974614.974632
• Mapping and sequencing complex genomes: Let's get physical!
  Meyers B, Scalabrin S, Morgante M.
  Nature Review Genetics. 2004; 5:8
  doi: 10.1038/nrg1404
• Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice.
  Antoniotti M, Mishra B, Piazza C, Policriti A, Simeoni M.
  Theoretical Computer Science. 2004; 325:1
  doi: 10.1016/j.tcs.2004.03.064