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Items: 42

1.

Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry.

Duckworth AD, Gherardini PF, Sykorova M, Yasin F, Nolan GP, Slupsky JR, Kalakonda N.

Nat Protoc. 2019 Feb 6. doi: 10.1038/s41596-018-0120-8. [Epub ahead of print]

PMID:
30728478
2.

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.

Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ.

Cell Rep. 2018 Jul 31;24(5):1377-1388. doi: 10.1016/j.celrep.2018.07.003.

3.

GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP.

Bioinformatics. 2018 Dec 1;34(23):4131-4133. doi: 10.1093/bioinformatics/bty430.

PMID:
29850785
4.

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells.

Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ.

Immunity. 2018 May 15;48(5):1029-1045.e5. doi: 10.1016/j.immuni.2018.04.026.

PMID:
29768164
5.

High response rate to PD-1 blockade in desmoplastic melanomas.

Eroglu Z, Zaretsky JM, Hu-Lieskovan S, Kim DW, Algazi A, Johnson DB, Liniker E, Ben Kong, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph RW, Postow MA, Carlino MS, Hwu WJ, Scolyer RA, Messina J, Cochran AJ, Long GV, Ribas A.

Nature. 2018 Jan 18;553(7688):347-350. doi: 10.1038/nature25187. Epub 2018 Jan 10.

6.

Systemic Immunity Is Required for Effective Cancer Immunotherapy.

Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG.

Cell. 2017 Jan 26;168(3):487-502.e15. doi: 10.1016/j.cell.2016.12.022. Epub 2017 Jan 19.

7.

High-throughput precision measurement of subcellular localization in single cells.

Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP.

Cytometry A. 2017 Feb;91(2):180-189. doi: 10.1002/cyto.a.23054. Epub 2017 Jan 17.

8.

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL.

J Immunol. 2016 Dec 1;197(11):4482-4492. Epub 2016 Oct 28.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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
14.

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.

15.

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

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

Mol Cell Proteomics. 2014 Sep;13(9):2198-212. doi: 10.1074/mcp.M114.039990. Epub 2014 May 15.

16.

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.

17.

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.

18.

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
19.

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
20.

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.

21.

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
22.

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
23.

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.

24.

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.

25.

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.

26.

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
27.

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.

28.

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.

29.

Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani.

Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF.

J Proteomics. 2011 Aug 24;74(9):1644-51. doi: 10.1016/j.jprot.2011.03.024. Epub 2011 Mar 26.

PMID:
21443974
30.

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.

31.

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71. doi: 10.1093/nar/gkq936. Epub 2010 Oct 21.

32.

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses.

Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF.

Proteomics. 2010 Nov;10(21):3868-83. doi: 10.1002/pmic.201000305.

PMID:
20960452
33.

Superpose3D: a local structural comparison program that allows for user-defined structure representations.

Gherardini PF, Ausiello G, Helmer-Citterich M.

PLoS One. 2010 Aug 5;5(8):e11988. doi: 10.1371/journal.pone.0011988.

34.

Modular architecture of nucleotide-binding pockets.

Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M.

Nucleic Acids Res. 2010 Jun;38(11):3809-16. doi: 10.1093/nar/gkq090. Epub 2010 Feb 25.

35.

Identification from chest x-rays: reliability of bone density patterns of the humerus.

Ciaffi R, De Angelis D, Gherardini PF, Arcudi G, Nessi R, Cornalba GP, Grandi M, Cattaneo C.

J Forensic Sci. 2010 Mar 1;55(2):478-81. doi: 10.1111/j.1556-4029.2009.01297.x. Epub 2010 Feb 11.

PMID:
20158592
36.

Structural motifs recurring in different folds recognize the same ligand fragments.

Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M.

BMC Bioinformatics. 2009 Jun 15;10:182. doi: 10.1186/1471-2105-10-182.

37.

Structure-based function prediction: approaches and applications.

Gherardini PF, Helmer-Citterich M.

Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302. doi: 10.1093/bfgp/eln030. Epub 2008 Jul 3. Review.

PMID:
18599513
38.

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.

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

39.

Convergent evolution of enzyme active sites is not a rare phenomenon.

Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ.

J Mol Biol. 2007 Sep 21;372(3):817-45. Epub 2007 Jun 14.

PMID:
17681532
40.

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W416-9. Epub 2007 May 8.

41.

False occurrences of functional motifs in protein sequences highlight evolutionary constraints.

Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M.

BMC Bioinformatics. 2007 Mar 1;8:68.

42.

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.

Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31. Epub 2006 Nov 16.

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