Publikationen

2013

125 Carotenuto M, Pedone E, Diana D, de Antonellis P, D?eroski S, Marino N, Navas L, Di Dato V, Scoppettuolo MN, Cimmino F, Correale S, Pirone L, Monti SM, Bruder E, Zenko B, Slavkov I, Pastorino F, Ponzoni M, Schulte JH, Schramm A, Eggert A, Westermann F, Arrigoni G, Accordi B, Basso G, Saviano M, Fattorusso R, Zollo M.  Neuroblastoma tumorigenesis is regulated through the Nm23-H1/h-Prune C-terminal interaction.  Sci Rep. 2013;3:1351. doi: 10.1038/srep01351. PubMed PMID: 23448979;PubMed Central PMCID: PMC3584926.

124 Kumps C, Fieuw A, Mestdagh P, Menten B, Lefever S, Pattyn F, De Brouwer S,Sante T, Schulte JH, Schramm A, Van Roy N, Van Maerken T, Noguera R, Combaret V, Devalck C, Westermann F, Laureys G, Eggert A, Vandesompele J, De Preter K, Speleman F.  Focal DNA copy number changes in neuroblastoma target MYCN regulated genes.  PLoS One. 2013;8(1):e52321. doi: 10.1371/journal.pone.0052321. Epub 2013 Jan 4. PubMed PMID: 23308108; PubMed Central PMCID: PMC3537730.

123 Brueckner LM, Hess EM, Schwab M, Savelyeva L. Instability at the FRA8I common fragile site disrupts the genomic integrity of the KIAA0146, CEBPD and PRKDC genes in colorectal cancer.  Cancer Lett. 2013 Apr 16. doi:pii: S0304-3835(13)00327-3. 10.1016/j.canlet.2013.04.007. PMID:23603433.

122 Gogolin, S., Batra, R., Harder, N., Ehemann, V., Pa hausen, T., Diessl, N.,Gade ,S., Nolte, I., Rohr, K., König, R., Westermann, F. MYCN-mediatedoverexpression of mitotic spindle regulatory genes and loss of p53-p21 functionjointly support the survival of tetraploid neuroblastoma cells.  CancerLetters, 331(1):35-45.

121 Berger E, Soldati R, Huebener Nicole, Hohn O, Stermann A, Durmus T, Lobitz S, Zenclussen AC, Christiansen H, Lode HN, Fest S. Salmonella SL7207 application is the most effective DNA vaccine delivery method for successful tumor eradication in a murine model for neuroblastoma.  Cancer Lett. 2013 Jan 18. doi:pii: S0304-3835(13)00032-3. 10.1016/j.canlet.2012.12.026.

120 Schelhorn SE, Fischer M, Tolosi L, Altmüller J, Nürnberg P, Pfister H, Lengauer T, Berthold F. Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol, in press.           
 
119 Gogolin S, Ehemann V, Becker G, Brueckner LM, Dreidax D, Bannert S, Nolte I, Savelyeva L, Bell E, Westermann F.  CDK4 inhibition restores G?-S arrest inMYCN-amplified neuroblastoma cells in the context of doxorubicin-induced DNA damage.  Cell Cycle. 2013 Apr 1;12(7):1091-104. doi: 10.4161/cc.24091. Epub 2013 Mar 5. PubMed PMID: 23462184.
 
118 Aschoff M, Hotz-Wagenblatt A, Glatting KH, Fischer M, Eils R, König R. SplicingCompass: differential splicing detection using RNA-Seq data.  Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.

117 Kocak H, Ackermann S, Hero B, Kahlert Y, Oberthuer A, Juraeva D, Roels F,Theissen J, Westermann F, Deubzer H, Ehemann V, Brors B, Odenthal M, Berthold F, Fischer M.  Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma.  Cell Death Dis. 2013 Apr 11;4:e586.

116 DEUBZER HE, Schier MC, Oehme I, Lodrini M, Haendler B, Sommer A, WITT O. HDAC11 is a novel drug target in carcinomas.  Int J Cancer. 2013 May 1;132(9):2200-8. doi: 10.1002/ijc.27876. Epub 2012 Oct 25.

115 Kieckbusch K, Beckers A, Odersky A, Mestdagh P, Köster J, Bray IM, Bryan K, Vandesompele J, Speleman F, Stallings RL, Schramm A, Eggert A, Sprüssel A, Schulte JH. MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.  Int J Cancer. 2013 Feb 7. doi: 10.1002/ijc.28091.

114 Schulte JH, Lindner S, Bohrer A, Maurer J, De Preter K, Lefever S, Heukamp L, Schulte S, Molenaar J, Versteeg R, Thor T, Künkele A, Vandesompele J, Speleman F, Schorle H, Eggert A, Schramm A. MYCN and ALKF1174L are sufficient to drive neuroblastoma development from neural crest progenitor cells. Oncogene, doi: 10.1038/onc.2012.106.

113 Dreidax D, Gogolin S, Schroeder C, Muth D, Brueckner LM, Hess EM, Zapatka M, Theißen J, Fischer M, Ehemann V, Schwab M, Savelyeva L, Westermann F. Low p14ARF expression in neuroblastoma cells is associated with repressed histone mark status, and enforced expression induces growth arrest and apoptosis.  Hum Mol Genet, 2013, 22(9): 1735-1745.
 
112 Lodrini M, Oehme I, Schroeder C, Milde T, Schier MC, Kopp-Schneider A, Schulte JH, Fischer M, De Preter K, Pattyn F, Castoldi M, Muckenthaler MU, Kulozik AE, Westermann F, Witt O, Deubzer HE.  MYCN and HDAC2 cooperate to repress miR-183 signaling in neuroblastoma. Nucleic Acids Res. 2013 Apr 26. [Epub ahead of print].
 
111 Brockmann M, Poon E, Berry T, Carstensen A, Deubzer HE, Rycak L, Jamin Y, Thway K, Robinson SP, Roels F, Witt O, Fischer M, Chesler L, Eilers M. Small molecule inhibitors of Aurora-A induce proteasomal degradation of N-Myc in childhood neuroblastoma.  Cancer Cell. 2013 Jun 19. pii: S1535-6108(13)00232-8. doi: 10.1016/j.ccr.2013.05.005. [Epub ahead of print].

2012

110 Ammar I, Izsvák Z, Ivics Z. The Sleeping Beauty transposon toolbox. Methods Mol Biol. 2012;859:229-40. doi: 10.1007/978-1-61779-603-6_13. PMID:22367875.

109 Asgharzadeh S, Salo JA, Ji L, Oberthuer A, Fischer M, Berthold F, Hadjidaniel M, Liu CW, Metelitsa LS, Pique-Regi R, Wakamatsu P, Villablanca JG, Kreissman SG, Matthay KK, Shimada H, London WB, Sposto R, Seeger RC. Clinical.

108 Batra R, Harder N, Gogolin S, Diessl N, Soons Z, Jäger-Schmidt C, Lawerenz C, Eils R, Rohr K, Westermann F, König R.  Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown.  PLoS One. 2012;7(12):e50988. doi:10.1371/journal.pone.0050988. Epub 2012 Dec 12. PubMed PMID: 23251412; PubMed Central PMCID: PMC3521006.

107 Brueckner LM, Sagulenko E, Hess EM, Zheglo D, Blumrich A, Schwab M, Savelyeva L.  Genomic rearrangements at the FRA2H common fragile site frequently involve non-homologous recombination events across LTR and L1(LINE) repeats.  Hum Genet. 2012 Apr 5.

106 Coco S, Theissen J, Scaruffi P, Stigliani S, Moretti S, Oberthuer A, Valdora F, Fischer M, Gallo F, Hero B, Bonassi S, Berthold F & Tonini GP Age-dependent accumulation of genomic aberrations and deregulation of cell cycle and telomerase genes in metastatic neuroblastoma.  Int J Cancer, 2012, 131(7): 1591-1600.

105 De Brouwer S, Mestdagh P, Lambertz I, Pattyn F, De Paepe A, Westermann F, Schroeder C, Schulte JH, Schramm A, De Preter K, Vandesompele J, Speleman F. Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma. Int J Cancer. 2012 Jun 1;130(11):2591-8. doi: 10.1002/ijc.26295. Epub 2011 Aug 30.

104 Eschenburg Georg, Angelika Eggert, Alexander Schramm, Holger N. Lode, Patrick Hundsdoerfer Smac mimetic LBW242 sensitizes XIAP-overexpressing neuroblastoma cells for TNF-a independent apoptosis  Cancer Research2012 May 15;72(10):2645-56. doi: 10.1158/0008-5472.CAN-11-4072. Epub 2012 Apr 9.

103 Fletcher JI, Gherardi S, Murray J, Burkhart CA, Russell A, Valli E, Smith J, Oberthuer A, Ashton LJ, London WB, Marshall GM, Norris MD, Perini G, Haber M. N-Myc regulates expression of the detoxifying enzyme glutathione transferase GSTP1, a marker of poor outcome in neuroblastoma Cancer Res. 2012 Feb 15;72(4):845-53.

102 Frommolt P, Abdallah AT, Altmüller J, Motameny S, Becker C, Stemshorn K, Fischer M, Freilinger T, Nürnberg P. Assessing the enrichment performance in targeted resequencing experiments.  Hum Mutat, 2012, 33(4): 635-641.

101 Garcia I, Mayol G, Ríos J, Domenech G, Cheung NK, Oberthuer A, Fischer M, Maris JM, Brodeur GM, Hero B, Rodríguez E, Suñol M, Galvan P, de Torres C, Mora J, Lavarino C. A Three-Gene Expression Signature Model for Risk Stratification of Patients with Neuroblastoma. Clin Cancer Res. 2012 Apr 1;18(7):2012-2023.

100 Henrich KO, Schwab M, Westermann F. 1p36 tumor suppression--a matter ofdosage?  Cancer Res. 2012 Dec 1;72(23):6079-88. doi:10.1158/0008-5472.CAN-12-2230. Epub 2012 Nov 20. Review. PubMed PMID: 23172308.

99 Höpker K, Hagmann H, Khurshid S, Chen S, Hasskamp P, Seeger-Nukpezah T, Schilberg K, Heukamp L, Lamkemeyer T, Sos M, Thomas R, Lowery D, Fischer M, Roels F, Liebau MC, Resch U, Kisner T, Röther F, Bartram MP, Müller RU, Fabretti F, Kurschat P, Schumacher B, Medema R, Yaffe MB, Schermer B, Reinhardt HC, Benzing T. AATF/Che1 acts as a phosphorylation-dependent molecular modulator to repress p53-driven apoptosis.  EMBO J, 2012, 31(20): 3961-3975.

98 Korshunov A, Remke M, Kool M, Hielscher T, Northcott PA, Williamson D, Pfaff E, Witt H, Jones DT, Ryzhova M, Cho YJ, Wittmann A, Benner A, Weiss WA, von Deimling A, Scheurlen W, Kulozik AE, Clifford SC, Peter Collins V, Westermann F, Taylor MD, Lichter P, Pfister SM. Biological and clinical heterogeneity of MYCN-amplified medulloblastoma. Acta Neuropathol. 2012 Apr;123(4):515-27.

97 Künkele A, De Preter K, Heukamp L, Thor T, Pajtler KW, Hartmann W, Mittelbronn M, Grotzer MA, Deubzer HE, Speleman F, Schramm A, Eggert A, Schulte JH.  Pharmacological activation of the p53 pathway by nutlin-3 exerts anti-tumoral effects in medulloblastomas.  Neuro Oncol. 2012 Jul;14(7):859-69. doi: 10.1093/neuonc/nos115. Epub 2012 May 16.

96 Milde T, Hielscher T, Witt H, Kool M, Mack SC, Deubzer HE, Oehme I, Lodrini M, Benner A, Taylor MD, von Deimling A, Kulozik AE, Pfister SM, Witt O, Korshunov A.  Nestin expression identifies ependymoma patients with poor outcome.  Brain Pathol. 2012 Nov;22(6):848-60. doi: 10.1111/j.1750-3639.2012.00600.x. Epub 2012 May 30.

95 Milde T, Kleber S, Korshunov A, Witt H, Hielscher T, Koch P, Kopp HG, Jugold M, DEUBZER HE, Oehme I, Lodrini M, Gröne HJ, Benner A, Brüstle O, Gilbertson RJ, von Deimling A, Kulozik AE, Pfister SM, Martin-Villalba A, WITT O.

94 Milde T, Lodrini M, Savelyeva L, Korshunov A, Kool M, Brueckner LM, Antunes AS, Oehme I, Pekrun A, Pfister SM, Kulozik AE, Witt O, Deubzer HE.  HD-MB03 is a novel Group 3 medulloblastoma model demonstrating sensitivity to histone deacetylase inhibitor treatment.  J Neurooncol. 2012 Dec;110(3):335-48. PMID:23054560.

93 Molenaar JJ, Domingo-Fernández R, Ebus ME, Lindner S, Koster J, Drabek K, Mestdagh P, van Sluis P, Valentijn LJ, van Nes J, Broekmans M, Haneveld F, Volckmann R, Bray I, Heukamp L, Sprüssel A, Thor T, Kieckbusch K, Klein-Hitpass L, Fischer M, Vandesompele J, Schramm A, van Noesel MM, Varesio  L, Speleman F, Eggert A, Stallings RL, Caron HN, Versteeg R, Schulte JH LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression.  Nat Genet. 2012 Nov;44(11):1199-206. doi: 10.1038/ng.2436. Epub 2012 Oct 7.

92 Oeltze St, Klemm P, Hillert R, Preim B, Schubert W Visualization and Exploration of 3D Toponome Data.  VCBM 2012 pp. 115-122. doi: 10.2312/VCBM/VCBM12/115-122.

91 Peifer M, Fernández-Cuesta L, Sos ML, George J, Kasper LH, Seidel D, Plenker D, Leenders F, Sun R, Zander T, Menon R, Koker M, Dahmen I, Müller C, Di Cerbo V, Schildhaus HU, Altmüller J, Baessmann I, Becker C, De Wilde B, Vandesompele J, Böhm D, Ansén S, Gabler F, Wilkening I, Heynck S, Heuckmann JM, Lu X, Cibulskis K, Banerji S, Getz G, Park KS, Rauh D, Grütter C, Fischer M, Pasqualucci L, Wright G, Wainer Z,  Russell P, Petersen I, Chen Y, Stoelben E, Ludwig C, Schnabel P, Hoffmann H, Muley T, Brockmann M, Engel-Riedel W, Muscarella LA, Fazio VM, Groen H, Timens W, Sietsma H, Thunnissen E, Smit E, Heideman DAM, Snijders PJF, Cappuzzo F, Ligorio C, Damiani S, Field J, Solberg S, Brustugun OT, Lund-Iversen M, Sänger J, Clement JH, Soltermann A, Moch H, Weder W, Solomon B, Soria JC, Validire P, Besse B, Brambilla E, Brambilla C, Lantuejoul S, Lorimier P, Schneider PM, Hallek M, Pao W, Meyerson M, Sage J, Shendure J, Schneider R, Büttner R, Wolf J, Nürnberg P, Perner S, Heukamp LC, Brindle PK, Haas S, Thomas RK. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.  Nat Genet, 2012, 44(10): 1104-1110.

90 Salm F, Cwiek P, Ghosal A, Lucia Buccarello A, Largey F, Wotzkow C, Höland K, Styp-Rekowska B, Djonov V, Zlobec I, Bodmer N, Gross N, Westermann F, Schäfer SC, Arcaro A.  RNA interference screening identifies a novel role for autocrine fibroblast growth factor signaling in neuroblastoma chemoresistance.  Oncogene. 2012 Oct 1. doi: 10.1038/onc.2012.416. [Epub ahead of print] PubMed PMID:23027129.

89 Schleiermacher G, Mosseri V, London WB, Maris JM, Brodeur GM, Attiyeh E, Haber M, Khan J, Nakagawara A, Speleman F, Noguera R, Tonini GP, Fischer M, Ambros I, Monclair T, Matthay KK, Ambros P, Cohn SL, Pearson ADJ. Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project.  Br J Cancer, 2012, 107(8): 1418-1422.

88 Schubert W, Gieseler A, Krusche A, Serocka P, Hillert R Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS.  N Biotechnol. 2012 Jun 15;29(5):599-610. doi: 10.1016/j.nbt.2011.12.004.

87 Stigliani, S., S. Coco, S. Moretti, A. Oberthuer, M. Fischer, J. Theissen, F. Gallo, A. Garavent, F. Berthold, S. Bonassi, G.P. Tonini, and P. Scaruffi High genomic instability predicts survival in metastatic high-risk neuroblastoma.  Neoplasia, 2012. 14(9): p. 823-32.

86 Swierczek M, Izsvák Z, Ivics Z The Sleeping Beauty transposon system for clinical applications. Expert Opin Biol Ther. 2012 Feb;12(2):139-53. doi: 10.1517/14712598.2012.642358. PMID:22176302.

85 Tonini, G.P., A. Nakagawara, and F. Berthold. Towards a turning point of neuroblastoma therapy.  Cancer Lett, 2012. 326(2): p. 128-34.

84 Witt O, Milde T, Deubzer HE, Oehme I, Witt R, Kulozik A, Eisenmenger A, Abel U, Karapanagiotou-Schenkel I.  Phase I/II intra-patient dose escalation study of vorinostat in children with relapsed solid tumor, lymphoma or leukemia.  Klin Padiatr. 2012 Oct;224(6):398-403. doi: 10.1055/s-0032-1323692. Epub 2012 Aug 22..

83 Zhao C, Shi L, Tong W, Shaughnessy JD Jr, Oberthuer A, Pusztai L, Deng Y, Symmans WF, Shi T. Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile. BMC Genomics. 2011 Dec 23;12 Suppl 5:S3.

2011

82 Ackermann S, Goeser F, Schulte JH, Schramm A, Ehemann V, Eggert A, Hero B, Berthold F, Fischer M. Polo-like kinase 1 is a therapeutic target in high-risk neuroblastoma. Clin Cancer Res, 2011, 17(4):731-741.

81 Afanasyeva EA, Mestdagh P, Kumps C, Vandesompele J, Ehemann V, Theissen J, Fischer M, Zapatka M, Brors B, Savelyeva L, Sagulenko V, Speleman F, Schwab M, Westermann F. MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival. Cell Death Differ. 2011 Jan 14. [Epub ahead  of print]

80 Bauer T, Eils R, König R. RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors, Bioinformatics, 27, 2239-47.

79 Blumrich A, Zapatka M, Brueckner LM, Zheglo D, Schwab M, Savelyeva L. The FRA2C common fragile site maps to the borders of MYCN amplicons in neuroblastoma and is associated with gross chromosomal rearrangements in different cancers. Hum Mol Genet 2011 Apr 15;20(8):1488-501.

78 Coco S, Valdora F, Bonassi S, Scaruffi P, Stigliani S, Oberthuer A, Berthold F, Andolfo I, Servidei T, Riccardi R, Basso E, Iolascon A, Tonini GP. Chromosome 9q and 16q Loss Identified by Genome-Wide Pooled-Analysis Are Associated with Tumor Aggressiveness in Patients with Classic Medulloblastoma. OMICS. 2011 Feb 24

77 Fiaschetti G, Castelletti D, Zoller S, Schramm A, Schroeder C, Nagaishi M,Stearns D, Mittelbronn M, Eggert A, Westermann F, Ohgaki H, Shalaby T, Pruschy M, Arcaro A, Grotzer MA. Bone morphogenetic protein-7 is a MYC target with prosurvival functions in childhood medulloblastoma. Oncogene. 2011 Feb 14. [Epub ahead of print]

76 Henrich KO, Bauer T, Schulte JH, Ehemann V, Deubzer HE, Gogolin S, Muth D, Fischer M, Benner A, König R, Schwab M, Westermann F. CAMTA1, a 1p36 tumor suppressor candidate, inhibits growth and activates differentiation programmes in neuroblastoma cells. Cancer Res. 2011 Mar 8. [Epub ahead of print]

75 Ivics Z, Izsvák Z, Chapman KM, Hamra FK. Sleeping Beauty transposon mutagenesis of the rat genome in spermatogonial stem cells. Methods. 2011 Apr;53(4):356-65. Epub 2010 Dec 28.PMID:21193047

74 Korshunov A, Remke M, Kool M, Hielscher T, Northcott PA, Williamson D, Pfaff E, Witt H, Jones DT, Ryzhova M, Cho YJ, Wittmann A, Benner A, Weiss WA, von Deimling A, Scheurlen W, Kulozik AE, Clifford SC, Peter Collins V, Westermann F, Taylor MD, Lichter P, Pfister SM. Biological and clinical heterogeneity of MYCN-amplified medulloblastoma. Acta Neuropathol. 2012 Apr;123(4):515-27. Epub 2011 Dec 9.

73 Kranz AL, Eils R, König R. Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res., 39, 8689-702.

72 Krupp M, Maass T, Marquardt JU, Staib F, Bauer T, König R, Biesterfeld S, Galle PR, Tresch A, Teufel A. The functional cancer map: a systems-level synopsis of genetic deregulation in cancer. BMC Med Genomics. 2011 Jun 30;4:53.

71 Ley S, Ley-Zaporozhan J, Günther P, Deubzer HE, Witt O, Schenk JP. Neuroblastoma imaging. Rofo. 2011 Mar;183(3):217-25. Epub 2010 Dec 17

70 Löffler H, Fechter A, Matuszewska M, Saffrich R, Mistrik M, Marhold J, HornungC, Westermann F, Bartek J, Krämer A. Cep63 Recruits Cdk1 to the Centrosome:Implications for Regulation of Mitotic Entry, Centrosome Amplification, andGenome Maintenance. Cancer Res. 2011 Mar 15;71(6):2129-2139.

69 London, W.B., V. Castel, T. Monclair, P.F. Ambros, A.D. Pearson, S.L. Cohn, F. Berthold, A. Nakagawara, R.L. Ladenstein, T. Iehara, and K.K. Matthay. Clinical and biologic features predictive of survival after relapse of neuroblastoma: a report from the International Neuroblastoma Risk Group project. J Clin Oncol, 2011. 29(24): p. 3286-92.

68 Moldt B, Miskey C, Staunstrup NH, Gogol-Döring A, Bak RO, Sharma N, Mátés L, Izsvák Z, Chen W, Ivics Z, Mikkelsen JG. Comparative Genomic Integration Profiling of Sleeping Beauty Transposons Mobilized With High Efficacy From Integrase-defective Lentiviral Vectors in Primary Human Cells. Mol Ther. 2011 Apr 5. [Epub ahead of print] PMID:21468003

67 Oeltze S, Freiler W, Hillert R, Doleisch H, Preim B, Schubert W. Interactive, graph-based visual analysis of high-dimensional, multi-parameter fluorescence microscopy data in toponomics. IEEE Trans Vis Comput Graph. 2011 Dec;17(12):1882-91, doi:10.1109/TVCG.2011.217

66 Remke M, Hielscher T, Korshunov A, Northcott PA, Bender S, Kool M, Westermann F, Benner A, Cin H, Ryzhova M, Sturm D, Witt H, Haag D, Toedt G, Wittmann A, Schöttler A, von Bueren AO, von Deimling A, Rutkowski S, Scheurlen W, Kulozik AE, Taylor MD, Lichter P, Pfister SM. FSTL5 is a marker of poor prognosis in non-WNT/non-SHH medulloblastoma. J Clin Oncol. 2011 Oct 10;29(29):3852-61. Epub 2011 Sep 12.

65 Schmitt, J., A. Keller, N. Nourkami-Tutdibi, S. Heisel, N. Habel, P. Leidinger, N. Ludwig, M. Gessler, N. Graf, F. Berthold, H.P. Lenhof, and E. Meese. Autoantibody signature differentiates wilms tumor patients from neuroblastoma patients. PLoS One, 2011. 6(12): p. e28951.

64 Schubert W, Gieseler A, Krusche A, Serocka P, Hillert R. Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS. N Biotechnol. 2011 Dec 21. (Epub ahead of print), doi:10.1016/j.nbt.2011.12.004

63 Schulte JH., H.S. Bachmann, B. Brockmeyer, K. Depreter, A. Oberthur, S. Ackermann, Y. Kahlert, K. Pajtler, J. Theissen, F. Westermann, J. Vandesompele, F. Speleman, F. Berthold, A. Eggert, B. Brors, B. Hero, A. Schramm, and M. Fischer. High ALK receptor tyrosine kinase expression supersedes ALK mutation as a determining factor of an unfavorable phenotype in primary neuroblastoma. Clin Cancer Res, 2011. 17(15): p. 5082-92.

62 Van Maerken T, Rihani A, Dreidax D, De Clercq S, Yigit N, Marine JC,Westermann F, De Paepe A, Vandesompele J, Speleman F. Functional analysis of the p53 pathway in neuroblastoma cells using the small-molecule MDM2 antagonistnutlin-3. Mol Cancer Ther. 2011 Apr 1. [Epub ahead of print]

2010

61 Barysenka A, Dress AW, Schubert W. An information theoretic thresholding method for detecting protein colocalizations in stacks of fluorescence images. Journal of Biotechnology, Volume 149, Issue 3, 1 September 2010, Pages 127-131, doi:10.1016/j.jbiotec.2010.01.009

60 De Preter K, Vermeulen J, Brors B, Delattre O, Eggert A, Fischer M, Janoueix-Lerosey I, Lavarino C, Maris J, Mora J, Nakagawara A, Oberthür A, Ohira M, Schleiermacher G, Schramm A, Schulte J, Wang Q, Westermann F, Speleman F, Vandesompele J. Accurate outcome prediction in neuroblastoma across independent datasets using a multi-gene signature. Clin Cancer Res, 2010, 16(5):1532-1541.

59 de Silva S, Mastrangelo MA, Lotta Jr LT, Burris CA, Izsvák Z, Ivics Z, Bowers WJ. HSV. Sleeping Beauty Vector-based Embryonic Gene Transfer Using the HSB5 Mutant: Loss of Apparent Transposition 'Hyperactivity' In Vivo. Hum Gene Ther. 2010 May 27; 21:1603-13. PMID: 20507234

58 Eggert A, Schulte JH. A small kiss of death for cancer. Nat Med. 2010;16:1079-81

57 Eschenburg G, Stermann A, Preissner R, Meyer HA, Lode HN. DNA vaccination: using the patient's immune system to overcome cancer. Clin Dev Immunol. 2010;2010:169484. Epub 2010 Dec 16

56 Fischer M, Bauer T, Oberthür A, Hero B, Theissen J, Ehrich M, Spitz R, Eils R, Westermann F, Brors B, König R, Berthold F. Integrated genomic profiling identifies two distinct molecular subtypes with divergent outcome in neuroblastoma with loss of chromosome 11q. Oncogene. 2010 Feb 11;29(6):865-75.

55 Gogolin S, Dreidax D, Becker G, Ehemann V, Schwab M, Westermann. F.MYCN/MYC-mediated drug resistance mechanisms in neuroblastoma. Int J ClinPharmacol Ther. 2010 Jul;48(7):489-91.

54 Herold J, Schubert W, Nattkemper TW. Automated detection and quantification of fluorescently labeled synapses in murine brain tissue sections for high throughput applications. Journal of Biotechnology, Volume 149, Issue 4, 15 September 2010, Pages 299-309, doi:10.1016/j.jbiotec.2010.03.004

53 Lacroix J, Leuchs B, Li J, Hristov G, Deubzer HE, Kulozik AE, Rommelaere J, Schlehofer JR, Witt O. Parvovirus H1 selectively induces cytotoxic effects on human neuroblastoma cells. Int J Cancer. 2010 Sep 1;127(5):1230-9.

52 Lewis, N., Schramm, G., Bordbar, A.,Schellenberger, J., Andersen, M., Cheng, J., Patel, M., Yee, A., Lewis, R., Eils, R., König, R., Palsson, B. Formulating multi-cellular models of metabolism in tissues: application to energy metabolism in the human brain, Nat. Biotechnology, 28, 1279

51 Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, A.J., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., Weitz, K.K., Eils, R., König, R., Smith, R.D. & Palsson, B.O. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models, Mol Sys Biol, 6, 390

50 Ma, L., J. Young, H. Prabhala, E. Pan, P. Mestdagh, D. Muth, J. Teruya-Feldstein, F. Reinhardt, T.T. Onder, S. Valastyan, F. Westermann, F. Speleman, J. Vandesompele, and R.A. Weinberg. miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nat Cell Biol, 2010. 12(3): p. 247-56. IF 17.623.

49 Mestdagh P, Fredlund E, Pattyn F, Rihani A, Van Maerken T, Vermeulen J, Kumps C, Menten B, De Preter K, Schramm A, Schulte J, Noguera R, Schleiermacher G, Janoueix-Lerosey I, Laureys G, Powel R, Nittner D, Marine JC, Ringnér M, Speleman F, Vandesompele J. An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours. Oncogene. 2010;29:3583-92.

48 Mestdagh P, Fredlund E, Pattyn F, Schulte JH, Muth D, Vermeulen J, Kumps C, Schlierf S, De Preter K, Van Roy N, Noguera R, Laureys G, Schramm A, Eggert A, Westermann F, Speleman F, Vandesompele J. MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors. Oncogene. 2010;29:1394-404.

47 Michaelis M, Kleinschmidt MC, Barth S, Rothweiler F, Geiler J, Breitling R, Mayer B, Deubzer H, Witt O, Kreuter J, Doerr HW, Cinatl J, Cinatl J Jr. Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines. Biochem Pharmacol. 2010 Jan 15;79(2):130-6. Epub 2009 Aug 19.

46 Milde T, Oehme I, Korshunov A, Kopp-Schneider A, Remke M, Northcott P, Deubzer HE, Lodrini M, Taylor MD, von Deimling A, Pfister S, Witt O. HDAC5 and HDAC9 in medulloblastoma: novel markers for risk stratification and role in tumor cell growth. Clin Cancer Res. 2010 Jun 15;16(12):3240-52. Epub 2010 Apr 22

45 Muth D, Ghazaryan S, Eckerle I, Beckett E, Pöhler C, Batzler J, Beisel C, Gogolin S, Fischer M, Henrich KO, Ehemann V, Gillespie P, Schwab M, Westermann F. Transcriptional repression of SKP2 is impaired in MYCN-amplified neuroblastoma. Cancer Res, 2010, 70(9):3791-3802.

44 Nevo I, Oberthür A, Edri-Botzer L, Sagi-Assif O, Pasmanik-Chor M, Kariv N, Fischer M, Yron I, Witz IP. Gene-expression-based analysis of local and metastatic neuroblastoma variants reveals a set of genes associated with tumor progression in neuroblastoma patients. Int J Cancer, 2010, 126(7):1570-81.

43 Oberthuer A, Hero B, Berthold F, Juraeva D, Faldum A, Kahlert Y,  Asgharzadeh S, Seeger R, Scaruffi P, Tonini GP, Janoueix-Lerosey I,  Delattre O, Schleiermacher G, Vandesompele J, Vermeulen J, Speleman F, Noguera R, Piqueras M, Benard J, Valent A, Avigad S, Yaniv I, Weber A, Christiansen H, Grundy RG, Schardt K, Schwab M, Eils R, Warnat P, Kaderali L, Simon T, DeCarolis B, Theissen J, Westermann F, Brors B, Fischer M. The prognostic impact of gene expression-based classification for neuroblastoma J Clin Oncol. 2010 Jul 20;28(21):3506-3515

42 Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, Berthold F, Shi L, Wolfinger RD, Fischer M, Brors B. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics J, 2010, 10:258-266.

41 Oberthuer, A., B. Hero, F. Berthold, D. Juraeva, A. Faldum, Y. Kahlert, S. Asgharzadeh, R. Seeger, P. Scaruffi, G.P. Tonini, I. Janoueix-Lerosey, O. Delattre, G. Schleiermacher, J. Vandesompele, J. Vermeulen, F. Speleman, R. Noguera, M. Piqueras, J. Benard, A. Valent, S. Avigad, I. Yaniv, A. Weber, H. Christiansen, R.G. Grundy, K. Schardt, M. Schwab, R. Eils, P. Warnat, L. Kaderali, T. Simon, B. Decarolis, J. Theissen, F. Westermann, B. Brors, and M. Fischer. Prognostic Impact of Gene Expression-Based Classification for Neuroblastoma. J Clin Oncol, 2010. 28(21): p. 3506-3515.

40 Parry RM, Jones W, Stokes TH, Phan JH, Moffitt RA, Fang H, Shi L, Oberthuer A, Fischer M, Tong W, Wang MD. k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction. Pharmacogenomics J, 2010, 10:292-309.

39 Riehl, A., Bauer, T., Brors, B., Busch, H., Németh, J., König, R., Gebhardt, C., Bierhaus, A., Nawroth, P., Eils, R., Angel, P. & Hess, J. Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation, BMC Genomics, 11:537.

38 Schramm, G., Kannabiran, N. & König, R. Regulation patterns in signaling networks of cancer, BMC Systems Biology, 4, 162.

37 Schramm, G., Surmann, E.M., Wiesberg, S., Oswald, M., Reinelt, G., Eils, R. & König, R. Analyzing the regulation of metabolic pathways in human breast cancer, BMC Medical Genomics, 3:39.

36 Schramm, G., Wiesberg, S., Diessl, N., Kranz, A.L., Sagulenko, V., Oswald, M., Reinelt, G., Westermann, F., Eils, R. & König, R. PathWave: Discovering patterns of differentially regulated enzymes in metabolic pathways, Bioinformatics, 2010 Mar 24. [Epub ahead of print]

35 Schubert W. On the origin of cell functions encoded in the toponome. Journal of Biotechnology, Volume 149, Issue 4, 15 September 2010, Pages 252-259, doi:10.1016/j.jbiotec.2010.03.0099

34 Schulte, J, Schowe, B, Mestdagh, P, Kaderali, L, Kalaghatgi, P, Schlierf, S, Vermeulen, J, Brockmeyer, B, Pajtler, K, Thor, T, de Preter, K, Speleman, F, Morik, K, Eggert, A, Vandesompele, J, Schramm, A. Accurate Prediction of Neuroblastoma Outcome based on miRNA Expression Profiles.  International Journal of Cancer, 27:2374-85

33 Schulte, JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, and Schramm A. Deep sequencing reveals differential expression of microRNAs in favourable versus unfavourable neuroblastoma.  Nucleic Acids Research, 38:5919-28

32 Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.. Nat Biotechnol, 2010, 28(8):827-838.

31 Suratanee, A., Rebhan, I., Matula, P., Kaderali, L., Rohr, K., Bartenschlager, R., Eils, R. & König, R. Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images, Bioinformatics, 26 ECCB 2010, i1-i6

2009

30 Bleeke M, Festa S, Huebener N, Landgraf C, Schraven B, Gerhard Gaedicke, Rudolf Volkmer, Holger N. LodeSystematic amino acid substitutions improved efficiency of GD2-peptide mimotope vaccination against neuroblastoma. EUROPEAN JOURNAL OF CANCER 4 5, 2009, 2915-2921.

29 Eckerle I, Muth D, Batzler J, Henrich KO, Lutz W, Fischer M, Witt O, Schwab M, Westermann F.Regulation of BIRC5 and ist isoform BIRC5-2B in neuroblastoma. Cancer Lett. 2009 Nov 18;285(1):99-107. Epub 2009 Jun 3

28 Gipp, M., Marcus, G., Harder, N., Suratanee, A., Rohr, K., König, R. & Männer, R. (2009). Haralick's Texture Features Computed by GPUs for Biological Applications, IAENG International Journal of Computer Science, 2009, 36:1, IJCS_36_1_09.

27 Harder N, Mora-Bermúdez F, Godinez WJ, Wünsche A, Eils R, Ellenberg J, Rohr K. Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time. Genome Res, (2009), 19, 2113-24.

26 Harel L, Tcherpakov M, Costa B, Zapatka M, Oberthuer A, Hansford LM, Levy Z, Avigad S, Yaniv I, Shi L, Eils R, Fischer M, Brors B, Kaplan DR, Fainzilber M.CCM2 mediates death signalling by the TrkA receptor tyrosine kinase. Neuron. 2009 Sep 10; 63(5):585-91

25 Hoene V, Fischer M, Ivanova A, Wallach T, Berthold F, Dame C. GATA factors in human neuroblastoma: distinctive expression patterns in clinical subtypes. Br J Cancer. 2009 Oct 20;101(8):1481-9. Epub 2009 Aug 25

24 Mestdagh, P., P. Van Vlierberghe, A. De Weer, D. Muth, F. Westermann, F. Speleman, and J. Vandesompele, A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol, 2009. 10(6): p. R64, IF 6.589.

23 Oberthuer A, Theissen J, Westermann F, Hero B, Fischer M.Molecular characterization and classification of neuroblastoma. Future Oncol, 2009, 5(5): 625-639.

22 Oehme I, Deubzer HE, Lodrini M, Milde T, Witt O.Targeting of HDAC8 and investigational inhibitors in neuroblastoma. Expert Opin Investig Drugs. 2009 Nov; 18(11):1605-17.

21 Oehme I, Deubzer HE, Wegener D, Pickert D, Linke JP, Hero B, Kopp-Schneider A, Westermann F, Ulrich S, Fischer M, Witt O.Histone deacetylase 8 in neuroblastoma tumorigenesis. Clin Cancer Res, 2009, 15(1): 91-99.

20 Schubert W, Gieseler A, Krusche A, Hillert R. Toponome mapping in prostate cancer: detection of 2000 cell surface protein clusters in a single tissue section and cell type specific annotation by using a three symbol code. J Proteome Res. 2009 Jun;8(6):2696-707. doi:10.1021/pr800944f

19 Theissen J, Boensch M, Spitz R, Betts D, Stegmaier S, Christiansen H, Niggli F, Schilling F, Schwab M, Simon T, Westermann F, Berthold F, Hero B. Heterogeneity of the MYCN oncogene in neuroblastoma. Clin Cancer Res, 2009. 15(6): p. 2085-90. IF 6.25.

18 Vermeulen J, De Preter K, Naranjo A, Vercruysse L, Van Roy N, Hellemans J, Swerts K, Bravo S, Scaruffi P, Tonini GP, De Bernardi B, Noguera R, Piqueras M, Canete A, Castel V, Janoueix-Lerosey I, Delattre O, Schleiermacher G, Michon J, Combaret V, Fischer M, Oberthuer A, Ambros P, Beiske K, Benard J, Marques B, Rubie H, Kohler J, Pötschger U, Ladenstein R, Hogarty MD, McGrady P, London WB, Laureys G, Speleman F, Vandesompele J.Predicting outcomes for children with neuroblastoma using a multigene-expression signature, a retrospective SIOPEN/COG/GPOH study. Lancet Oncol, 2009, 10(7): 663-671.

17 Voth H, Oberthuer A, Simon T, Kahlert Y, Berthold F, Fischer M. Co-regulated expression of HAND2 and DEIN by a bidirectional promoter with asymmetrical activity in neuroblastoma. BMC Mol Biol. 2009 Apr 6;10:28

16 Voth H, Oberthuer A, Simon T, Kahlert Y, Berthold F, Fischer M. Co-regulated expression of HAND2 and DEIN by a bidirectional promoter with asymmetrical activity in neuroblastoma. BMC Mol Biol. 2009 Apr 6;10:28

15 Witt O, Deubzer HE, Lodrini M, Milde T, Oehme I.Targeting histone deacetylases in neuroblastoma. Curr Pharm Des. 2009;15(4):436-47.

14 Witt O, Deubzer HE, Milde T, Oehme I.HDAC family: What are the cancer relevant targets. Cancer Lett. 2009 May 8;277(1):8-21. Epub 2008 Sep 27.

13 Witt O, Lindemann R.HDAC inhibitors: magic bullets, dirty drugs or just another targeted therapy. Cancer Lett. 2009 Aug 8;280(2):123-4. Epub 2009 Mar 19

2008

12 Bénard J, Raguénez G, Kauffmann A, Valent A, Ripoche H, Joulin V, Job B, Danglot G, Cantais S, Robert T, Terrier-Lacombe MJ, Chassevent A, Koscielny S, Fischer M, Berthold F, Lipinski M, Tursz T, Dessen P, Lazar V, Valteau-Couanet D.MYCN-non-amplified metastatic neuroblastoma with good prognosis and spontaneous regression: A molecular portrait of stage 4S. Mol Onc, 2008, 2(3): 261-271.

11 Bode M, Irmler M, Friedenberger M, May C, Jung K, Stephan C, Meyer HE,Lach C, Hillert R, Krusche A, Beckers J, Marcus K, Schubert W. Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus. Proteomics 2008; 8(6):1170-8; doi 10.1002/pmic.200700742

10 Deubzer HE, Ehemann V, Kulozik AE, Westermann F, Savelyeva L, Kopp-Schneider A, Riester D, Schwab M, Witt O. Anti-neuroblastoma activity of Helminthosporium carbonum (HC)-toxin is superior to that of other differentiating compounds in vitro. Cancer Lett. 2008 Jun 8;264(1):21-8. Epub 2008 Feb 8.

9 Deubzer HE, Ehemann V, Westermann F, Heinrich R, Mechtersheimer G, Kulozik AE, Schwab M, Witt O. Histone deacetylase inhibitor Helminthosporium carbonum (HC)-toxin suppresses the malignant phenotype of neuroblastoma cells. Int J Cancer. 2008 Apr 15;122(8):1891-900.

8 Frühwald MC, Witt O.The epigenetics of cancer in children. Klin Padiatr. 2008 Nov-Dec;220(6):333-41. Epub 2008 Oct 23.

7 Michaelis M, Bliss J, Arnold SC, Hinsch N, Rothweiler F, Deubzer HE, Witt O, Langer K, Doerr HW, Wels WS, Cinatl J Jr. Cisplatin-resistant neuroblastoma cells express enhanced levels of epidermal growth factor receptor (EGFR) and are sensitive to treatment with EGFR-specific toxins. Clin Cancer Res. 2008 Oct 15;14(20):6531-7.

6 Oberthuer A, Kaderali L, Kahlert Y, Hero B, Westermann F, Berthold F, Brors B, Eils R, Fischer M.Sub-classification and individual survival time prediction from gene-expression data of neuroblastoma patients using CASPAR. Clin Cancer Res, 2008, 14(20): 6590-6601.

5 Schubert W, Bode M, Hillert R, Krusche A, Friedenberger M. Toponomics and neurotoponomics: a new way to medical systems biology. Expert Rev Proteomics. 2008 Apr;5(2):361-9. Review. doi:10.1586/14789450.5.2.361

4 Schubert W, Friedenberger M, Bode M, Krusche A, Hillert R. Functional architecture of the cell nucleus: towards comprehensive toponome reference maps of apoptosis. Biochim Biophys Acta. 2008 Nov;1783(11):2080-8. Epub 2008 Jul 31. doi:10.1016/j.bbamcr.2008.07.019

3 Schulte JH, Kirfel J, Lim S, Schramm A, Friedrichs N, Deubzer HE, Witt O, Eggert A, Buettner R.Transcription factor AP2alpha (TFAP2a) regulates differentiation and proliferation of neuroblastoma cells. Cancer Lett. 2008 Nov 18;271(1):56-63. Epub 2008 Jul 11.

2 Wegener D, Deubzer HE, Oehme I, Milde T, Hildmann C, Schwienhorst A, Witt O.HKI 46F08, a novel potent histone deacetylase inhibitor, exhibits antitumoral activity against embryonic childhood cancer cells. Anticancer Drugs. 2008 Oct;19(9):849-57.

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.