Publications
Selected publications of project partners relevant for CancerTelSys
Holger Erfle
Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H et al. & Pepperkok R. (2012), Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Nat Cell Biol. 14, 764-774
Reiss S, Rebhan I, Backes P, Romero-Brey I, Erfle H et al. & Bartenschlager R. (2011). Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe 9, 32-45.
Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H et al. & Ellenberg J. (2010). Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721-727.
Reymann, J., Beil, N., Beneke, J., Kaletta, PP, Burkert, K. and Erfle, H. (2009) Next generation 9216 microwell cell array for high content screening microscopy. Biotechniques 47, 877-878.
Erfle H, Neumann B, Liebel U, Rogers P, Held M, WalterT, Ellenberg J and Pepperkok R (2007), Reverse transfection on cell arrays for high content screening microscopy, Nature Protocols 2, 392-399.
Rainer König
Kranz AL, Eils R, König R (2011). Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 39, 8689–8702.
Bauer T, Eils R, König R: RIP: the regulatory interaction predictor—a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 2011, 27(16):2239-2247.
Schramm G, Surmann EM, Wiesberg S, Oswald M, Reinelt G, Eils R, König R: Analyzing the regulation of metabolic pathways in human breast cancer. BMC Med Genomics 2010, 3(1):39.
Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ: Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol 2010, 28(12):1279-1285.
Schramm G, Kannabiran N, König R: Regulation patterns in signaling networks of cancer. BMC Syst Biol 2010, 4:162.
Brian Luke
Luke-Glaser S, Poschke H and Luke B (2012) Getting in (and out of) the loop: regulating higher order telomere structures. Frontiers in Oncology. 2, 180.
Poschke H, Dees M, Chang M, Kaderali L, Amberkar S, Rothstein R and Luke B (2012). Rif2 promotes a telomere fold-back structure through Rpd3L recruitment in budding yeast. PloS Genetics. 8, e1002960.
Maicher A, Kastner L, Dees M and Luke B (2012). Deregulated telomere transcription causes replication dependent telomere shortening and promotes cellular senescence. Nucleic Acids Research. 40, 6649-59.
Iglesias N, Redon S, Pfeiffer V, Dees M, Lingner J, Luke B (2011). Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast. (2012). EMBO Rep. 12, 587-593
Maicher A, Kastner L, and Luke B (2012). Telomeres and Disease - Enter TERRA. RNA Biology 9, 843-9.
Website: https://www.imb-mainz.de/research/luke
Stefan Pfister
Northcott PA, Jones DT, Kool M, Robinson GW, Gilbertson RJ, Cho YJ, Pomeroy SL, Korshunov A, Lichter P, Taylor MD, Pfister SM. (2012). Medulloblastomics: the end of the beginning. Nat Rev Cancer. 2012 Dec;12: 818-34.
Sturm D, Witt H, Hovestadt V, et al. & Plass C, Jabado N, Pfister SM. (2012). Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma. Cancer Cell. 22: 425-37.
Jones DT, Jäger N, Kool M et al. & A, Eils R*, Pfister SM*, Lichter P*. (2012) Dissecting the genomic complexity underlying medulloblastoma. Nature. 2012 Jul 25.
Schwartzentruber J, Korshunov A, Liu XY, et al. &, Plass C, Majewski J, Pfister SM, Jabado N. (2012). Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012 Jan 29;482(7384):226-31.
Rausch T, Jones DT, Zapatka M et al. & Pfister SM, Korbel JO. (2012)Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012 Jan 20;148(1-2):59-71.
Website:http://www.pediatric-neurooncology.com
Christoph Plass
Claus R, Lucas DM, Stilgenbauer S, et al. & Plass C, Byrd JC. (2012). Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia. J Clin Oncol, 30, 2483-2491.
Raval, A., Tanner, S. M., Byrd, J. C., et al. & Plass, C. (2007). Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell 129, 879-890.
Yu L, Liu C, Vandeusen J, Becknell B, et al. & Plass C. Global assessment of promoter methylation in a murine model of cancer identifies ID4 as a putative novel tumor suppressor gene in human leukemia. Nat. Genet., 37:265-274, 2005.
Raval, A., Lucas, D. M., Matkovic, J. J., et al. & Plass C. (2005). TWIST2 demonstrates differential methylation in immunoglobulin variable heavy chain mutated and unmutated chronic lymphocytic leukemia. J. Clin. Oncol. 23, 3877-85.
Costello JF, Frühwald MC, Smiraglia DJ, et al. & Plass C. (2000) Aberrant CpG island methylation has non-random and tumor type specific patterns. Nat. Genet., 25:132-138.
Website: http://www.dkfz.de/en/tox/plass.php
Karsten Rippe
Chung, I., Osterwald, S., Deeg, K. & Rippe, K. (2012). PML body meets telomere: The beginning of an ALTernate ending. Nucleus 3, 263-275.
Osterwald, S., Wörz, S., Reymann, J., Sieckmann, F., Rohr, K., Erfle, H. & Rippe, K. (2012). A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathway. Biotechnol. J. 7, 103-116.
Chung, I., Leonhardt, H. & Rippe, K. (2011). De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation. J. Cell Sci. 124, 3603-3618.
Lang, M., Jegou, T., Chung, I., Richter, K., Udvarhelyi, A., Münch, S., Cremer, C., Hemmerich, P., Engelhardt, J., Hell, S. W. & Rippe, K. (2010). Three-dimensional organization of PML nuclear bodies. J. Cell Sci. 123, 392-400.
Jegou, T., Chung, I., Heuvelmann, G., Wachsmuth, M., Görisch, S. M., Greulich-Bode, K., Boukamp, P., Lichter, P. & Rippe, K. (2009). Dynamics of telomeres and promyelocytic leukemia nuclear bodies in a telomerase negative human cell line. Mol Biol Cell 20, 2070-2082.
Website: https://malone.bioquant.uni-heidelberg.de
Karl Rohr
Bergeest JP, Rohr K. (2012) Efficient globally optimal segmentation of cells in fluorescence microscopy images using level sets and convex energy functionals. Medical Image Analysis 16 (7), 1436-1444, 2012
Chang, L., Godinez, W.J., Kim, I.H., Tektonidis, M., de Lanerolle, P., Eils, R., Rohr, K., Knipe, D.M. (2011) Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 108:21, E136-E144
Godinez WJ, Lampe M, Wörz S, Müller B, Eils R, Rohr K. (2009) Deterministic and Probabilistic Approaches for Tracking Virus Particles in Time-lapse Fluorescence Microscopy Image Sequences, Medical Image Analysis 13:2, 325-342
Harder N, Mora-Bermúdez F, Godinez WJ, A. Wünsche, Eils R, Ellenberg J, and Rohr K. (2009) Automatic Analysis of Dividing Cells in Live Cell Movies to Detect Mitotic Delays and Correlate Phenotypes in Time, Genome Research 19:11, 2113-2124.
Wörz S, Sander P, Pfannmöller M, Rieker RJ, Joos S, Mechtersheimer G, Boukamp P, Lichter P, and Rohr K. (2010) 3D Geometry-Based Quantification of Colocalizations in Multi-Channel 3D Microscopy Images of Human Soft Tissue Tumors, IEEE Transactions on Medical Imaging 29:8, 1474-1484
Website http://www.bioquant.uni-heidelberg.de/bmcv
Guido Sauter
Weischenfeldt J, Simon R, Feuerbach L. et al. & Sauter G, Plass C, Brors B, Yaspo ML, Korbel JO, Schlomm T (2013). Integrative genomic analyses reveal androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell, in press.
Slamon D, Eiermann W, Robert N, Pienkowski T, Martin M, Press M, Mackey J, Glaspy J, Chan A, Pawlicki M, Pinter T, Valero V, Liu MC, Sauter G, von Minckwitz G, Visco F, Bee V, Buyse M, Bendahmane B, Tabah-Fisch I, Lindsay MA, Riva A, Crown J (2011). Adjuvant trastuzumab in HER2-positive breast cancer, NEJM 365, 1273-1283.
Schinke T, Schilling AF, Baranowsky A et al. & Sauter G, Amling M (2009). Impaired gastric acidification negatively affects calcium homeostasis and bone mass, Nat Med 15, 674-681
Holst F, Stahl PR, Ruiz C, Hellwinkel O, Jehan Z, Wendland M, Lebeau A, Terracciano L, Al-Kuraya K, Janicke F, Sauter G, Simon R (2007). Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer, Nat Genet 39, 655-660.
Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP (1998). Tissue microarrays for high-throughput molecular profiling of tumor specimens, Nat Med 4, 844-847.
Website: http://www.uke.de/institute/pathologie/index.php
