Publikationen

2013

55 Kamburov A, Stelzl U, Lehrach H, Herwig R.  The ConsensusPathDB interactiondatabase: 2013 update.  Nucleic Acids Res. 2013 Jan;41(Database issue):D793-800.

54 Petrakis S, Schaefer MH, Wanker EE, Andrade-Navarro MA. Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners.  BioEssays 35 (6): 503-507.

53  Suter B, Fontaine JF, Yildirimman R, Rasko T, Schaefer MH, Rasche A, Porras P, Vazquez-Alvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE.  Development and application of a DNA microarray-based yeast two-hybrid system.  Nucleic Acids Research 41 (3): 1496-507.

52 Weimann M, Grossmann A, Woodsmith J, Ozkan Z, Birth P, Meierhofer D, Benlasfer N, Valovka T, Timmermann B, Wanker EE, Sauer S, Stelzl U.  A Y2H-seq approach defines the human protein methyltransferase interactome.  Nat Methods. 2013 10:  doi: 10.1038/nmeth.2397.

2012

51 Bieschke J, Herbst M, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, Lopez Del Amo JM, Gruening BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Faendrich M, Frank RF, Reif B, Guenther S, Walsh DM, Wanker EE. Small-molecule conversion of toxic oligomers to nontoxic {beta}-sheet-rich amyloid fibrils.  Nat Chemical Biology 8 (1): 93-101.

50 Chua JJ, Butkevich E, Worseck JM, Kittelmann M, Grønborg M, Behrmann E, Stelzl U, Pavlos NJ, Lalowski MM, Eimer S, Wanker EE, Klopfenstein DR, Jahn R.  Phosphorylation-regulated axonal dependent transport of syntaxin 1 is mediated by a Kinesin-1 adapter.  Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5862-7.

49 Haupt A., G. Joberty, M. Bantscheff, H. Fröhlich, H. Stehr, M. R. Schweiger, A. Fischer, M. Kerick, S.T. Boerno, A. Dahl, M. Lappe, H. Lehrach, C. Gonzalez, G. Drewes and B.M.H. Lange. Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics. BMC Cancer, 12(1):38. [Epub ahead of print], (2012).

48 Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, Will CL, Pena V, Lührmann R, Stelzl U.  Dynamic protein-protein interaction wiring of the human spliceosome.  Mol Cell. 2012 Feb 24;45(4):567-80.

47 Kamburov A, Grossmann A, Herwig R, Stelzl U.  Cluster-based assessment ofprotein-protein interaction confidence.  BMC Bioinformatics. 2012 Oct 10;13:262.doi: 10.1186/1471-2105-13-262.

46 Kamburov A, Stelzl U, Herwig R.  IntScore: a web tool for confidence scoring ofbiological interactions.  Nucleic Acids Res. 2012 Jul;40(Web Server issue):W140-6. doi: 10.1093/nar/gks492.

45 Petrakis S, Rasko T, Russ J, Friedrich RP, Stroedicke M, Riechers SP, Muehlenberg K, Moeller A, Reinhardt A, Vinayagam A, Schaefer MH, Boutros M, Tricoire H, Andrade-Navarro MA, Wanker EE.  Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1.  PLoS Genetics 8 (8): e1002897.

44 Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.  HIPPIE: Integrating protein interaction networks with experiment based quality scores.  PLoS One. 2012;7(2):e31826.

43 Schaefer MH, Wanker EE, Andrade-Navarro MA.  Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks.  Nucleic Acids Res. 2012 Jan 28.

2011

42 Barbosa-Silva, A., J.F. Fontaine, E.R. Donnard, F. Stussi, J. Miguel-Ortega and M.A. Andrade-Navarro. 2011. PESCADOR, a web-based tool to extract and study biointeractions from PubMed queries. BMC Bioinformatics. 12:435.

41 Bieschke J, Herbst M, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, Lopez del Amo JM, Grüning BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Fändrich M, Frank RF, Reif B, Günther S, Walsh DM, Wanker EE. Small-molecule conversion of toxic oligomers to nontoxic ?-sheet-rich amyloid fibrils. Nat Chem Biol. 2011 Nov 20;8(1):93-101.

40 Dasari M, Espargaro A, Sabate R, Lopez Del Amo JM, Fink U, Grelle G, Bieschke J, Ventura S, Reif B. Bacterial inclusion bodies of Alzheimer's disease beta-amyloid peptides can be employed to study native-like aggregation intermediate states. Chembiochem. 2011 Feb 11;12(3).

39 Donnard, E., A. Barbosa-Silva, R.M. Guedes, G. Fernandes, H. Velloso, M.J. Kohn, M.A. Andrade-Navarro, J.M. Ortega. 2011. Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics 2011, 12 Suppl 4:S3.

38 Elefsinioti A, Sarac OS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. Large-scale de novo prediction of physical protein-protein association. Mol Cell Proteomics. 2011 Nov;10(11):M111.010629.

37 Fontaine, J.F., F. Priller, A. Barbosa-Silva, M.A. Andrade-Navarro. 2011. Génie: literature-basedgene prioritization at multi genomic scale. Nucleic Acids Research. 39:W455-W461.

36 Gilbert DF, Erdmann G, Zhang X, Fritzsche A, Demir K, Jaedicke A, Muehlenberg K, Wanker EE, Boutros M. A novel multiplex cell viability assay for high-throughput RNAi screening. PLoS One. 2011;6(12):e28338. doi:10.1371/journal.pone.0028338

35 Grelle G, Otto A, Lorenz M, Frank RF, Wanker EE, Bieschke. Black tea theaflavins inhibit formation of toxic amyloid-? and ?-synuclein fibrils. Biochemistry. 2011 Dec 13;50(49):10624-36.

34 Krallinger, M., M. Vazquez, F. Leitner, D. Salgado, A. Chatr-aryamontri, A. Winter, L. Perfetto, L. Briganti, L. Licata, M. Iannuccelli, L. Castagnoli, G. Cesareni, M. Tyers, G. Schneider, F. Rinaldi, R. Leaman, G. Gonzalez, S. Matos, S. Kim, W.J. Wilbur, L. Rocha, H. Shatkay, A.V. Tendulkar, S. Agarwal, F. Liu, X. Wang, R. Rak, K. Noto, C. Elkan, Z. Lu, R.I. Dogan, J.F. Fontaine, M.A. Andrade-Navarro and A. Valencia. 2011. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics. 12 Suppl 8:S3.

33 Lopes, T.J., M. Schaefer, J. Schoemaker, Y. Matsuoka, J.F. Fontaine, G. Neumann, M.A. Andrade-Navarro, Y. Kawaoka and H. Kitano. 2011. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics. 27:2414-2421.

32 Paul FE; Hosp F; Selbach M. Analyzing protein-protein interactions by quantitative mass spectrometry. Methods : (2011-03-04)

31 Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., Selbach, M. (2011). Global quantification of mammalian gene expression control. Nature. 2011 May 19;473(7347):337-42.

30 Soler-Lopez M, Zanzoni A, Lluis R, Stelzl U, Aloy P. Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome Res. 2011 Mar;21(3):364-76.

29 Stehr H.; Jang, S.-H.J.; Duarte, J.M.; Wierling, C.; Lehrach, H.; Lappe, M.; Lange, B.M.H. The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. Molecular Cancer, 10:54. (2011).

28 Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE. A directed protein interaction network for investigating intracellular signal transduction. Sci Signal. 2011 Sep 6;4(189):rs8.

2010

27 Barbosa-Silva A, Soldatos TG, Magalhães ILF, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR - literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics 2010; 11:70. doi 10.1186/1471-2105-11-70

26 Bieschke J, Russ J, Friedrich RP, Ehrnhoefer DE, Wobst H, Neugebauer K, Wanker, EE. EGCG remodels mature [alpha]-synuclein and amyloid-[beta] fibrils and reduces cellular toxicity. Proceedings of the National Academy of Sciences. 2010 Apr; (Epub ahead of print). doi 10.1073/pnas.0910723107

25 Bieschke J. Gruener Tee - neue Einsichten fuer einen alten Wirkstoff [Green tea - new insights for an old drug]. Chemie in unserer Zeit 44 (4): 306-307 (2010-08).

24 Enokido Y, Tamura T, Ito H, Arumughan A, Komuro A, Shiwaku H, Sone M, Foulle R, Sawada H, Ishiguro H, Ono T, Murata M, Kanazawa I, Tomilin N, Tagawa K, Wanker EE, Okazawa H. Mutant huntingtin impairs Ku70-mediated DNA repair. J Cell Biol. 189:425-43

23 Goehler H, Dröge A, Lurz R, Schnoegl S, Chernoff YO, Wanker EE. Pathogenic polyglutamine tracts are potent inducers of spontaneous Sup35 and Rnq1 amyloidogenesis. PLoS ONE. 2010 Mar; 5 (3):e9642. doi 10.1371/journal.pone.0009642

22 Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol. 2010 Mar 1; 11(3):R24. doi 10.1186/gb-2010-11-3-r24

21 Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression.PLoS Comput Biol.  2010 Sep 9;6(9). pii: e1000925.

20 Luber CA; Cox J; Lauterbach H; Fancke B; Selbach M; Tschopp J; Akira S; Wiegand M; Hochrein H; O'Keeffe M; Mann M. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells Immunity 32 (2): 279-289 (2010-02-26)

19 Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 2010 Jan; 38(Database issue):D190-195. doi 10.1093/nar/gkp951

18 Müller, H.; Mirgorodskaya, E.; Steinbrink, S.; Schmidt, D.; Lehmann, V.; Habermann, K.; Gustavsson, N.; Kessler, T.; Ploubidou, A.; Lehrach, H.; Gobom, J.; Boutros, M.; Lange, B.M.H. Proteomic and functional analysis of the Drosophila centrosome. The EMBO Journal advance online publication 3 September 2010; doi:10.1038/emboj.2010.210

17 Scholz, A.-K.; Klebl, B.M.; Morkel, M; Lehrach, H.; Dahl, A.; Lange, B.M.H. A flexible multi-well format for immunofluorescence screening microscopy of small molecule inhibitors. Assay Drug Dev Technol. 8:571-80 (2010).

16 Soler-Lopez M, Zanzoni A, Lluis R, Stelzl U, Aloy P. Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome Res. 2011 Mar;21(3):364-76.

15 Sury MD; Chen JX; Selbach M. The SILAC fly allows for accurate protein quantification in vivo Molecular & Cellular Proteomics 9 (10): 2173-2183 (2010-10)

14 Sylvester M, Kliche S, Lange S, Geithner S, Klemm C, Schlosser A, Grossmann A, Stelzl U, Schraven B, Krause E, Freund C. Adhesion and degranulation promoting adapter protein (ADAP) is a central hub for phosphotyrosine-mediated interactions in T cells. PLoS One. 2010 Jul 22;5(7):e11708.

13 Vinayagam A, Stelzl U, Wanker EE. Repeated two-hybrid screening detects transient protein-protein interactions. Theoretical Chemistry Accounts 125 (3-6): 613-619 (2010-03).

2009

12 Bundesministerium für Bildung und Forschung, ed. Was Alzheimer und Parkinson verbindet. In: Impulsgeber Lebenswissenschaften. Forschung für die Innovationen der Zukunft. Bielefeld: Bertelsmann 2009, p. 54.

11 Chaurasia G, Malhotra S, Russ J, Schnoegl S, Hänig C, Wanker EE, Futschik Me. UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. Nucl. Acids Res. 2009 Jan; 37 (suppl_1):D657-660. doi 10.1093/nar/gkn841

10 Chirasani SR, Markovic DS, Synowitz M, Eichler SA, Wisniewski P, Kaminska B, Otto A, Wanker E, Schäfer M, Chiarugi P, Meier JC, Kettenmann H, Glass R. Transferrin-receptor-mediated iron accumulation controls proliferation and glutamate release in glioma cells. Journal of Molecular Medicine (Berlin, Germany). 2009 Feb; 87 (2):153-167. doi 10.1007/s00109-008-0414-3

9 Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, Mann M. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nature Protocols. 2009 Apr; 4(5):698-705. doi 10.1038/nprot.2009.36

8 Fontaine J, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA. MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Research 2009; 37:W141-W146. doi 10.1093/nar/gkp353

7 Kegel KB, Schewkunow V, Sapp E, Masso N, Wanker EE, DiFiglia M, Goldmann WH. Polyglutamine expansion in huntingtin increases its insertion into lipid bilayers. Biochemical and Biophysical Research Communications. 2009 Sep;  387 (3):472-475. doi 10.1016/j.bbrc.2009.07.039

6 Müller, H.; Mirgorodskaya, E.; Steinbrink, S.; Schmidt, D.; Lehmann, V.; Habermann, K.; Gustavsson, N.; Kessler, T.; Ploubidou, A.; Lehrach, H.; Gobom, J.; Boutros, M.; Lange, B.M.H. Proteomic and functional analysis of the Drosophila centrosome. The EMBO Journal advance online publication 3 September 2010; doi:10.1038/emboj.2010.210

5 Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, Arumughan A, Foulle R, Porras P, Sanchez-Pulido L, Wanker EE, Andrade-Navarro MA. Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput Biol. 2009 5: e1000304. doi 110.1371/journal.pcbi.1000304

4 Schwanhäusser B, Gossen M, Dittmar G, Selbach M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics. 2009 Jan; 9(1):205-209. doi 10.1002/pmic.200800275

3 Tamura T, Sone M, Yamashita M, Wanker EE, Okazawa H. Glial cell lineage expression of mutant ataxin-1 and huntingtin induces developmental and late-onset neuronal pathologies in Drosophila models. PLoS ONE. 2009 Jan; 4 (1):e4262. doi 10.1371/journal.pone.0004262

2 Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, SmolyarA, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M. An empiricalframework for binary interactome mapping. Nature Methods. 2009 Jan; 6 (1):83-90. doi 10.1038/nmeth.1280

1 Vermeulen M, Selbach M. Quantitative proteomics: a tool to assess cell differentiation. Current Opinion in Cell Biology. 2009 Dec; 21(6):761-766. doi 10.1016/j.ceb.2009.09.003