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Items: 14

1.

Kinome-wide identification of phosphorylation networks in Eukaryotic proteomes.

Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M.

Bioinformatics. 2018 Jul 17. doi: 10.1093/bioinformatics/bty545. [Epub ahead of print]

PMID:
30016513
2.

Quantifying compartment-associated variations of protein abundance in proteomics data.

Parca L, Beck M, Bork P, Ori A.

Mol Syst Biol. 2018 Jul 2;14(7):e8131. doi: 10.15252/msb.20178131.

3.

Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC).

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M.

Mol Cell Proteomics. 2018 Apr;17(4):810-825. doi: 10.1074/mcp.RA117.000189. Epub 2018 Jan 23.

4.

Systematic identification of phosphorylation-mediated protein interaction switches.

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB.

PLoS Comput Biol. 2017 Mar 27;13(3):e1005462. doi: 10.1371/journal.pcbi.1005462. eCollection 2017 Mar.

5.

Spatiotemporal variation of mammalian protein complex stoichiometries.

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M.

Genome Biol. 2016 Mar 14;17:47. doi: 10.1186/s13059-016-0912-5.

6.

In situ structural analysis of the human nuclear pore complex.

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M.

Nature. 2015 Oct 1;526(7571):140-143. doi: 10.1038/nature15381. Epub 2015 Sep 23.

7.

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M.

Mol Cell Proteomics. 2015 May;14(5):1350-60. doi: 10.1074/mcp.M114.042499. Epub 2015 Mar 9.

8.

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D494-502. doi: 10.1093/nar/gku1081. Epub 2014 Oct 31.

9.

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.

10.

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.

11.

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.

Minguez P, Letunic I, Parca L, Bork P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D306-11. doi: 10.1093/nar/gks1230. Epub 2012 Nov 28.

12.

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.

13.

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

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

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. Epub 2011 May 26.

14.

Phosphate binding sites identification in protein structures.

Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G.

Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. Epub 2010 Oct 24.

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