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Results: 1 to 20 of 82

1.

Computational methods for analysis and inference of kinase/inhibitor relationships.

Ferrè F, Palmeri A, Helmer-Citterich M.

Front Genet. 2014 Jun 30;5:196. doi: 10.3389/fgene.2014.00196. eCollection 2014. Review.

PMID:
25071826
[PubMed]
Free PMC Article
2.

A proteome-wide Domain-centric Perspective on Protein Phosphorylation.

Palmeri A, Ausiello G, Ferre F, Helmer-Citterich M, Gherardini PF.

Mol Cell Proteomics. 2014 May 15. pii: mcp.M114.039990. [Epub ahead of print]

PMID:
24830415
[PubMed - as supplied by publisher]
Free PMC Article
3.

A novel approach to represent and compare RNA secondary structures.

Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M.

Nucleic Acids Res. 2014;42(10):6146-57. doi: 10.1093/nar/gku283. Epub 2014 Apr 21.

PMID:
24753415
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D.

Mol Cell Proteomics. 2014 Jul;13(7):1787-99. doi: 10.1074/mcp.M114.037705. Epub 2014 Apr 16.

PMID:
24741111
[PubMed - in process]
5.

Role of CTCF protein in regulating FMR1 locus transcription.

Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferrè F, Helmer-Citterich M, Tabolacci E, Neri G.

PLoS Genet. 2013;9(7):e1003601. doi: 10.1371/journal.pgen.1003601. Epub 2013 Jul 18.

PMID:
23874213
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics.

Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M.

BMC Bioinformatics. 2013;14 Suppl 7:S1. doi: 10.1186/1471-2105-14-S7-S1. Epub 2013 Apr 22.

PMID:
23815154
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

DBATE: database of alternative transcripts expression.

Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferrè F, Helmer-Citterich M.

Database (Oxford). 2013 Jul 9;2013:bat050. doi: 10.1093/database/bat050. Print 2013.

PMID:
23842462
[PubMed - indexed for MEDLINE]
Free Article
8.

Alternative splicing tends to avoid partial removals of protein-protein interaction sites.

Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F.

BMC Genomics. 2013 Jun 7;14:379. doi: 10.1186/1471-2164-14-379.

PMID:
23758645
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

webPDBinder: a server for the identification of ligand binding sites on protein structures.

Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W308-13. doi: 10.1093/nar/gkt457. Epub 2013 Jun 3.

PMID:
23737450
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

Parca L, Ferré F, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W281-5. doi: 10.1093/nar/gkt390. Epub 2013 May 22.

PMID:
23703207
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif.

Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D.

J Proteome Res. 2013 Jul 5;12(7):3405-12. doi: 10.1021/pr4002492. Epub 2013 Jun 11.

PMID:
23688256
[PubMed - indexed for MEDLINE]
12.

Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound.

Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF.

J Proteomics. 2013 Jun 28;86:97-104. doi: 10.1016/j.jprot.2013.05.002. Epub 2013 May 16.

PMID:
23684787
[PubMed - indexed for MEDLINE]
13.

Peamaclein--a new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3.

Tuppo L, Alessandri C, Pomponi D, Picone D, Tamburrini M, Ferrara R, Petriccione M, Mangone I, Palazzo P, Liso M, Giangrieco I, Crescenzo R, Bernardi ML, Zennaro D, Helmer-Citterich M, Mari A, Ciardiello MA.

Clin Exp Allergy. 2013 Jan;43(1):128-40. doi: 10.1111/cea.12028.

PMID:
23278887
[PubMed - indexed for MEDLINE]
14.

Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity.

Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G.

PLoS One. 2012;7(11):e50240. doi: 10.1371/journal.pone.0050240. Epub 2012 Nov 27.

PMID:
23209685
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Experimental and computational methods for the analysis and modeling of signaling networks.

Gherardini PF, Helmer-Citterich M.

N Biotechnol. 2013 Mar 25;30(3):327-32. doi: 10.1016/j.nbt.2012.11.007. Epub 2012 Nov 16. Review.

PMID:
23165097
[PubMed - in process]
16.

Exploring the diversity of SPRY/B30.2-mediated interactions.

Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G.

Trends Biochem Sci. 2013 Jan;38(1):38-46. doi: 10.1016/j.tibs.2012.10.001. Epub 2012 Nov 17. Review.

PMID:
23164942
[PubMed - indexed for MEDLINE]
17.

Mapping the human phosphatome on growth pathways.

Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G.

Mol Syst Biol. 2012;8:603. doi: 10.1038/msb.2012.36.

PMID:
22893001
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

B-Pred, a structure based B-cell epitopes prediction server.

Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A.

Adv Appl Bioinform Chem. 2012;5:11-21. doi: 10.2147/AABC.S30620. Epub 2012 Jul 25.

PMID:
22888263
[PubMed]
Free PMC Article
19.

Deciphering a global network of functionally associated post-translational modifications.

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P.

Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31.

PMID:
22806145
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Modeling gene regulatory network motifs using Statecharts.

Fioravanti F, Helmer-Citterich M, Nardelli E.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S20. doi: 10.1186/1471-2105-13-S4-S20.

PMID:
22536967
[PubMed - indexed for MEDLINE]
Free PMC Article

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