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Items: 1 to 50 of 79

1.

Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity.

Soste M, Charmpi K, Lampert F, Gerez JA, van Oostrum M, Malinovska L, Boersema PJ, Prymaczok NC, Riek R, Peter M, Vanni S, Beyer A, Picotti P.

Cell Syst. 2019 Aug 29. pii: S2405-4712(19)30267-4. doi: 10.1016/j.cels.2019.07.010. [Epub ahead of print]

2.

Publisher Correction: Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Sep;16(9):932. doi: 10.1038/s41592-019-0546-0.

PMID:
31406386
3.

Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Aug;16(8):743-749. doi: 10.1038/s41592-019-0495-7. Epub 2019 Jul 29. Erratum in: Nat Methods. 2019 Sep;16(9):932.

PMID:
31363225
4.

Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis.

Wild P, Susperregui A, Piazza I, Dörig C, Oke A, Arter M, Yamaguchi M, Hilditch AT, Vuina K, Chan KC, Gromova T, Haber JE, Fung JC, Picotti P, Matos J.

Mol Cell. 2019 Aug 22;75(4):859-874.e4. doi: 10.1016/j.molcel.2019.06.022. Epub 2019 Jul 24.

5.

A cullin-RING ubiquitin ligase targets exogenous α-synuclein and inhibits Lewy body-like pathology.

Gerez JA, Prymaczok NC, Rockenstein E, Herrmann US, Schwarz P, Adame A, Enchev RI, Courtheoux T, Boersema PJ, Riek R, Peter M, Aguzzi A, Masliah E, Picotti P.

Sci Transl Med. 2019 Jun 5;11(495). pii: eaau6722. doi: 10.1126/scitranslmed.aau6722.

PMID:
31167929
6.

TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates.

Laferrière F, Maniecka Z, Pérez-Berlanga M, Hruska-Plochan M, Gilhespy L, Hock EM, Wagner U, Afroz T, Boersema PJ, Barmettler G, Foti SC, Asi YT, Isaacs AM, Al-Amoudi A, Lewis A, Stahlberg H, Ravits J, De Giorgi F, Ichas F, Bezard E, Picotti P, Lashley T, Polymenidou M.

Nat Neurosci. 2019 Jan;22(1):65-77. doi: 10.1038/s41593-018-0294-y. Epub 2018 Dec 17.

PMID:
30559480
7.

Phosphorylation of nuclear Tau is modulated by distinct cellular pathways.

Ulrich G, Salvadè A, Boersema P, Calì T, Foglieni C, Sola M, Picotti P, Papin S, Paganetti P.

Sci Rep. 2018 Dec 7;8(1):17702. doi: 10.1038/s41598-018-36374-4.

8.

Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date.

Boersema PJ, Melnik A, Hazenberg BPC, Rezeli M, Marko-Varga G, Kamiie J, Portelius E, Blennow K, Zubarev RA, Polymenidou M, Picotti P.

J Proteome Res. 2018 Dec 7;17(12):4072-4084. doi: 10.1021/acs.jproteome.8b00401. Epub 2018 Sep 28.

PMID:
30137990
9.

The multi-subunit GID/CTLH E3 ubiquitin ligase promotes cell proliferation and targets the transcription factor Hbp1 for degradation.

Lampert F, Stafa D, Goga A, Soste MV, Gilberto S, Olieric N, Picotti P, Stoffel M, Peter M.

Elife. 2018 Jun 18;7. pii: e35528. doi: 10.7554/eLife.35528.

10.

High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds.

Zampieri M, Szappanos B, Buchieri MV, Trauner A, Piazza I, Picotti P, Gagneux S, Borrell S, Gicquel B, Lelievre J, Papp B, Sauer U.

Sci Transl Med. 2018 Feb 21;10(429). pii: eaal3973. doi: 10.1126/scitranslmed.aal3973.

11.

Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides.

Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M.

J Biol Chem. 2018 Apr 13;293(15):5600-5612. doi: 10.1074/jbc.RA117.001484. Epub 2018 Feb 16.

12.

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication.

Piazza I, Kochanowski K, Cappelletti V, Fuhrer T, Noor E, Sauer U, Picotti P.

Cell. 2018 Jan 11;172(1-2):358-372.e23. doi: 10.1016/j.cell.2017.12.006. Epub 2018 Jan 4.

13.

FKBP12 contributes to α-synuclein toxicity by regulating the calcineurin-dependent phosphoproteome.

Caraveo G, Soste M, Cappelleti V, Fanning S, van Rossum DB, Whitesell L, Huang Y, Chung CY, Baru V, Zaichick S, Picotti P, Lindquist S.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11313-E11322. doi: 10.1073/pnas.1711926115. Epub 2017 Dec 11.

14.

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry.

Schopper S, Kahraman A, Leuenberger P, Feng Y, Piazza I, Müller O, Boersema PJ, Picotti P.

Nat Protoc. 2017 Nov;12(11):2391-2410. doi: 10.1038/nprot.2017.100. Epub 2017 Oct 26.

PMID:
29072706
15.

Mitotic Disassembly of Nuclear Pore Complexes Involves CDK1- and PLK1-Mediated Phosphorylation of Key Interconnecting Nucleoporins.

Linder MI, Köhler M, Boersema P, Weberruss M, Wandke C, Marino J, Ashiono C, Picotti P, Antonin W, Kutay U.

Dev Cell. 2017 Oct 23;43(2):141-156.e7. doi: 10.1016/j.devcel.2017.08.020.

16.

Reversible protein aggregation is a protective mechanism to ensure cell cycle restart after stress.

Saad S, Cereghetti G, Feng Y, Picotti P, Peter M, Dechant R.

Nat Cell Biol. 2017 Oct;19(10):1202-1213. doi: 10.1038/ncb3600. Epub 2017 Aug 28.

PMID:
28846094
17.

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability.

Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P.

Science. 2017 Feb 24;355(6327). pii: eaai7825. doi: 10.1126/science.aai7825.

PMID:
28232526
18.

Corrigendum: Cortical dynamics during cell motility are regulated by CRL3KLHL21 E3 ubiquitin ligase.

Courtheoux T, Enchev RI, Lampert F, Gerez J, Beck J, Picotti P, Sumara I, Peter M.

Nat Commun. 2016 Oct 31;7:13487. doi: 10.1038/ncomms13487. No abstract available.

19.

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity.

Geiger R, Rieckmann JC, Wolf T, Basso C, Feng Y, Fuhrer T, Kogadeeva M, Picotti P, Meissner F, Mann M, Zamboni N, Sallusto F, Lanzavecchia A.

Cell. 2016 Oct 20;167(3):829-842.e13. doi: 10.1016/j.cell.2016.09.031. Epub 2016 Oct 13.

20.

Cortical dynamics during cell motility are regulated by CRL3(KLHL21) E3 ubiquitin ligase.

Courtheoux T, Enchev RI, Lampert F, Gerez J, Beck J, Picotti P, Sumara I, Peter M.

Nat Commun. 2016 Sep 19;7:12810. doi: 10.1038/ncomms12810. Erratum in: Nat Commun. 2016 Oct 31;7:13487.

21.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

22.

Erratum: Phosphoproteomics takes it easy.

Picotti P.

Nat Biotechnol. 2016 Apr;34(4):441. doi: 10.1038/nbt0416-441b. No abstract available.

PMID:
27054998
23.

Voices of biotech.

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T.

Nat Biotechnol. 2016 Mar;34(3):270-5. doi: 10.1038/nbt.3502. No abstract available.

PMID:
26963549
24.

The Replisome-Coupled E3 Ubiquitin Ligase Rtt101Mms22 Counteracts Mrc1 Function to Tolerate Genotoxic Stress.

Buser R, Kellner V, Melnik A, Wilson-Zbinden C, Schellhaas R, Kastner L, Piwko W, Dees M, Picotti P, Maric M, Labib K, Luke B, Peter M.

PLoS Genet. 2016 Feb 5;12(2):e1005843. doi: 10.1371/journal.pgen.1005843. eCollection 2016 Feb.

25.

Preparation and Characterization of Stable α-Synuclein Lipoprotein Particles.

Eichmann C, Campioni S, Kowal J, Maslennikov I, Gerez J, Liu X, Verasdonck J, Nespovitaya N, Choe S, Meier BH, Picotti P, Rizo J, Stahlberg H, Riek R.

J Biol Chem. 2016 Apr 15;291(16):8516-27. doi: 10.1074/jbc.M115.707968. Epub 2016 Feb 4.

26.

Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide.

Feng Y, Picotti P.

Methods Mol Biol. 2016;1394:43-56. doi: 10.1007/978-1-4939-3341-9_4.

PMID:
26700040
27.

Relative Infestation Level and Sensitivity of Grapevine Cultivars to the Leafhopper Empoasca vitis (Hemiptera: Cicadellidae).

Fornasiero D, Pavan F, Pozzebon A, Picotti P, Duso C.

J Econ Entomol. 2016 Feb;109(1):416-25. doi: 10.1093/jee/tov313. Epub 2015 Oct 26.

PMID:
26503344
28.

Phosphoproteomics takes it easy.

Picotti P.

Nat Biotechnol. 2015 Sep;33(9):929-30. doi: 10.1038/nbt.3345. No abstract available. Erratum in: Nat Biotechnol. 2016 Apr;34(4):441.

PMID:
26348962
29.

Mitotic redistribution of the mitochondrial network by Miro and Cenp-F.

Kanfer G, Courthéoux T, Peterka M, Meier S, Soste M, Melnik A, Reis K, Aspenström P, Peter M, Picotti P, Kornmann B.

Nat Commun. 2015 Aug 11;6:8015. doi: 10.1038/ncomms9015.

30.

Proteomics beyond large-scale protein expression analysis.

Boersema PJ, Kahraman A, Picotti P.

Curr Opin Biotechnol. 2015 Aug;34:162-70. doi: 10.1016/j.copbio.2015.01.005. Epub 2015 Jan 28. Review.

PMID:
25636126
31.

Modules, networks and systems medicine for understanding disease and aiding diagnosis.

Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M.

Genome Med. 2014 Oct 17;6(10):82. doi: 10.1186/s13073-014-0082-6. eCollection 2014.

32.

Global analysis of protein structural changes in complex proteomes.

Feng Y, De Franceschi G, Kahraman A, Soste M, Melnik A, Boersema PJ, de Laureto PP, Nikolaev Y, Oliveira AP, Picotti P.

Nat Biotechnol. 2014 Oct;32(10):1036-44. doi: 10.1038/nbt.2999. Epub 2014 Sep 14.

PMID:
25218519
33.

A sentinel protein assay for simultaneously quantifying cellular processes.

Soste M, Hrabakova R, Wanka S, Melnik A, Boersema P, Maiolica A, Wernas T, Tognetti M, von Mering C, Picotti P.

Nat Methods. 2014 Oct;11(10):1045-8. doi: 10.1038/nmeth.3101. Epub 2014 Sep 7.

PMID:
25194849
34.

Stepwise priming by acidic pH and a high K+ concentration is required for efficient uncoating of influenza A virus cores after penetration.

Stauffer S, Feng Y, Nebioglu F, Heilig R, Picotti P, Helenius A.

J Virol. 2014 Nov;88(22):13029-46. doi: 10.1128/JVI.01430-14. Epub 2014 Aug 27.

35.

Calcineurin determines toxic versus beneficial responses to α-synuclein.

Caraveo G, Auluck PK, Whitesell L, Chung CY, Baru V, Mosharov EV, Yan X, Ben-Johny M, Soste M, Picotti P, Kim H, Caldwell KA, Caldwell GA, Sulzer D, Yue DT, Lindquist S.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):E3544-52. doi: 10.1073/pnas.1413201111. Epub 2014 Aug 13.

36.

Accumulation of oligomer-prone α-synuclein exacerbates synaptic and neuronal degeneration in vivo.

Rockenstein E, Nuber S, Overk CR, Ubhi K, Mante M, Patrick C, Adame A, Trejo-Morales M, Gerez J, Picotti P, Jensen PH, Campioni S, Riek R, Winkler J, Gage FH, Winner B, Masliah E.

Brain. 2014 May;137(Pt 5):1496-513. doi: 10.1093/brain/awu057. Epub 2014 Mar 24.

37.

A Complete Mass-spectrometric Map of a Eukaryotic Proteome.

Soste M, Picotti P.

Chimia (Aarau). 2013 Sep;67(9):684. No abstract available.

PMID:
24388350
38.

Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring.

Di Girolamo F, Righetti PG, Soste M, Feng Y, Picotti P.

J Proteomics. 2013 Aug 26;89:215-26. doi: 10.1016/j.jprot.2013.05.037. Epub 2013 Jun 7.

PMID:
23747450
39.

Host cell entry of respiratory syncytial virus involves macropinocytosis followed by proteolytic activation of the F protein.

Krzyzaniak MA, Zumstein MT, Gerez JA, Picotti P, Helenius A.

PLoS Pathog. 2013;9(4):e1003309. doi: 10.1371/journal.ppat.1003309. Epub 2013 Apr 11.

40.

Proteomic analysis of F1F0-ATP synthase super-assembly in mitochondria of cardiomyoblasts undergoing differentiation to the cardiac lineage.

Bisetto E, Comelli M, Salzano AM, Picotti P, Scaloni A, Lippe G, Mavelli I.

Biochim Biophys Acta. 2013 Jul;1827(7):807-16. doi: 10.1016/j.bbabio.2013.04.002. Epub 2013 Apr 12.

41.

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.

Zampar GG, Kümmel A, Ewald J, Jol S, Niebel B, Picotti P, Aebersold R, Sauer U, Zamboni N, Heinemann M.

Mol Syst Biol. 2013;9:651. doi: 10.1038/msb.2013.11.

42.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3645-50. doi: 10.1073/pnas.1216918110. Epub 2013 Feb 6.

43.

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis.

Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R.

Nature. 2013 Feb 14;494(7436):266-70. doi: 10.1038/nature11835. Epub 2013 Jan 20.

44.

Proteomics meets the scientific method.

Picotti P, Bodenmiller B, Aebersold R.

Nat Methods. 2013 Jan;10(1):24-7. doi: 10.1038/nmeth.2291. No abstract available.

PMID:
23269373
45.

Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export.

Altvater M, Chang Y, Melnik A, Occhipinti L, Schütz S, Rothenbusch U, Picotti P, Panse VG.

Mol Syst Biol. 2012;8:628. doi: 10.1038/msb.2012.63.

46.

Regulation of yeast central metabolism by enzyme phosphorylation.

Oliveira AP, Ludwig C, Picotti P, Kogadeeva M, Aebersold R, Sauer U.

Mol Syst Biol. 2012;8:623. doi: 10.1038/msb.2012.55.

47.

Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions.

Picotti P, Aebersold R.

Nat Methods. 2012 May 30;9(6):555-66. doi: 10.1038/nmeth.2015. Review.

PMID:
22669653
48.

RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.

Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm LJ, Kaufman E, Wollscheid B, Simard MJ, Miska EA, Aebersold R, Gerber AP, Hengartner MO.

Genome Res. 2012 Jul;22(7):1360-71. doi: 10.1101/gr.133330.111. Epub 2012 Mar 27.

49.

Protein significance analysis in selected reaction monitoring (SRM) measurements.

Chang CY, Picotti P, Hüttenhain R, Heinzelmann-Schwarz V, Jovanovic M, Aebersold R, Vitek O.

Mol Cell Proteomics. 2012 Apr;11(4):M111.014662. doi: 10.1074/mcp.M111.014662. Epub 2011 Dec 21.

50.

IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.

Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, Bauman AT, Picotti P, Schmidt A, van Belle G, Aebersold R, Kolker E.

J Proteomics. 2011 Dec 10;75(1):116-21. doi: 10.1016/j.jprot.2011.06.003. Epub 2011 Jun 21.

PMID:
21718813

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