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Items: 41

1.

A semi-automated protocol for NGS metabarcoding and fungal analysis in forensic.

Giampaoli S, De Vittori E, Frajese GV, Paytuví A, Sanseverino W, Anselmo A, Barni F, Berti A.

Forensic Sci Int. 2019 Nov 15;306:110052. doi: 10.1016/j.forsciint.2019.110052. [Epub ahead of print]

PMID:
31778923
2.

LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells.

Cebrià-Costa JP, Pascual-Reguant L, Gonzalez-Perez A, Serra-Bardenys G, Querol J, Cosín M, Verde G, Cigliano RA, Sanseverino W, Segura-Bayona S, Iturbide A, Andreu D, Nuciforo P, Bernado-Morales C, Rodilla V, Arribas J, Yelamos J, de Herreros AG, Stracker TH, Peiró S.

Oncogene. 2019 Aug 28. doi: 10.1038/s41388-019-0969-1. [Epub ahead of print]

PMID:
31462706
3.

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.

Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A.

Cell Rep. 2019 Jul 9;28(2):352-367.e9. doi: 10.1016/j.celrep.2019.06.037.

4.

Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi.

Borgognone A, Sanseverino W, Aiese Cigliano R, Castanera R.

Int J Genomics. 2019 May 2;2019:9702342. doi: 10.1155/2019/9702342. eCollection 2019.

5.

A de novo transcriptome assembly approach elucidates the dynamics of ovarian maturation in the swordfish (Xiphias gladius).

Gioacchini G, Marisaldi L, Basili D, Candelma M, Pignalosa P, Aiese Cigliano R, Sanseverino W, Hardiman G, Carnevali O.

Sci Rep. 2019 May 14;9(1):7375. doi: 10.1038/s41598-019-43872-6.

6.

A Walkthrough to the Use of GreeNC: The Plant lncRNA Database.

Paytuvi-Gallart A, Sanseverino W, Aiese Cigliano R.

Methods Mol Biol. 2019;1933:397-414. doi: 10.1007/978-1-4939-9045-0_25.

PMID:
30945200
7.

Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing.

Russo MT, Aiese Cigliano R, Sanseverino W, Ferrante MI.

PeerJ. 2018 Oct 5;6:e5507. doi: 10.7717/peerj.5507. eCollection 2018.

8.

Broad phenotypic spectrum and genotype-phenotype correlations in GMPPB-related dystroglycanopathies: an Italian cross-sectional study.

Astrea G, Romano A, Angelini C, Antozzi CG, Barresi R, Battini R, Battisti C, Bertini E, Bruno C, Cassandrini D, Fanin M, Fattori F, Fiorillo C, Guerrini R, Maggi L, Mercuri E, Morani F, Mora M, Moro F, Pezzini I, Picillo E, Pinelli M, Politano L, Rubegni A, Sanseverino W, Savarese M, Striano P, Torella A, Trevisan CP, Trovato R, Zaraieva I, Muntoni F, Nigro V, D'Amico A, Santorelli FM; Italian CMD Network.

Orphanet J Rare Dis. 2018 Sep 26;13(1):170. doi: 10.1186/s13023-018-0863-x.

9.

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.

Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J.

Sci Rep. 2018 May 24;8(1):8088. doi: 10.1038/s41598-018-26416-2.

10.

Author Correction: The hypothesis that Helicobacter pylori predisposes to Alzheimer's disease is biologically plausible.

Contaldi F, Capuano F, Fulgione A, Aiese Cigliano R, Sanseverino W, Iannelli D, Medaglia C, Capparelli R.

Sci Rep. 2018 Apr 11;8(1):6061. doi: 10.1038/s41598-018-23613-x.

11.

Genomic diversity in ochratoxigenic and non ochratoxigenic strains of Aspergillus carbonarius.

Castellá G, Bragulat MR, Puig L, Sanseverino W, Cabañes FJ.

Sci Rep. 2018 Apr 3;8(1):5439. doi: 10.1038/s41598-018-23802-8.

12.

Sequencing, De Novo Assembly, and Annotation of the Complete Genome of a New Thraustochytrid Species, Strain CCAP_4062/3.

Seddiki K, Godart F, Aiese Cigliano R, Sanseverino W, Barakat M, Ortet P, Rébeillé F, Maréchal E, Cagnac O, Amato A.

Genome Announc. 2018 Mar 15;6(11). pii: e01335-17. doi: 10.1128/genomeA.01335-17.

13.

PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes.

Osuna-Cruz CM, Paytuvi-Gallart A, Di Donato A, Sundesha V, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1197-D1201. doi: 10.1093/nar/gkx1119.

14.

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuono C, Bostan H, Termolino P, Aversano R, Batelli G, Cammareri M, Carputo D, Chiusano ML, Conicella C, Consiglio F, D'Agostino N, De Palma M, Di Matteo A, Grandillo S, Sanseverino W, Tucci M, Grillo S.

DNA Res. 2018 Apr 1;25(2):149-160. doi: 10.1093/dnares/dsx045.

15.

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription.

Forestan C, Farinati S, Aiese Cigliano R, Lunardon A, Sanseverino W, Varotto S.

BMC Plant Biol. 2017 Oct 12;17(1):161. doi: 10.1186/s12870-017-1108-1.

16.

The hypothesis that Helicobacter pylori predisposes to Alzheimer's disease is biologically plausible.

Contaldi F, Capuano F, Fulgione A, Aiese Cigliano R, Sanseverino W, Iannelli D, Medaglia C, Capparelli R.

Sci Rep. 2017 Aug 10;7(1):7817. doi: 10.1038/s41598-017-07532-x. Erratum in: Sci Rep. 2018 Apr 11;8(1):6061.

17.

Careful with That Axe, Gene, Genome Perturbation after a PEG-Mediated Protoplast Transformation in Fusarium verticillioides.

Scala V, Grottoli A, Aiese Cigliano R, Anzar I, Beccaccioli M, Fanelli C, Dall'Asta C, Battilani P, Reverberi M, Sanseverino W.

Toxins (Basel). 2017 May 31;9(6). pii: E183. doi: 10.3390/toxins9060183.

18.

Transcriptomic response of durum wheat to nitrogen starvation.

Curci PL, Aiese Cigliano R, Zuluaga DL, Janni M, Sanseverino W, Sonnante G.

Sci Rep. 2017 Apr 26;7(1):1176. doi: 10.1038/s41598-017-01377-0.

19.

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP.

Ruggieri V, Anzar I, Paytuvi A, Calafiore R, Cigliano RA, Sanseverino W, Barone A.

DNA Res. 2017 Feb 1;24(1):81-91. doi: 10.1093/dnares/dsw050.

20.

Spermatozoa from infertile patients exhibit differences of DNA methylation associated with spermatogenesis-related processes: an array-based analysis.

Camprubí C, Salas-Huetos A, Aiese-Cigliano R, Godo A, Pons MC, Castellano G, Grossmann M, Sanseverino W, Martin-Subero JI, Garrido N, Blanco J.

Reprod Biomed Online. 2016 Dec;33(6):709-719. doi: 10.1016/j.rbmo.2016.09.001. Epub 2016 Sep 15.

PMID:
27692602
21.

Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.

Forestan C, Aiese Cigliano R, Farinati S, Lunardon A, Sanseverino W, Varotto S.

Sci Rep. 2016 Jul 27;6:30446. doi: 10.1038/srep30446.

22.

Pentatricopeptide repeat 336 as the candidate gene for paternal sorting of mitochondria (Psm) in cucumber.

Del Valle-Echevarria AR, Sanseverino W, Garcia-Mas J, Havey MJ.

Theor Appl Genet. 2016 Oct;129(10):1951-9. doi: 10.1007/s00122-016-2751-x. Epub 2016 Jul 16.

23.

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.

Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P.

Nat Genet. 2016 Jun;48(6):657-66. doi: 10.1038/ng.3565. Epub 2016 May 9.

PMID:
27158781
24.

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.

Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R.

Genome Biol. 2016 Feb 25;17:32. doi: 10.1186/s13059-016-0883-6.

25.

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling.

Vacca M, Tripathi KP, Speranza L, Aiese Cigliano R, Scalabrì F, Marracino F, Madonna M, Sanseverino W, Perrone-Capano C, Guarracino MR, D'Esposito M.

BMC Bioinformatics. 2016 Jan 20;17 Suppl 2:14. doi: 10.1186/s12859-015-0859-7.

26.

Flowering and trichome development share hormonal and transcription factor regulation.

Matías-Hernández L, Aguilar-Jaramillo AE, Cigliano RA, Sanseverino W, Pelaz S.

J Exp Bot. 2016 Mar;67(5):1209-19. doi: 10.1093/jxb/erv534. Epub 2015 Dec 17. Review.

PMID:
26685187
27.

GREENC: a Wiki-based database of plant lncRNAs.

Paytuví Gallart A, Hermoso Pulido A, Anzar Martínez de Lagrán I, Sanseverino W, Aiese Cigliano R.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1161-6. doi: 10.1093/nar/gkv1215. Epub 2015 Nov 17.

28.

Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle.

Zaccaria M, Ludovici M, Sanzani SM, Ippolito A, Cigliano RA, Sanseverino W, Scarpari M, Scala V, Fanelli C, Reverberi M.

Toxins (Basel). 2015 Oct 23;7(10):4315-29. doi: 10.3390/toxins7104315.

29.

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM.

Mol Biol Evol. 2015 Oct;32(10):2760-74. doi: 10.1093/molbev/msv152. Epub 2015 Jul 14.

PMID:
26174143
30.

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives.

Aversano R, Contaldi F, Ercolano MR, Grosso V, Iorizzo M, Tatino F, Xumerle L, Dal Molin A, Avanzato C, Ferrarini A, Delledonne M, Sanseverino W, Cigliano RA, Capella-Gutierrez S, Gabaldón T, Frusciante L, Bradeen JM, Carputo D.

Plant Cell. 2015 Apr;27(4):954-68. doi: 10.1105/tpc.114.135954. Epub 2015 Apr 14.

31.

Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius.

Cabañes FJ, Sanseverino W, Castellá G, Bragulat MR, Cigliano RA, Sánchez A.

Sci Rep. 2015 Mar 13;5:9086. doi: 10.1038/srep09086.

32.

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly.

Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J.

BMC Genomics. 2015 Jan 22;16:4. doi: 10.1186/s12864-014-1196-3.

33.

Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis.

Yang L, Koo DH, Li D, Zhang T, Jiang J, Luan F, Renner SS, Hénaff E, Sanseverino W, Garcia-Mas J, Casacuberta J, Senalik DA, Simon PW, Chen J, Weng Y.

Plant J. 2014 Jan;77(1):16-30. doi: 10.1111/tpj.12355. Epub 2013 Dec 3.

34.

Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles.

Aiese Cigliano R, Sanseverino W, Cremona G, Ercolano MR, Conicella C, Consiglio FM.

BMC Genomics. 2013 Jan 28;14:57. doi: 10.1186/1471-2164-14-57.

35.

In silico approach to predict candidate R proteins and to define their domain architecture.

Sanseverino W, Ercolano MR.

BMC Res Notes. 2012 Dec 8;5:678. doi: 10.1186/1756-0500-5-678.

36.

Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics.

Andolfo G, Sanseverino W, Rombauts S, Van de Peer Y, Bradeen JM, Carputo D, Frusciante L, Ercolano MR.

New Phytol. 2013 Jan;197(1):223-37. doi: 10.1111/j.1469-8137.2012.04380.x. Epub 2012 Nov 19.

37.

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.

Sanseverino W, Hermoso A, D'Alessandro R, Vlasova A, Andolfo G, Frusciante L, Lowy E, Roma G, Ercolano MR.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1167-71. doi: 10.1093/nar/gks1183. Epub 2012 Nov 17.

38.

The genome of melon (Cucumis melo L.).

Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P.

Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11872-7. doi: 10.1073/pnas.1205415109. Epub 2012 Jul 2.

39.

Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects.

Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L.

Plant Cell Rep. 2012 Jun;31(6):973-85. doi: 10.1007/s00299-012-1234-z. Epub 2012 Feb 18. Review.

40.

Evolution of parallel spindles like genes in plants and highlight of unique domain architecture#.

Cigliano RA, Sanseverino W, Cremona G, Consiglio FM, Conicella C.

BMC Evol Biol. 2011 Mar 24;11:78. doi: 10.1186/1471-2148-11-78.

41.

PRGdb: a bioinformatics platform for plant resistance gene analysis.

Sanseverino W, Roma G, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR.

Nucleic Acids Res. 2010 Jan;38(Database issue):D814-21. doi: 10.1093/nar/gkp978. Epub 2009 Nov 11.

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