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Items: 1 to 20 of 34

1.

Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State.

Sacco F, Silvestri A, Posca D, Pirrò S, Gherardini PF, Castagnoli L, Mann M, Cesareni G.

Cell Syst. 2016 Mar 23;2(3):159-71. doi: 10.1016/j.cels.2016.02.005. Epub 2016 Mar 3.

PMID:
27135362
2.

Highly multiplexed simultaneous detection of RNAs and proteins in single cells.

Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF.

Nat Methods. 2016 Mar;13(3):269-75. doi: 10.1038/nmeth.3742. Epub 2016 Jan 25.

PMID:
26808670
3.

IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.

Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP.

Science. 2015 Jul 10;349(6244):1259425. doi: 10.1126/science.1259425.

4.

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus.

O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM.

J Allergy Clin Immunol. 2015 Nov;136(5):1326-36. doi: 10.1016/j.jaci.2015.04.008. Epub 2015 May 30.

5.

AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation.

Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F.

Nat Cell Biol. 2015 May;17(5):706. doi: 10.1038/ncb3171. No abstract available.

PMID:
25925585
6.

AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation.

Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F.

Nat Cell Biol. 2015 Jan;17(1):20-30. doi: 10.1038/ncb3072. Epub 2014 Dec 1. Erratum in: Nat Cell Biol. 2015 May;17(5):706.

PMID:
25438055
7.

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]

8.

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.

9.

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.

10.

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
11.

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
12.

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.

13.

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
14.

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
15.

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.

16.

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.

17.

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S17. doi: 10.1186/1471-2105-13-S4-S17.

18.

What has proteomics taught us about Leishmania development?

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

Parasitology. 2012 Aug;139(9):1146-57. doi: 10.1017/S0031182012000157. Epub 2012 Feb 28. Review.

PMID:
22369930
19.

PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae.

Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M.

BMC Genomics. 2011 Dec 19;12:614. doi: 10.1186/1471-2164-12-614.

20.

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.

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