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26
Facchin S, Vitulo N, Calgaro M, Buda A, Romualdi C, Pohl D, Perini B, Lorenzon G, Marinelli C, D’Incà R, Sturniolo GC, Savarino EV. Microbiota changes induced by microencapsulated sodium butyrate in patients with inflammatory bowel disease. Neurogastroenterol Motil 2020;32:e13914. [PMID: 32476236 PMCID: PMC7583468 DOI: 10.1111/nmo.13914] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/06/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022]
27
Calgaro M, Romualdi C, Waldron L, Risso D, Vitulo N. Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data. Genome Biol 2020;21:191. [PMID: 32746888 PMCID: PMC7398076 DOI: 10.1186/s13059-020-02104-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]  Open
28
Pinosio S, Marroni F, Zuccolo A, Vitulo N, Mariette S, Sonnante G, Aravanopoulos FA, Ganopoulos I, Palasciano M, Vidotto M, Magris G, Iezzoni A, Vendramin GG, Morgante M. A draft genome of sweet cherry (Prunus avium L.) reveals genome-wide and local effects of domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020;103:1420-1432. [PMID: 32391598 DOI: 10.1111/tpj.14809] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 05/26/2023]
29
Balzan S, Carraro L, Merlanti R, Lucatello L, Capolongo F, Fontana F, Novelli E, Larini I, Vitulo N, Cardazzo B. Microbial metabarcoding highlights different bacterial and fungal populations in honey samples from local beekeepers and market in north-eastern Italy. Int J Food Microbiol 2020;334:108806. [PMID: 32805512 DOI: 10.1016/j.ijfoodmicro.2020.108806] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023]
30
Palumbo F, Vitulo N, Vannozzi A, Magon G, Barcaccia G. The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. Int J Mol Sci 2020;21:E4664. [PMID: 32630002 PMCID: PMC7370444 DOI: 10.3390/ijms21134664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 01/12/2023]  Open
31
Urciuolo A, Serena E, Ghua R, Zatti S, Giomo M, Mattei N, Vetralla M, Selmin G, Luni C, Vitulo N, Valle G, Vitiello L, Elvassore N. Engineering a 3D in vitro model of human skeletal muscle at the single fiber scale. PLoS One 2020;15:e0232081. [PMID: 32374763 PMCID: PMC7202609 DOI: 10.1371/journal.pone.0232081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/07/2020] [Indexed: 01/07/2023]  Open
32
Scalabrin S, Toniutti L, Di Gaspero G, Scaglione D, Magris G, Vidotto M, Pinosio S, Cattonaro F, Magni F, Jurman I, Cerutti M, Suggi Liverani F, Navarini L, Del Terra L, Pellegrino G, Ruosi MR, Vitulo N, Valle G, Pallavicini A, Graziosi G, Klein PE, Bentley N, Murray S, Solano W, Al Hakimi A, Schilling T, Montagnon C, Morgante M, Bertrand B. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm. Sci Rep 2020;10:4642. [PMID: 32170172 PMCID: PMC7069947 DOI: 10.1038/s41598-020-61216-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022]  Open
33
Bargelloni L, Babbucci M, Ferraresso S, Papetti C, Vitulo N, Carraro R, Pauletto M, Santovito G, Lucassen M, Mark FC, Zane L, Patarnello T. Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures. Commun Biol 2019;2:443. [PMID: 31815198 PMCID: PMC6884616 DOI: 10.1038/s42003-019-0685-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/08/2019] [Indexed: 11/10/2022]  Open
34
Lovato A, Pignatti A, Vitulo N, Vandelle E, Polverari A. Inhibition of Virulence-Related Traits in Pseudomonas syringae pv. actinidiae by Gunpowder Green Tea Extracts. Front Microbiol 2019;10:2362. [PMID: 31681224 PMCID: PMC6797950 DOI: 10.3389/fmicb.2019.02362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/27/2019] [Indexed: 12/23/2022]  Open
35
Vitulo N, Lemos WJF, Calgaro M, Confalone M, Felis GE, Zapparoli G, Nardi T. Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity. Front Microbiol 2019;9:3203. [PMID: 30671035 PMCID: PMC6331396 DOI: 10.3389/fmicb.2018.03203] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/11/2018] [Indexed: 12/30/2022]  Open
36
Ambrosino L, Ruggieri V, Bostan H, Miralto M, Vitulo N, Zouine M, Barone A, Bouzayen M, Frusciante L, Pezzotti M, Valle G, Chiusano ML. Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. BMC Bioinformatics 2018;19:435. [PMID: 30497367 PMCID: PMC6266932 DOI: 10.1186/s12859-018-2420-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
37
Fasoli M, Richter CL, Zenoni S, Bertini E, Vitulo N, Dal Santo S, Dokoozlian N, Pezzotti M, Tornielli GB. Timing and Order of the Molecular Events Marking the Onset of Berry Ripening in Grapevine. PLANT PHYSIOLOGY 2018;178:1187-1206. [PMID: 30224433 PMCID: PMC6236592 DOI: 10.1104/pp.18.00559] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 05/08/2023]
38
Nigris S, Baldan E, Tondello A, Zanella F, Vitulo N, Favaro G, Guidolin V, Bordin N, Telatin A, Barizza E, Marcato S, Zottini M, Squartini A, Valle G, Baldan B. Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera. BMC Microbiol 2018;18:133. [PMID: 30326838 PMCID: PMC6192205 DOI: 10.1186/s12866-018-1306-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/07/2018] [Indexed: 12/14/2022]  Open
39
Pauletto M, Manousaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Quoc VH, Carraro R, Bertotto D, Franch R, Maroso F, Aslam ML, Sonesson AK, Simionati B, Malacrida G, Cestaro A, Caberlotto S, Sarropoulou E, Mylonas CC, Power DM, Patarnello T, Canario AVM, Tsigenopoulos C, Bargelloni L. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 2018;1:119. [PMID: 30271999 PMCID: PMC6123679 DOI: 10.1038/s42003-018-0122-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022]  Open
40
Palumbo F, Vannozzi A, Vitulo N, Lucchin M, Barcaccia G. The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants. Sci Rep 2018;8:10459. [PMID: 29993007 PMCID: PMC6041299 DOI: 10.1038/s41598-018-28775-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/29/2018] [Indexed: 02/06/2023]  Open
41
De Iudicibus S, Lucafò M, Vitulo N, Martelossi S, Zimbello R, De Pascale F, Forcato C, Naviglio S, Di Silvestre A, Gerdol M, Stocco G, Valle G, Ventura A, Bramuzzo M, Decorti G. High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. Int J Mol Sci 2018;19:ijms19051399. [PMID: 29738455 PMCID: PMC5983624 DOI: 10.3390/ijms19051399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 01/02/2023]  Open
42
Santi C, Molesini B, Guzzo F, Pii Y, Vitulo N, Pandolfini T. Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti. Genes (Basel) 2017;8:E396. [PMID: 29257077 PMCID: PMC5748714 DOI: 10.3390/genes8120396] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 12/23/2022]  Open
43
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 2017. [DOI: 10.1177/117693430700300007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
44
Vitulo N, Dalla Valle L, Skobo T, Valle G, Alibardi L. Downregulation of lizard immuno-genes in the regenerating tail and myogenes in the scarring limb suggests that tail regeneration occurs in an immuno-privileged organ. PROTOPLASMA 2017;254:2127-2141. [PMID: 28357509 DOI: 10.1007/s00709-017-1107-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/20/2017] [Indexed: 06/06/2023]
45
Bertoldi L, Forcato C, Vitulo N, Birolo G, De Pascale F, Feltrin E, Schiavon R, Anglani F, Negrisolo S, Zanetti A, D'Avanzo F, Tomanin R, Faulkner G, Vezzi A, Valle G. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. BMC Bioinformatics 2017;18:225. [PMID: 28454514 PMCID: PMC5410040 DOI: 10.1186/s12859-017-1654-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/26/2017] [Indexed: 11/21/2022]  Open
46
Pagliarani C, Vitali M, Ferrero M, Vitulo N, Incarbone M, Lovisolo C, Valle G, Schubert A. The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine. PLANT PHYSIOLOGY 2017;173:2180-2195. [PMID: 28235889 PMCID: PMC5373040 DOI: 10.1104/pp.16.01119] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
47
Vitulo N, Dalla Valle L, Skobo T, Valle G, Alibardi L. Transcriptome analysis of the regenerating tail vs. the scarring limb in lizard reveals pathways leading to successful vs. unsuccessful organ regeneration in amniotes. Dev Dyn 2017;246:116-134. [DOI: 10.1002/dvdy.24474] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/12/2016] [Accepted: 11/16/2016] [Indexed: 12/29/2022]  Open
48
Vannozzi A, Donnini S, Vigani G, Corso M, Valle G, Vitulo N, Bonghi C, Zocchi G, Lucchin M. Transcriptional Characterization of a Widely-Used Grapevine Rootstock Genotype under Different Iron-Limited Conditions. FRONTIERS IN PLANT SCIENCE 2017;7:1994. [PMID: 28105035 PMCID: PMC5214570 DOI: 10.3389/fpls.2016.01994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/16/2016] [Indexed: 05/06/2023]
49
Alboresi A, Perin G, Vitulo N, Diretto G, Block M, Jouhet J, Meneghesso A, Valle G, Giuliano G, Maréchal E, Morosinotto T. Light Remodels Lipid Biosynthesis in Nannochloropsis gaditana by Modulating Carbon Partitioning between Organelles. PLANT PHYSIOLOGY 2016;171:2468-82. [PMID: 27325666 PMCID: PMC4972283 DOI: 10.1104/pp.16.00599] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/20/2016] [Indexed: 05/18/2023]
50
Campagna D, Gasparini F, Franchi N, Vitulo N, Ballin F, Manni L, Valle G, Ballarin L. Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. BMC Genomics 2016;17:275. [PMID: 27038623 PMCID: PMC4818882 DOI: 10.1186/s12864-016-2598-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/15/2022]  Open
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