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Items: 1 to 50 of 52

1.

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives.

Ambrosino L, Tangherlini M, Colantuono C, Esposito A, Sangiovanni M, Miralto M, Sansone C, Chiusano ML.

Mar Drugs. 2019 Oct 11;17(10). pii: E576. doi: 10.3390/md17100576. Review.

2.

Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway.

Esposito A, Tamburini S, Triboli L, Ambrosino L, Chiusano ML, Jousson O.

Microbiologyopen. 2019 Oct 1:e938. doi: 10.1002/mbo3.938. [Epub ahead of print]

3.

Functional conserved non-coding elements among tunicates and chordates.

Ambrosino L, Vassalli QA, D'Agostino Y, Esposito R, Cetrangolo V, Caputi L, Amoroso A, Aniello F, D'Aniello S, Chatzigeorgiou M, Chiusano ML, Locascio A.

Dev Biol. 2019 Apr 15;448(2):101-110. doi: 10.1016/j.ydbio.2018.12.012. Epub 2018 Dec 20.

PMID:
30579696
4.

Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine.

Ambrosino L, Ruggieri V, Bostan H, Miralto M, Vitulo N, Zouine M, Barone A, Bouzayen M, Frusciante L, Pezzotti M, Valle G, Chiusano ML.

BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):435. doi: 10.1186/s12859-018-2420-y.

5.

GLOSSary: the GLobal Ocean 16S subunit web accessible resource.

Tangherlini M, Miralto M, Colantuono C, Sangiovanni M, Dell' Anno A, Corinaldesi C, Danovaro R, Chiusano ML.

BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):443. doi: 10.1186/s12859-018-2423-8.

6.

Complete Genome Sequencing of 10 Brucella abortus Biovar 3 Strains Isolated from Water Buffalo.

Paradiso R, Orsini M, Criscuolo D, Borrelli R, Valvini O, Cammà C, Chiusano ML, Galiero G, Borriello G.

Genome Announc. 2018 Apr 19;6(16). pii: e00180-18. doi: 10.1128/genomeA.00180-18.

7.

Complete Genome Sequencing of Eight Brucella abortus Biovar 1 Strains Isolated from Water Buffalo.

Paradiso R, Orsini M, Riccardi MG, Cecere B, Cerrone A, Cammà C, Chiusano ML, Galiero G, Borriello G.

Genome Announc. 2018 Mar 29;6(13). pii: e00179-18. doi: 10.1128/genomeA.00179-18.

8.

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.

9.

Shaping the evolutionary tree of green plants: evidence from the GST family.

Monticolo F, Colantuono C, Chiusano ML.

Sci Rep. 2017 Oct 30;7(1):14363. doi: 10.1038/s41598-017-14316-w.

10.

Bioinformatics Resources for Plant Genomics: Opportunities and Bottlenecks in The -omics Era.

Ambrosino L, Colantuono C, Monticolo F, Chiusano ML.

Curr Issues Mol Biol. 2018;27:71-88. doi: 10.21775/cimb.027.071. Epub 2017 Sep 8. Review.

PMID:
28885175
11.

Trichoderma harzianum enhances tomato indirect defense against aphids.

Coppola M, Cascone P, Chiusano ML, Colantuono C, Lorito M, Pennacchio F, Rao R, Woo SL, Guerrieri E, Digilio MC.

Insect Sci. 2017 Dec;24(6):1025-1033. doi: 10.1111/1744-7917.12475. Epub 2017 Jul 10.

PMID:
28475289
12.

Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships.

Ambrosino L, Chiusano ML.

Bioinform Biol Insights. 2017 Feb 23;11:1177932217690136. doi: 10.1177/1177932217690136. eCollection 2017.

13.

Distinct gene networks drive differential response to abrupt or gradual water deficit in potato.

Ambrosone A, Batelli G, Bostan H, D'Agostino N, Chiusano ML, Perrotta G, Leone A, Grillo S, Costa A.

Gene. 2017 Jan 15;597:30-39. doi: 10.1016/j.gene.2016.10.024. Epub 2016 Oct 19.

PMID:
27771448
14.

Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum.

Simm S, Scharf KD, Jegadeesan S, Chiusano ML, Firon N, Schleiff E.

Bioinform Biol Insights. 2016 Sep 26;10:185-207. eCollection 2016.

15.

Bioinformatics resources for pollen.

Ambrosino L, Bostan H, Ruggieri V, Chiusano ML.

Plant Reprod. 2016 Jun;29(1-2):133-47. doi: 10.1007/s00497-016-0284-8. Epub 2016 Jun 8. Review.

PMID:
27271281
16.

Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato.

Iovieno P, Punzo P, Guida G, Mistretta C, Van Oosten MJ, Nurcato R, Bostan H, Colantuono C, Costa A, Bagnaresi P, Chiusano ML, Albrizio R, Giorio P, Batelli G, Grillo S.

Front Plant Sci. 2016 Mar 31;7:371. doi: 10.3389/fpls.2016.00371. eCollection 2016.

17.

Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato.

Ruggieri V, Bostan H, Barone A, Frusciante L, Chiusano ML.

Plant Mol Biol. 2016 Jul;91(4-5):397-412. doi: 10.1007/s11103-016-0469-4. Epub 2016 Mar 23.

PMID:
27007138
18.

Self-DNA inhibitory effects: Underlying mechanisms and ecological implications.

Cartenì F, Bonanomi G, Giannino F, Incerti G, Vincenot CE, Chiusano ML, Mazzoleni S.

Plant Signal Behav. 2016;11(4):e1158381. doi: 10.1080/15592324.2016.1158381. Review.

19.

Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana.

Di Salle P, Incerti G, Colantuono C, Chiusano ML.

Brief Bioinform. 2017 Mar 1;18(2):215-225. doi: 10.1093/bib/bbw002.

PMID:
26891982
20.

pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana.

Ambrosino L, Bostan H, di Salle P, Sangiovanni M, Vigilante A, Chiusano ML.

Evol Bioinform Online. 2016 Jan 11;12:1-7. doi: 10.4137/EBO.S32536. eCollection 2016. Review.

21.

Suppression Subtractive Hybridization analysis provides new insights into the tomato (Solanum lycopersicum L.) response to the plant probiotic microorganism Trichoderma longibrachiatum MK1.

De Palma M, D'Agostino N, Proietti S, Bertini L, Lorito M, Ruocco M, Caruso C, Chiusano ML, Tucci M.

J Plant Physiol. 2016 Jan 15;190:79-94. doi: 10.1016/j.jplph.2015.11.005. Epub 2015 Nov 17.

PMID:
26705844
22.

Identification of novel small ncRNAs in pollen of tomato.

Bokszczanin KL, Krezdorn N, Fragkostefanakis S, Müller S, Rycak L, Chen Y, Hoffmeier K, Kreutz J, Paupière MJ, Chaturvedi P, Iannacone R, Müller F, Bostan H, Chiusano ML, Scharf KD, Rotter B, Schleiff E, Winter P; SPOT-ITN Consortium (Solanaceae Pollen Thermotolerance Initial Training Network Consortium).

BMC Genomics. 2015 Sep 18;16:714. doi: 10.1186/s12864-015-1901-x.

23.

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome.

Bostan H, Chiusano ML.

BMC Plant Biol. 2015 Feb 13;15:48. doi: 10.1186/s12870-014-0412-2.

24.

Inhibitory effects of extracellular self-DNA: a general biological process?

Mazzoleni S, Cartenì F, Bonanomi G, Senatore M, Termolino P, Giannino F, Incerti G, Rietkerk M, Lanzotti V, Chiusano ML.

New Phytol. 2015 Apr;206(1):127-32. doi: 10.1111/nph.13306. Epub 2015 Jan 28.

25.

A DArT marker-based linkage map for wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes.

Iorizzo M, Gao L, Mann H, Traini A, Chiusano ML, Kilian A, Aversano R, Carputo D, Bradeen JM.

BMC Genet. 2014 Nov 18;15:123. doi: 10.1186/s12863-014-0123-6.

26.

Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks?

Mazzoleni S, Bonanomi G, Incerti G, Chiusano ML, Termolino P, Mingo A, Senatore M, Giannino F, Cartenì F, Rietkerk M, Lanzotti V.

New Phytol. 2015 Feb;205(3):1195-210. doi: 10.1111/nph.13121. Epub 2014 Oct 29.

27.

Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations.

Ercolano MR, Sacco A, Ferriello F, D'Alessandro R, Tononi P, Traini A, Barone A, Zago E, Chiusano ML, Buson G, Delledonne M, Frusciante L.

BMC Genomics. 2014 Feb 18;15:138. doi: 10.1186/1471-2164-15-138.

28.

Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck.

Licciardello C, D'Agostino N, Traini A, Recupero GR, Frusciante L, Chiusano ML.

BMC Plant Biol. 2014 Feb 3;14:39. doi: 10.1186/1471-2229-14-39.

29.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

Traini A, Iorizzo M, Mann H, Bradeen JM, Carputo D, Frusciante L, Chiusano ML.

Int J Genomics. 2013;2013:257218. doi: 10.1155/2013/257218. Epub 2013 May 8.

30.

Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana.

Sangiovanni M, Vigilante A, Chiusano ML.

Biology (Basel). 2013 Dec 9;2(4):1465-87. doi: 10.3390/biology2041465.

31.

Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences.

Di Filippo M, Traini A, D'Agostino N, Frusciante L, Chiusano ML.

Gene. 2012 May 10;499(1):176-81. doi: 10.1016/j.gene.2012.02.044. Epub 2012 Feb 26.

PMID:
22391094
32.

Evolutionary meta-analysis of solanaceous resistance gene and solanum resistance gene analog sequences and a practical framework for cross-species comparisons.

Quirin EA, Mann H, Meyer RS, Traini A, Chiusano ML, Litt A, Bradeen JM.

Mol Plant Microbe Interact. 2012 May;25(5):603-12. doi: 10.1094/MPMI-12-11-0318-R.

33.

Evolution of anterior Hox regulatory elements among chordates.

Natale A, Sims C, Chiusano ML, Amoroso A, D'Aniello E, Fucci L, Krumlauf R, Branno M, Locascio A.

BMC Evol Biol. 2011 Nov 15;11:330. doi: 10.1186/1471-2148-11-330.

34.

Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.

Zenoni S, D'Agostino N, Tornielli GB, Quattrocchio F, Chiusano ML, Koes R, Zethof J, Guzzo F, Delledonne M, Frusciante L, Gerats T, Pezzotti M.

Plant J. 2011 Oct;68(1):11-27. doi: 10.1111/j.1365-313X.2011.04661.x. Epub 2011 Jul 14.

35.

Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs.

Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A.

Am J Pathol. 2010 May;176(5):2113-30. doi: 10.2353/ajpath.2010.090837. Epub 2010 Mar 26.

36.

SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes.

D'Agostino N, Traini A, Frusciante L, Chiusano ML.

BMC Plant Biol. 2009 Nov 30;9:142. doi: 10.1186/1471-2229-9-142.

37.

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development.

Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G.

BMC Genomics. 2009 Aug 26;10:399. doi: 10.1186/1471-2164-10-399.

38.

ISOL@: an Italian SOLAnaceae genomics resource.

Chiusano ML, D'Agostino N, Traini A, Licciardello C, Raimondo E, Aversano M, Frusciante L, Monti L.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S7. doi: 10.1186/1471-2105-9-S2-S7.

39.

Structural and functional genomics of tomato.

Barone A, Chiusano ML, Ercolano MR, Giuliano G, Grandillo S, Frusciante L.

Int J Plant Genomics. 2008;2008:820274. doi: 10.1155/2008/820274.

40.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. Epub 2007 Dec 18.

41.

An EST database from saffron stigmas.

D'Agostino N, Pizzichini D, Chiusano ML, Giuliano G.

BMC Plant Biol. 2007 Oct 9;7:53.

42.

Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome.

D'Agostino N, Traini A, Frusciante L, Chiusano ML.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S9.

43.

TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species.

D'Agostino N, Aversano M, Frusciante L, Chiusano ML.

Nucleic Acids Res. 2007 Jan;35(Database issue):D901-5. Epub 2006 Nov 16.

44.

ParPEST: a pipeline for EST data analysis based on parallel computing.

D'Agostino N, Aversano M, Chiusano ML.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S9.

45.

A possible flip-flop genetic mechanism for reciprocal gene expression.

Chiusano ML, Di Giaimo R, Potenza N, Russo GM, Geraci G, del Gaudio R.

FEBS Lett. 2005 Sep 12;579(22):4919-22.

46.
47.

Genome properties of the diatom Phaeodactylum tricornutum.

Scala S, Carels N, Falciatore A, Chiusano ML, Bowler C.

Plant Physiol. 2002 Jul;129(3):993-1002.

48.

Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A).

Facchiano AM, Stiuso P, Chiusano ML, Caraglia M, Giuberti G, Marra M, Abbruzzese A, Colonna G.

Protein Eng. 2001 Nov;14(11):881-90.

PMID:
11742107
49.

Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code.

Chiusano ML, Alvarez-Valin F, Di Giulio M, D'Onofrio G, Ammirato G, Colonna G, Bernardi G.

Gene. 2000 Dec 30;261(1):63-9.

PMID:
11164038
50.

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

Chiusano ML, D'Onofrio G, Alvarez-Valin F, Jabbari K, Colonna G, Bernardi G.

Gene. 1999 Sep 30;238(1):23-31.

PMID:
10570980

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