88 Dreher F., Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, Karl Schellander, Hans Lehrach, Bodo M.H. Lange and Ralf Herwig. DIPSBC - Data Integration Platform for Systems Biology Collaborations BMC Bioinformatics 2012, 13:85 [Epub ahead of print], (2012).

87 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, Jan 25;12(1):38. [Epub ahead of print], (2012).

86 Jurmeister S, Baumann M, Balwierz A, Keklikoglou I, Ward A, Uhlmann S, Zhang JD, Wiemann S, Sahin O.  MicroRNA-200c Represses Migration and Invasion of Breast Cancer Cells by Targeting Actin-Regulatory Proteins FHOD1 and PPM1F.  Mol Cell Biol 32: 633-651.

85 Keklikoglou I, Koerner C, Schmidt C, Zhang JD, Heckmann D, Shavinskaya A, Allgayer H, Guckel B, Fehm T, Schneeweiss A, Sahin O, Wiemann S, Tschulena U.  MicroRNA-520/373 family functions as a tumor suppressor in estrogen receptor negative breast cancer by targeting NF-kappaB and TGF-beta signaling pathways.  Oncogene. Epub

84 Lisauskas T, Matula P, Claas C, Reusing S, Wiemann S, Erfle H, Lehmann L, Fischer P, Rohr K, Starkuviene V. Live-cell assays to identify regulators of ER-to-Golgi trafficking Traffic 13: 416-432.

83 Shamu C, Wiemann S, Boutros M.  On target: A public repository for large-scale RNAi experiments. Nat Cell Biology 14: 115.

82 Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H, Bexiga MG, Singan VR, Heriche JK, Neumann B, Mateos A, Blake J, Bechtel S, Benes V, Wiemann S, Ellenberg J, Pepperkok R. Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway.  Nat Cell Biology: accepted.

81 Uhlmann S, Mannsperger H, Zhang JD, Horvat E-A, Schmidt C, Küblbeck M, Henjes F, Ward A, Tschulena U, Zweig K, Korf U, Wiemann S, Sahin O.  Global microRNA level regulation of EGFR-driven cell cycle protein network in breast cancer.  Mol Syst Biol 8: 570.

80 van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC.  Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol.  2012;8:571. PMID: 22373819.

79 Walde S, Thakar K, Hutten S, Spillner C, Nath A, Rothbauer U, Wiemann S, Kehlenbach RH.  The Nucleoporin Nup358/RanBP2 Promotes Nuclear Import in a Cargo- and Transport Receptor-Specific Manner.  Traffic 13: 218-233.

78 Ward A, Balwierz A, Zhang JD, Küblbeck M, Pawitan Y, Hielscher T, Wiemann S, Sahin O.  Re-expression of microRNA-375 reverts both tamoxifen resistance and accompanied EMT-like properties in breast cancer.  Oncogene: 10.1038/onc.2012.128.


77 Bai SW, Herrera-Abreu MT, Rohn J, Racine V, Tajadura V, Suryavanshi N, Bechtel S, Wiemann S, Baum B, Ridley AJ. A novel strategy to identify and characterize a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. BMC Biology 9: 54.

76 Becla, L., Lunshof, J.E., Gurwitz, D., Schulte In den Bäumen, T., Westerhoff, H.V., Lange, B.M.H., Brand, A. Health technology assessment in the era of personalized health care. Int J Technol Assess Health Care, 30:1-9

75 Bender C, von der Heyde S, Henjes F, Wiemann S, Korf U, Beissbarth T. Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. BMC Bioinformatics 12: 291.

74 Brase JC, Johannes M, Mannsperger H, Fälth M, Metzger J, Meister L, Meister M, Kacprzyk LA, Andrasiuk T, Sirma H, Sauter G, Simon R, Schlomm T, Beissbarth B, Korf U, Kuner R, Sültmann H. TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling. BMC Cancer 11, 507.PMID: 22142399

73 Chiocchetti A, Pakalapati G, Duketis E, Wiemann S, Poustka A, Poustka F, Klauck SM. Mutation and expression analyses of the ribosomal protein gene RPL10 in an extended German sample of patients with autism spectrum disorder. Am J Med Genet A 155: 1472-1475.

72 Conrad C, Wünsche A, Tan TH, Bulkescher J, Sieckmann F, Verissimo F, Edelstein A, Walter T, Liebel U, Pepperkok R, Ellenberg J. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods. 2011 Mar;8(3):246-9. Epub 2011 Jan 23.

71 Grade M, Hummon AB, Camps J, Emons G, Spitzner M, Gaedcke J, Hoermann P, Ebner R, Becker H, Difilippantonio MJ, Ghadimi BM, Beissbarth T, Caplen NJ, Ried T. A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets. Int J Cancer. 2011; 128(5):1069-79.

70 Jung K, Becker B, Brunner B, Beißbarth T. Comparison of Global Tests for Functional Gene Sets in Two-Group Designs and Selection of Potentially Effect-causing Genes. Bioinformatics, 2011, epub.

69 Keklikoglou I, Koerner C, Schmidt C, Zhang JD, Heckmann D, Shavinskaya A, Allgayer H, Guckel B, Fehm T, Schneeweiss A, Sahin O, Wiemann S, Tschulena U. MicroRNA-520/373 family functions as a tumor suppressor in estrogen receptor negative breast cancer by targeting NF-kappaB and TGF-beta signaling pathways. Oncogene. Epub

68 Ritzerfeld J, Remmele S, Wang T, Temmerman K, Brügger B, Wegehingel S, Tournaviti S, Strating JR, Wieland FT, Neumann B, Ellenberg J, Lawerenz C, Hesser J, Erfle H, Pepperkok R, Nickel W. Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases. Genome Research

67 Seebacher J, Gavin AC. SnapShot: Protein-protein interaction networks. Cell. 2011;144(6):1000. PMID:21414489

66 Stehr H, Seon-Hi J Jang, José M Duarte, Christoph Wierling, Hans Lehrach, Michael Lappe and Bodo MH Lange. The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. Molecular Cancer, May 16;10:54. (2011).

65 Zhang JD, Koerner C, Bechtel S, Bender C, Keklikoglou I, Schmidt C, Irsigler A, Ernst U, Sahin O, Wiemann S, Tschulena U. Time-resolved human kinome RNAi screen identifies a network regulating mitotic-events as early regulators of cell proliferation. PLoS ONE 6: e22176.


64 Bender C, Henjes F, Fröhlich H, Wiemann S, Korf U and Beißbarth T. Dynamic Deterministic Effects Propagation Networks for learning signalling pathways from reverse phase protein array time series data. Bioinformatics 2010, 26, i596-602.

63 Brase JC, Johannes M, Schlomm T, Falth M, Haese A, Steuber T, Beissbarth T, Kuner R, Sultmann H. Circulating miRNAs are correlated with tumor progression in prostate cancer. Int J Cancer. doi:10.1002/ijc.25376

62 Brase JC, Mannsperger H, Frohlich H, Gade S, Schmidt C, Wiemann S, Beissbarth T, Schlomm T, Sultmann H, Korf U. Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification. Proteome Sci 8: 36.

61 Domschke C, Schuetz F, Sommerfeldt N, Rom J, Scharf A, Sohn C, Schneeweiss A, Beckhove P. Effects of distant metastasis and peripheral CA 15-3 on the induction of spontaneous T cell responses in breast cancer patients. Cancer Immunol Immunother 59: 479-486.

60 Ebert AD, Laussmann M, Wegehingel S, Kaderali L, Erfle H, Reichert J, Lechner J, Beer HD, Pepperkok R, Nickel W. Tec-Kinase-mediated Phosphorylation of Fibroblast Growth Factor 2 Is Essential for Unconventional Secretion. Traffic. doi:10.1111/j.1600-0854.2010.01059.

59 Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods 7: S56-68.

58 Grecco HE, Roda-Navarro P, Girod A, Hou J, Frahm T, Truxius DC, Pepperkok R, Squire A, Bastiaens PI. In situ analysis of tyrosine phosphorylation networks by FLIM on cell arrays. Nat Methods 7: 467-472.

57 Haller F, Von Heydebreck A, Zhang J, Gunawan B, Langer C, Ramadori G, Wiemann S, Sahin O. Localisation- and mutation-dependent microRNA (miRNA) expression signatures in gastrointestinal stromal tumors (GISTs), with a cluster of coexpressed miRNAs located at 14q32.31. J Pathol 220: 71-86.

56 Jöcker A, Sonntag J, Henjes F, Goetschel F, Tresch A, Beißbarth T, Wiemann S, Korf U. QuantProReloaded: Quantitative Analysis of Microspot Immunoassays. Bioinformatics, 2010, 26(19):2480-1.

55 Jung K, Grade M, Gaedcke J, Jo P, Opitz L, Becker H, Ghadimi BM, Beissbarth T. A new sensitivity-preferred strategy to build prediction rules for therapy response of cancer patients using gene expression data. Comput Methods Programs Biomed. 2010 Apr 9.

54 Mannsperger H, Gade S, Wiemann S, Sültmann H, Beißbarth T, Korf U. RPPanalyzer: Analysis of reverse phase protein array data. Bioinformatics, 2010, 26(17):2202-3.

53 Mannsperger HA, Uhlmann S, Schmidt C, Wiemann S, Sahin O, Korf U RNAi-based validation of antibodies for reverse phase protein arrays. Proteome Sci 8: 69.

52 Marmé F, Werft W, Benner A, Burwinkel B, Sinn P, Sohn C, Lichter P, Hahn M, Schneeweiss A. FGFR4 Arg388 genotype is associated with pathological complete response to neoadjuvant chemotherapy for primary breast cancer. Ann Oncol. 2010 Feb 10. [Epub ahead of print]PMID: 20147743 [PubMed - as supplied by publisher]Related articles

51 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. EMBO Journal, 29:3344-3357 (2010).

50 Neumann B, Walter T, Heriche JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wunsche A, Satagopam V, Schmitz MH, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters JM, Hyman AA, Durbin R, Pepperkok R, Ellenberg J. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464: 721-727.

49 O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Heriche JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B. Visualizing biological data-now and in the future. Nat Methods 7: S2-4.

48 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).

47 Subramanian D, Laketa V, Muller R, Tischer C, Zarbakhsh S, Pepperkok R, Schultz C. Activation of membrane-permeant caged PtdIns(3)P induces endosomal fusion in cells. Nat Chem Biol 6: 324-326.

46 Uhlmann S, Zhang JD, Mannsperger H, Schwäger A, Ward A, Burmester S, Riazalhosseini Y, Korf U, Wiemann S, Sahin Ö. miR-200bc/429 cluster targets PLCgamma1 and differentially regulates proliferation and EGF-driven invasion than miR-200a/141 in breast cancer. Oncogene 29: 4297-4306.

45 Walter T, Held M, Neumann B, Heriche JK, Conrad C, Pepperkok R, Ellenberg J. Automatic identification and clustering of chromosome phenotypes in a genome wide RNAi screen by time-lapse imaging. J Struct Biol 170: 1-9.

44 Will, R. et al. Myomasp/LRRC39, a Heart- and Muscle-Specific Protein, Is a Novel Component of the Sarcomeric M-Band and Is Involved in Stretch Sensing. Circ Res. Nov 12;107(10):1253-64. Epub 2010 Sep 16.


43 Bartz F, Kern L, Erz D, Zhu M, Gilbert D, Meinhof T, Wirkner U, Erfle H, Muckenthaler M, Pepperkok R, Runz H (2009) Identification of cholesterol-regulating genes by targeted RNAi screening. Cell Metab 2009 10: 63-75.

42 Chan S, Romieu G, Huober J, Delozier T, Tubiana-Hulin M, Schneeweiss A, Lluch A, Llombart A, du Bois A, Kreienberg R, Mayordomo JI, Antón A, Harrison M, Jones A, Carrasco E, Vaury AT, Frimodt-Moller B, Fumoleau P. Phase III study of gemcitabine plus docetaxel compared with capecitabine plus docetaxel for anthracycline-pretreated patients with metastatic breast cancer. J Clin Oncol. 2009 Apr 10;27(11):1753-60. Epub 2009 Mar 9.

41 Domschke C, Schuetz F, Ge Y, Seibel T, Falk C, Brors B, Vlodavsky I, Sommerfeldt N, Sinn HP, Kühnle MC, Schneeweiss A, Scharf A, Sohn C, Schirrmacher V, Moldenhauer G, Momburg F, Beckhove P. Intratumoral cytokines and tumor cell biology determine spontaneous breast cancer-specific immune responses and their correlation to prognosis. Cancer Res. 2009 Nov 1;69(21):8420-8. Epub 2009 Oct 20.

40 Eichbaum M, Bischofs E, Nehls K, Schneeweiss A, Sohn C. Bendamustine hydrochloride ? A renaissance of alkylating strategies in anticancer medicine. Drugs Today (Barc) 45:431-444, 2009.

39 Eichbaum MH, Weiss LM, Bruckner T, Schneeweiss A, Sinn HP, Gebauer G, Fersis N, Kussmaul J, Sohn C. Prognostic impact of hemoglobin levels before and during carboplatin/taxane-based chemotherapy in patients with primary invasive epithelial ovarian cancer. Med Sci Monit 15:CR156-63, 2009.

38 Froehlich H, Sahin Ö, Arlt D, Bender C, Beissbarth T. Deterministic Effects Propagation Networks for Reconstructing Protein Signaling Networks from Multiple Interventions. BMC Bioinformatics, 2009, 10(10):R104.

37 Froehlich H, Tresch A, Beissbarth T. Nested Effects Models for Learning Signaling Networks from Perturbation Data. Biometrical Journal, 2009, 51(2):304-23.

36 George AJ, Gordon L, Beissbarth T, Koukoulas I, Holsinger DRM, Perreau V, Cappai R, Tan SS, Masters CL, Scott HS, Li QX. A Serial Analysis of Gene Expression (SAGE) profile of the Alzheimer's disease Tg2576 mouse model.  Neurotoxicity Research, Volume 17, Number 4, 360-379, DOI: 10.1007/s12640-009-9112-3.

35 Guipponi M, Li QX, Hyde L, Beissbarth T, Smyth GK, Masters CL, Scott HS. SAGE Analysis of Genes Differentially Expressed in Presymptomatic TgSOD1(G93A) Transgenic Mice Identified Cellular Processes Involved in Early Stage of ALS Pathology. J Mol Neurosci. 2010 May;41(1):172-82. Epub 2009 Dec 2.

34 Hartmann M, Jackisch C, Raab G, Schneeweiss A, Possinger K, Oyee J, Harbeck N. Cost-utility analysis for advanced breast cancer therapy in Germany: results of the fulvestrant sequencing model. Breast Cancer Res Treat. 2009 Sep;117(2):305-17. Epub 2009 Jan 8.

33 Heck S, Rom J, Thewes V, Becker N, Blume B, Sinn HP, Deuschle U, Sohn C, Schneeweiss A, Lichter P. Estrogen-related receptor alpha expression and function is associated with the transcriptional coregulator AIB1 in breast carcinoma. Cancer Res. 2009 Jun 15;69(12):5186-93. Epub 2009 Jun 2.

32 Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, Paton NW (2009) Modeling and managing experimental data using FuGE. OMICS 2009 13: 239-251.

31 Korf U, Lobke C, Sahin O, Haller F, Sultmann H, Arlt D, Poustka A. Reverse-phase protein arrays for application-orientated cancer research. Proteomics Clinical Applications. 2009. 3(10):1140-1150. DOI: 10.1002/prca.200780035 

30 Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castano-Diez D, Chen WH, Devos D, Guell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Bottcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC (2009) Proteome organization in a genome-reduced bacterium. Science 2009 326: 1235-1240.

29 Ling KH, Hewitt CA, Beissbarth T, Hyde L, Banerjee K, Cheah PS, Cannon PZ, Hahn CN, Thomas PQ, Smyth GK, Tan SS, Thomas S, Scott HS. Transcriptome profiling of the developing mouse cerebral cortex reveals spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts. Genom Biol, 2009, 10(10):R104.

28 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

27 Rochet N, Sterzing F, Jensen AD, Dinkel J, Herfarth KK, Schubert K, Eichbaum MH, Schneeweiss A, Sohn C, Debus J, Harms W. Intensity-modulated whole abdominal radiotherapy after surgery and carboplatin/taxane chemotherapy for advanced ovarian cancer: phase I study. Int J Radiat Oncol Biol Phys 2009 [Epub ahead of print].

26 Rom J, von Minckwitz G, Marmé F, Ataseven B, Kozian D, Sievert M, Schlehe B, Schuetz F, Scharf A, Kaufmann M, Sohn C, Schneeweiss A. Phase I study of apoptosis gene modulation with oblimersen within preoperative chemotherapy in patients with primary breast cancer. Ann Oncol. 2009 Nov;20(11):1829-35. Epub 2009 Jul 15.

25 Sahin O, Froehlich H, Löbke C, Korf U, Burmester S, Majety M, Mattern J, Schupp I, Chaouiya C, Thieffry D, Poustka A, Wiemann S, Beissbarth T, Arlt D. Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol. 2009 Jan 1;3:1.

24 Sahin O, Wiemann S. Functional genomics and proteomics approaches to study the ERBB network in cancer. FEBS Lett. 2009 Jun 5;583(11):1766-71. Epub 2009 Mar 20.

23 Schuetz F, Ehlert K, Ge Y, Schneeweiss A, Rom J, Inzkirweli N, Sohn C, Schirrmacher V, Beckhove P. Treatment of advanced metastasized breast cancer with bone marrow-derived tumour-reactive memory T cells: a pilot clinical study. Cancer Immunol Immunother. 2009 Jun;58(6):887-900. Epub 2008 Nov 8.

22 Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. MGC Project Team.  The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-33. Epub 2009 Sep 18.

21 Untch M, Möbus V, Kuhn W, Muck BR, Thomssen C, Bauerfeind I, Harbeck N, Werner C, Lebeau A, Schneeweiss A, Kahlert S, von Koch F, Petry KU, Wallwiener D, Kreienberg R, Albert US, Lück HJ, Hinke A, Jänicke F, Konecny GE. Intensive dose-dense compared with conventionally scheduled preoperative chemotherapy for high-risk primary breast cancer. J Clin Oncol. 2009 Jun 20;27(18):2938-45. Epub 2009 Apr 13.

20 Zhang, J. D. & Wiemann, S. KEGGgraph: a graph approach to KEGG PATHWAY in R and Bioconductor. Bioinformatics. 2009 Jun; 25(11):1470-1.

19 Zhang, JD., Duda, A., Schmidt, C., Irsigler, A., Wiemann, S. and Tschulena, U. (2009). Analyzing the Effect of Gene Knock-Down in Real-Time Using Roche?s xCELLigence System. Biochemica, 09/02.

18 Zhang, JD., Ernst, U., Irsigler, A., Wiemann, S. and Tschulena, U. (2009). qPCR Identification of Genes Involved in Apoptosis and Cell Cycle Regulation. Biochemica, 09/02.


17 Bender C, Froehlich H, Johannes M, Beissbarth T. Extending pathways with inferred regulatory interactions from microarray data and protein domain signatures. Proceedings of CAMDA, 2008.

16 Froehlich H, Beissbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F. Analyzing Gene Perturbation Screens With Nested Effects Models in R and Bioconductor. Bioinformatics, 2008, 24(21):2549-50.

15 Froehlich H, Fellmann M, Sueltmann H, Poustka A, Beissbarth T. Estimating Large Scale Signaling Networks through Nested Effects Models from Intervention Effects in Microarray Data. Bioinformatics, 2008, 24(22):2650-6

14 Froehlich H, Fellmann M, Sueltmann H, Poustka A, Beissbarth T. Predicting Pathway Membership via Domain Signatures. Bioinformatics, 2008, 24(19):2137-42.

13 Hahne F, Mehrle A, Arlt D, Poustka A, Wiemann S, Beissbarth T. Extending pathways based on gene list signatures using InterPro domains. BMC Bioinformatics 2008; 4;9(1):3

12 Kissling C, Retz W, Wiemann S, Coogan AN, Clement RM, Hunnerkopf R, Conner AC, Freitag CM, Rosler M, Thome J (2008) A polymorphism at the 3'-untranslated region of the CLOCK gene is associated with adult attention-deficit hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2008 147: 333-338.

11 Kohl T, Schmidt C, Wiemann S, Poustka A, Korf U (2008) Automated production of recombinant human proteins as resource for proteome research. Proteome Science 2008 6: 4.7.

10 Korf U, Derdak S, Tresch A, Henjes F, Schumacher S, Schmidt C, Hahn B, Lehmann WD, Poustka A, Beissbarth T, Klingmuller U (2008a) Quantitative protein microarrays for time-resolved measurements of protein phosphorylation. Proteomics 2008 8: 4603-4612.8.

9 Korf U, Henjes F, Schmidt C, Tresch A, Mannsperger H, Lobke C, Beissbarth T, Poustka A (2008b) Antibody microarrays as an experimental platform for the analysis of signal transduction networks. Adv Biochem Eng Biotechnol 2008 110: 153-175.9.

8 Lobke C, Laible M, Rappl C, Ruschhaupt M, Sahin O, Arlt D, Wiemann S, Poustka A, Sultmann H, Korf U (2008) Contact spotting of protein microarrays coupled with spike-in of normalizer protein permits time-resolved analysis of ERBB receptor signaling. Proteomics 2008 8: 1586-1594.10.

7 Mathivanan, S. et al. (2008). Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 26, 164-7.

6 Michaud J, Simpson KM, Escher R, Buchet-Poyau K, Beissbarth T, Carmichael C, Ritschie ME, Schutz F, Cannon P, Liu M, Shen X, Ito Y, Raskind WH, Horwitz MS, Sato M, Urner DR, Speed TP, Kavallaris M, Smyth GK, Scott HS. Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics, 2008, 9:363

5 Sansone, S.A. et al. (2008). The first RSBI (ISA-TAB) workshop: can a simple format work for complex studies? Omics 12, 143-9.

4 Sauermann M, Sahin Ö, Sültmann H, Hahne F, Blaszkiewicz S, Majety M, Füzesi L, Poustka A, Wiemann S, Arlt D. Reduced expression of the Vacuole membrane protein 1 (Vmp1) affects the invasion capacity of tumor cells. Oncogene 2008; 27:1320-6.

3 Taylor, C.F. et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26, 889-96.

2 Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthuer A, Brors B, Beissbarth T, Vandesompele J, Pattyn F, Hero B, König R, Fischer M, Schwab M.Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblasotmas. Genome Biol, 2008, 9(10): R150.

1 Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2008 36: D793-799.