46 Börno ST, Fischer A, Kerick M, Fälth M, Laible M, Brase JC, Kuner R, Dahl A, Grimm C, Sayanjali B, Isau M, Röhr C, Wunderlich A, Timmermann B, Claus R, Plass C, Graefen M, Simon R, Demichelis F, Rubin MA, Sauter G, Schlomm T, Sültmann H, Lehrach H, Schweiger MR. Increase in genome-wide differential DNA methylation in TMPRSS2:ERG fusion negative prostate cancers with miRNA-26a hypermethylation. Cancer Discov. 2012 Nov;2(11):1024-35. doi: 10.1158/2159-8290.CD-12-0041. Epub 2012 Aug 28.                                                                                                 
45 Haupt A, Joberty G, Bantscheff M, Frohlich H, Stehr H, Schweiger MR, Fischer A, Kerick M, Boerno ST, Dahl A, Lappe M, Lehrach H, Gonzalez C, Drewes G, Lange BM. Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics. BMC Cancer. 2012 Jan 25;12(1):38

44 Krohn A, Diedler T, Burkhardt L, Mayer PS, De Silva C, Meyer-Kornblum M, Kötschau D, Tennstedt P, Huang J, Gerhäuser C, Mader M, Kurtz S, Sirma H, Saad F, Steuber T, Graefen M, Plass C, Sauter G, Simon R, Minner S, Schlomm T.  Genomic deletion of PTEN is associated with tumor progression and early PSA recurrence in ERG fusion positive and fusion negative prostate cancer.  Am J Pathol. 2012 Aug;181(2):401-12. doi: 10.1016/j.ajpath.2012.04.026. Epub 2012 Jun 13.

43 Kuner R, Brase JC, Sültmann H, Wuttig D Gade S.  miRNA biomarkers in body fluids of prostate cancer patients.  Methods. 2013 Jan;59(1):132-7. doi: 10.1016/j.ymeth.2012.05.004. Epub 2012 May 29.

42 Ummanni R, Barreto F, Venz S, Scharf C, Barret C, Mannsperger HA, Brase JC, Kuner R, Schlomm T, Sauter G, Sültmann H, Korf U, Bokemeyer C, Walther R, Brümmendorf TH, Balabanov S.  Peroxiredoxins 3 and 4 are overexpressed in prostate cancer tissue and affect the proliferation of prostate cancer cells in vitro.  J Proteome Res. 2012


41 Brase JC, Johannes M, Mannsperger H, Fälth M, Metzger J, Kacprzyk LA, Andrasiuk T, Gade S, Meister M, Sirma H, Sauter G, Simon R, Schlomm T, Beißbarth T, Korf U, Kuner R, Sültmann H, TMPRSS2-ERG -specific transcriptional modulation is associated with prostate cancer biomarkers and TGF-? signaling. BMC Cancer, 2011, 11(1):507

40 Brase JC, Johannes M, Schlomm T, Fälth M, Haese A, Steuber T, Beissbarth T, Kuner R, Sültmann H. Circulating miRNAs are correlated with tumor progression in prostate cancer. Int J Cancer. 2011;128:608-16

39 Gade S, Porzelius C, Faelth M, Brase JC, Wuttig D, Kuner R, Binder H, Sültmann H, Beissbarth T. Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. BMC Bioinformatics. 2011;12:488

38 Johannes M, Fröhlich H, Sültmann H, Beißbarth T. pathClass: An R-Package for Integration of Pathway Knowledge into Support Vector Machines for Biomarker DiscoveryBioinformatics. 2011, in press.

37 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 ORIGINAL PAPER Vol. 27 no. 10 2011, pages 1377–1383. doi:10.1093/bioinformatics/btr152"

36 Minner S, Enodien M, Sirma H, Luebke AM, Krohn A, Mayer PS, Simon R, Tennstedt P, Müller J, Scholz L, Brase JC, Liu AY, Schlüter H, Pantel K, Schumacher U, Bokemeyer C, Steuber T, Graefen M, Sauter G, Schlomm T. ERG status is unrelated to PSA recurrence in radically operated prostate cancer in the absence of antihormonal therapy. Clin Cancer Res. 2011 Sep 15;17(18):5878-88

35 Porzelius C, Johannes M, Binder H, Beissbarth T. Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients. Biometrical J. 2011; 53(2):190-2011.

34 Rupp A-K, Rupp C, Keller S, Brase JC, Ehehalt R, Fogel M, Moldenhauer G, Marmé F, Sültmann H, Altevogt P. Loss of EpCAM expression in breast cancer derived serum exosomes: role of proteolytic cleavage. Gynecol Oncol. 2011 Aug;122(2):437-46. Epub 2011 May 20

33 Schweiger M.R., Kerick M., Timmermann B. and M.Isau. The power of NGS technologies to delineate the genome organization in cancer: From mutations to structural variations and epigenetic alterations. Cancer Metastasis Rev. 2011 Jan 27.

32 Ummanni R, Jost E, Braig M, Lohmann F, Mundt F, Barett C, Schlomm T, Sauter G, Senff T, Bokemeyer C, Sültmann H, Meyer-Schwesinger C, Brümmendorf TH, Balabanov S. Ubiquitin carboxyl-terminal hydrolase 1 (UCHL1) is a potential tumour suppressor in prostate cancer and is frequently silenced by promoter methylation. Mol Cancer. 2011;10:129

31 Ummanni R, Mundt F, Pospisil H, Venz S, Barett C, Fälth M, Köllermann J, Walther R, Schlomm T, Sauter G, Bokemeyer C, Sültmann H, Schuppert A, Brümmendorf TH, Balabanov S. Identification of clinically relevant protein targets in prostate cancer with 2D-DIGE coupled mass spectrometry and systems biology network platform. PLOS One 2011 Feb 11;6(2):e16833

30 Wittig-Blaich SM, Kacprzyk LA, Eismann T, Bewerunge-Hudler M, Kruse P, Winkler E, Strauss WS, Hibst R, Steiner R, Schrader M, Mertens D, Sültmann H, Wittig R. Matrix-dependent regulation of AKT in Hepsin-overexpressing PC3 prostate cancer cells. Neoplasia, 2011, 13(7):579-89


29 Boerno S.T., Grimm C., Lehrach H. and Michal-Ruth Schweiger. Next Generation Sequencing Technologies for DNA Methylation Analyses in Cancer Genomics. Epigenomics 2010 April; 2(2): 199-209,

28 Borgmann, K., Raabe, A., Reuther, S., Szymczak, S., Schlomm, T., Isbarn, H., Gomolka, M., Busjahn, A., Bonin, M., Ziegler, A., Dikomey E.  The potential role of G2- but not of G0-radiosensitivity for predisposition of prostate cancer. Radiotherapy & Oncology 2010;96(1):19-24

27 Brase JC, Johannes M, Schlomm T, Fälth M, Haese A, Steuber T,  Beissbarth T, Kuner R, Sültmann H. Circulating miRNAs are correlated with tumor progression in prostate cancer. 2010 April. Int J Cancer. In press

26 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. 2010 Jun 22;8(1):36.

25 Budäus L, Isbarn H, Eichelberg C, Lughezzani G, Sun M, Perrotte P, Chun FKH, Steuber T, Ahyai SA, Zacharias M, Suardi M, Fisch M, Schlomm T, Haese A, Heinzer H, Huland H, Montorsi F, Graefen M, Karakiewicz PI. Biochemical recurrence after radical prostatectomy: A case of multiplicative interactionbetween surgical margin status and pathological stage. J Urol, in press, 2010

24 El Gammal AT, Bruchmann M, Zustin J, Isbarn H, Hellwinkel OJ, Kollermann J, Sauter G, Simon R, Wilczak W, Schwarz J, Bokemeyer C, Brummendorf TH, Izbicki JR, Yekebas E, Fisch M, Huland H, Graefen M, Schlomm T. Chromosome 8p deletions and 8q gains are associated with tumor progression and poor prognosis in prostate cancer. Clin Cancer Res 2010;16:56-64.

23 Isbarn H, Wanner M, Salomon G, Steuber T, Schlomm T, Köllermann J, Sauter G, Haese A, Heinzer H, Huland H, Graefen M. Long-term data on the survival of patients with prostate cancer treated with radical prostatectomy in the prostate-specific antigen era. BJU Int, 2010 Jul;106(1):37-43

22 Johannes M, Brase JC, Fröhlich H, Gade S, Gehrmann M, Fälth M, Sültmann H, Beissbarth T. Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients.  Bioinformatics. 2010; 26(17):2136-44.

21 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.

20 Mannsperger H, Gade S, Wiemann S, Sültmann H, Beissbarth T, and Korf U. RPPanalyzer: Analysis of reverse phase protein array data. Bioinformatics 2010, 26, 2202-3.

19 Mannsperger HM, Uhlmann S, Wiemann S, Sahin Ö, Korf U. RNAi-based validation of antibodies reverse phase protein arrays. Proteome Science 2010, 8, 69

18 Minner S, Jessen B, Stiedenroth L, Burandt E, Kollermann J, Mirlacher M, Erbersdobler A, Eichelberg C, Fisch M, Brummendorf TH, Bokemeyer C, Simon R, Steuber T, Graefen M, Huland H, Sauter G, Schlomm T. Low level HER2 overexpression is associated with rapid tumor cell proliferation and poor prognosis in prostate cancer. Clin Cancer Res 2010;16:1553-1560.

17 Minner S, Wittmer C, Graefen M, Salomon G, Steuber T, Haese A, Huland H, Bokemeyer C, Yekebas E, Dierlamm J, Balabanov S, Kilic E, Wilczak W, Simon R, Sauter G, Schlomm T. High level PSMA expression is associated with early PSA recurrence in surgically treated prostate cancer. Prostate, Epub 2010 Aug 31.    


16 Calabro A, Beissbarth T, Kuner R, Stojanov M, Benner A, Asslaber M, Ploner F, Zatloukal K, Samonigg H, Poustka A, Sültmann H. Effects of infiltrating lymphocytes and estrogen receptor on gene expression and prognosis in breast cancer. Breast Cancer Res Treat. 2009 Jul;116(1):69-77.

15 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.

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

13 Gaedcke J, Grade M, Jung K, Schirmer M, Jo P, Obermeyer C, Wolff HA, Herrmann MK, Beissbarth T, Becker H, Ried T, Ghadimi M. KRAS and BRAF mutations in patients with rectal cancer treated with preoperative chemoradiotherapy. Radiother Oncol. 2009.

12 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, 2009.

11 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.

10 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 

9 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.

8 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.

7 Sprenger T, Rothe H, Homayounfar K, Beissbarth T, Ghadimi BM, Becker H, Liersch T. Preoperative Chemoradiotherapy Does Not Necessarily Reduce Lymph Node Retrieval in Rectal Cancer Specimens-Results from a Prospective Evaluation with Extensive Pathological Work-up. J Gastrointest Surg. 2009.


6 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.

5 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

4 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

3 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

2 Van Laere S, Beissbarth T, Auwera VI, Eynden VG, Trinh XB, Elst H, Hummelen P, Dam P, Marck E, Vermeulen P, Dirix L. Relapse-free survival in breast cancer patients is associated with a gene expression signature characteristic for inflammatory breast cancer. Clin Cancer Res, 2008, 14(22):7452-60.

1 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.