IGA Publications

•   ERNE-BS5: Aligning BS-treated Sequences by Multiple Hits on a 5-letters Alphabet.
  Prezza N., Del Fabbro C., Vezzi F., De Paoli E., and Policriti A.
  Proceedings of The 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2012), Orlando (Florida), U.S.A., October 7-10, 2012, Association for Computing Machinery, 0:12-19, ISBN: 978-1-4503-1670-5
•  mrNA: the MPI randomized Numerical Aligner.
  Del Fabbro C., Vezzi F., and Policriti A.
  Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta (Georgia) U.S.A., November 12-15, 2011, IEEE Computer Society 0:139-142, ISBN 978-0-7695-4574-5
  doi: 10.1109/BIBM.2011.17
•  Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm.
  Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C.
  PLoS ONE. 2012; Epub ahead of print
  doi: 10.1371/journal.pone.0035668
• 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. 2012; 124:2
  doi: 10.1007/s00122-011-1703-8
• Feature-by-Feature - Evaluating De Novo Sequence Assembly.
  Vezzi F, Narzisi G, Mishra B.
  PLoS One. 2012; 7:2
  doi: 10.1371/journal.pone.0031002
• rNA: a Fast and Accurate Short Reads Numerical Aligner.
  Vezzi F, Del Fabbro C, Tomescu AI, Policriti A.
  Bioinformatics. 2012; 28:1
  doi: 10.1093/bioinformatics/btr617
• Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions.
  Buti M, Giordani T, Cattonaro F, Cossu RM, Pistelli L, Vukich M, Morgante M, Cavallini A, Natali L.
  Theor Appl Genet. 2011 Sep;123(5):779-91.
  doi: 10.1007/s00122-011-1626-4
• Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene.
  Marroni F, Pinosio S, Zaina G, Fogolari F, Felice N, Cattonaro F, Morgante M.
  Tree Genetics & Genomes 2011 Oct; 7(5):1011-1023.
  doi: 10.1007/s11295-011-0391-5
• An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.).
  Giordani T, Buti M, Natali L, Pugliesi C, Cattonaro F, Morgante M, Cavallini A.
  Theor Appl Genet. 2011 Apr;122(6):1039-49.
  doi: 10.1007/s00122-010-1509-0
• Genetic dissection of barley morphology and development.
  Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R.
  Plant Physiol. 2011 Feb;155(2):617-27.
  doi: 10.1104/​pp.​110.​166249
• Bud set in poplar--genetic dissection of a complex trait in natural and hybrid populations.
  Rohde A, Storme V, Jorge V, Gaudet M, Vitacolonna N, Fabbrini F, Ruttink T, Zaina G, Marron N, Dillen S, Steenackers M, Sabatti M, Morgante M, Boerjan W, Bastien C.
  New Phytol. 2011 Jan;189(1):106-21.
  doi: 10.1111/j.1469-8137.2010.03469.x
• 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; 157:4
  doi: 10.1104/pp.111.183921
• 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; 67:4
  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