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Items: 26

1.

Transcriptome Profiles of Strawberry (Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages.

Haile ZM, Nagpala-De Guzman EG, Moretto M, Sonego P, Engelen K, Zoli L, Moser C, Baraldi E.

Front Plant Sci. 2019 Sep 18;10:1131. doi: 10.3389/fpls.2019.01131. eCollection 2019.

2.

First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

Moretto M, Sonego P, Villaseñor-Altamirano AB, Engelen K.

BMC Bioinformatics. 2019 Jan 28;20(1):54. doi: 10.1186/s12859-019-2643-6.

3.

Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change.

Malacarne G, Pilati S, Valentini S, Asnicar F, Moretto M, Sonego P, Masera L, Cavecchia V, Blanzieri E, Moser C.

Front Plant Sci. 2018 Sep 21;9:1385. doi: 10.3389/fpls.2018.01385. eCollection 2018.

4.

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).

Buti M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ.

Gigascience. 2018 Apr 1;7(4):1-14. doi: 10.1093/gigascience/giy010. Erratum in: Gigascience. 2018 Nov 1;7(11):.

5.

Dual RNA-Seq of Lysobacter capsici AZ78 - Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses.

Tomada S, Sonego P, Moretto M, Engelen K, Pertot I, Perazzolli M, Puopolo G.

Environ Microbiol. 2017 Oct;19(10):4113-4125. doi: 10.1111/1462-2920.13861. Epub 2017 Aug 14.

PMID:
28745426
6.

Abscisic Acid Is a Major Regulator of Grape Berry Ripening Onset: New Insights into ABA Signaling Network.

Pilati S, Bagagli G, Sonego P, Moretto M, Brazzale D, Castorina G, Simoni L, Tonelli C, Guella G, Engelen K, Galbiati M, Moser C.

Front Plant Sci. 2017 Jun 21;8:1093. doi: 10.3389/fpls.2017.01093. eCollection 2017.

7.

Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence.

Haile ZM, Pilati S, Sonego P, Malacarne G, Vrhovsek U, Engelen K, Tudzynski P, Zottini M, Baraldi E, Moser C.

Plant Cell Environ. 2017 Aug;40(8):1409-1428. doi: 10.1111/pce.12937. Epub 2017 Apr 12.

PMID:
28239986
8.

Insights into the Role of the Berry-Specific Ethylene Responsive Factor VviERF045.

Leida C, Dal Rì A, Dalla Costa L, Gómez MD, Pompili V, Sonego P, Engelen K, Masuero D, Ríos G, Moser C.

Front Plant Sci. 2016 Dec 9;7:1793. doi: 10.3389/fpls.2016.01793. eCollection 2016.

9.

Complete genome sequence of Bacillus amyloliquefaciens subsp. plantarum S499, a rhizobacterium that triggers plant defences and inhibits fungal phytopathogens.

Molinatto G, Puopolo G, Sonego P, Moretto M, Engelen K, Viti C, Ongena M, Pertot I.

J Biotechnol. 2016 Nov 20;238:56-59. doi: 10.1016/j.jbiotec.2016.09.013. Epub 2016 Sep 28.

10.

VESPUCCI: Exploring Patterns of Gene Expression in Grapevine.

Moretto M, Sonego P, Pilati S, Malacarne G, Costantini L, Grzeskowiak L, Bagagli G, Grando MS, Moser C, Engelen K.

Front Plant Sci. 2016 May 10;7:633. doi: 10.3389/fpls.2016.00633. eCollection 2016.

11.

The Lysobacter capsici AZ78 Genome Has a Gene Pool Enabling it to Interact Successfully with Phytopathogenic Microorganisms and Environmental Factors.

Puopolo G, Tomada S, Sonego P, Moretto M, Engelen K, Perazzolli M, Pertot I.

Front Microbiol. 2016 Feb 5;7:96. doi: 10.3389/fmicb.2016.00096. eCollection 2016.

12.

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.

Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.

Nucleic Acids Res. 2016 Jan 4;44(D1):D620-3. doi: 10.1093/nar/gkv1251. Epub 2015 Nov 19.

13.

Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.

Lòpez-Fernàndez S, Sonego P, Moretto M, Pancher M, Engelen K, Pertot I, Campisano A.

Front Microbiol. 2015 May 26;6:419. doi: 10.3389/fmicb.2015.00419. eCollection 2015.

14.

Comparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.

Sonego P, Meysman P, Moretto M, Viola R, Laukens K, Cavalieri D, Engelen K.

Methods Mol Biol. 2015;1231:125-35. doi: 10.1007/978-1-4939-1720-4_8.

PMID:
25343862
15.

Draft Genome Sequence of Lysobacter capsici AZ78, a Bacterium Antagonistic to Plant-Pathogenic Oomycetes.

Puopolo G, Sonego P, Engelen K, Pertot I.

Genome Announc. 2014 Apr 24;2(2). pii: e00325-14. doi: 10.1128/genomeA.00325-14.

16.

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.

Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K.

Nucleic Acids Res. 2014 Jan;42(Database issue):D649-53. doi: 10.1093/nar/gkt1086. Epub 2013 Nov 8.

17.

Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients.

Sigalotti L, Covre A, Fratta E, Parisi G, Sonego P, Colizzi F, Coral S, Massarut S, Kirkwood JM, Maio M.

J Transl Med. 2012 Sep 5;10:185. doi: 10.1186/1479-5876-10-185.

18.

ROC analysis: applications to the classification of biological sequences and 3D structures.

Sonego P, Kocsor A, Pongor S.

Brief Bioinform. 2008 May;9(3):198-209. doi: 10.1093/bib/bbm064. Epub 2008 Jan 11. Review.

PMID:
18192302
19.

Benchmarking protein classification algorithms via supervised cross-validation.

Kertész-Farkas A, Dhir S, Sonego P, Pacurar M, Netoteia S, Nijveen H, Kuzniar A, Leunissen JA, Kocsor A, Pongor S.

J Biochem Biophys Methods. 2008 Apr 24;70(6):1215-23. Epub 2007 May 31.

PMID:
17604112
20.

A Protein Classification Benchmark collection for machine learning.

Sonego P, Pacurar M, Dhir S, Kertész-Farkas A, Kocsor A, Gáspári Z, Leunissen JA, Pongor S.

Nucleic Acids Res. 2007 Jan;35(Database issue):D232-6. Epub 2006 Nov 16.

21.

Surface-antigen expression profiling of B cell chronic lymphocytic leukemia: from the signature of specific disease subsets to the identification of markers with prognostic relevance.

Zucchetto A, Sonego P, Degan M, Bomben R, Dal Bo M, Bulian P, Benedetti D, Rupolo M, Del Poeta G, Campanini R, Gattei V.

J Transl Med. 2006 Mar 1;4:11.

22.

A scoring system based on the expression of six surface molecules allows the identification of three prognostic risk groups in B-cell chronic lymphocytic leukemia.

Zucchetto A, Bomben R, Dal Bo M, Sonego P, Nanni P, Rupolo M, Bulian P, Dal Maso L, Del Poeta G, Del Principe MI, Degan M, Gattei V.

J Cell Physiol. 2006 May;207(2):354-63.

PMID:
16331666
23.

Surface-antigen expression profiling (SEP) in B-cell chronic lymphocytic leukemia (B-CLL): Identification of markers with prognostic relevance.

Zucchetto A, Sonego P, Degan M, Bomben R, Dal Bo M, Russo S, Attadia V, Rupolo M, Buccisano F, Steffan A, Del Poeta G, Pucillo C, Colombatti A, Campanini R, Gattei V.

J Immunol Methods. 2005 Oct 20;305(1):20-32. Epub 2005 Aug 8.

PMID:
16198366
24.

Neurogenic potential of human mesenchymal stem cells revisited: analysis by immunostaining, time-lapse video and microarray.

Bertani N, Malatesta P, Volpi G, Sonego P, Perris R.

J Cell Sci. 2005 Sep 1;118(Pt 17):3925-36. Epub 2005 Aug 9.

25.

Mutational status of IgV(H) genes in B-cell chronic lymphocytic leukemia and prognosis: percent mutations or antigen-driven selection?

Bomben R, Dal Bo M, Zucchetto A, Zaina E, Nanni P, Sonego P, Del Poeta G, Degan M, Gattei V.

Leukemia. 2005 Aug;19(8):1490-2. No abstract available.

PMID:
15944717
26.

Signature of B-CLL with different prognosis by Shrunken centroids of surface antigen expression profiling.

Zucchetto A, Sonego P, Degan M, Bomben R, Dal Bo M, Russo S, Attadia V, Rupolo M, Buccisano F, Del Principe MI, Del Poeta G, Pucillo C, Colombatti A, Campanini R, Gattei V.

J Cell Physiol. 2005 Jul;204(1):113-23.

PMID:
15605425

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