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CancerTelSys

Publications

2022

Gunkel, M., J. P. Eberle, R. Bulkescher, J. Reymann, I. Chung, R. Simon, G. Sauter, V. Starkuviene, K. Rippe, and H. Erfle. 2022. "Multiscale Fluorescence Imaging." In Single Molecule Science, 38–48. doi.org/10.1017/9781108525909.006

2021

Wollmann, T., and K. Rohr (2021). "Deep Consensus Network: Aggregating predictions to improve object detection in microscopy images." Medical Image Analysis 70: 102019. CancerTelSys  doi.org/10.1016/j.media.2021.102019.

2020

Eichenauer, T., F. Federlein, K. Moller, V. Chirico, S. Kind, M. Lennartz, F. Lutz, C. Hube-Magg, D. Hoflmayer, M. Fisch, H. Huland, H. Heinzer, M. Graefen, A. Haese, C. Schroeder, P. Lebok, S. Minner, R. Simon, G. Sauter, T. Schlomm, W. Wilczak, S. Steurer, and A. M. Luebke (2020). "High CHK2 protein expression is a strong and independent prognostic feature in ERG negative prostate cancer." PATHOLOGY 52(4): 421–430. doi.org/10.1016/j.pathol.2020.03.001.

Fraune, C., L. Harms, F. Buscheck, D. Hoflmayer, M. C. Tsourlakis, T. S. Clauditz, R. Simon, K. Moller, A. M. Luebke, C. Moller-Koop, S. Steurer, C. Hube-Magg, G. Sauter, S. Weidemann, P. Lebok, D. Dum, S. Kind, S. Minner, J. R. Izbicki, T. Schlomm, H. Huland, H. Heinzer, E. Burandt, A. Haese, M. Graefen, and C. Schroeder (2020). "Upregulation of the transcription factor TFAP2D is associated with aggressive tumor phenotype in prostate cancer lacking the TMPRSS2:ERG fusion." Molecular Medicine 26(1): 13. doi.org/10.1186/s10020-020-00148-4.

Hassan, M. I. A., J. M. Kruse, T. Krueger, H.-M. Dahse, Z. Cseresnyes, M. G. Blango, H. Slevogt, F. Hoerhold, V. Ast, R. Koenig, M. T. Figge, O. Kniemeyer, A. A. Brakhage, and K. Voigt (2020). "Functional surface proteomic profiling reveals the host heat-shock proteinA8 as a mediator ofLichtheimia corymbiferarecognition by murine alveolar macrophages." Environ Microbiol. doi.org/10.1111/1462-2920.15140EarlyAccess:JUL2020DocumentType:Article;EarlyAccess.

Hoerhold, F., D. Eisel, M. Oswald, A. Kolte, D. Roell, W. Osen, S. B. Eichmueller, and R. Koenig (2020). "Reprogramming of macrophages employing gene regulatory and metabolic network models." PLoS Comput Biol 16(2). doi.org/10.1371/journal.pcbi.1007657.

Höflmayer, D., A. Steinhoff, C. Hube-Magg, M. Kluth, R. Simon, E. Burandt, M. C. Tsourlakis, S. Minner, G. Sauter, F. Büscheck, W. Wilczak, S. Steurer, H. Huland, M. Graefen, A. Haese, H. Heinzer, T. Schlomm, F. Jacobsen, A. Hinsch, A. M. Poos, M. Oswald, K. Rippe, R. König, and C. Schroeder (2020). "Expression of CCCTC‐binding factor (CTCF) is linked to poor prognosis in prostate cancer." Mol Oncol 14(1): 129. doi.org/10.1002/1878-0261.12597.

Sieverling, L., C. Hong, S. D. Koser, P. Ginsbach, K. Kleinheinz, B. Hutter, D. M. Braun, I. Cortés-Ciriano, R. Xi, R. Kabbe, P. J. Park, R. Eils, M. Schlesner, B. Brors, K. Rippe, D. T. W. Jones, L. Feuerbach, K. C. Akdemir, E. G. Alvarez, A. Baez-Ortega, R. Beroukhim, P. C. Boutros, D. D. L. Bowtell, B. Brors, K. H. Burns, P. J. Campbell, K. Chan, K. Chen, I. Cortés-Ciriano, A. Dueso-Barroso, A. J. Dunford, P. A. Edwards, X. Estivill, D. Etemadmoghadam, L. Feuerbach, J. L. Fink, M. Frenkel-Morgenstern, D. W. Garsed, M. Gerstein, D. A. Gordenin, D. Haan, J. E. Haber, J. M. Hess, B. Hutter, M. Imielinski, D. T. W. Jones, Y. S. Ju, M. D. Kazanov, L. J. Klimczak, Y. Koh, J. O. Korbel, K. Kumar, E. A. Lee, J. J.-K. Lee, Y. Li, A. G. Lynch, G. Macintyre, F. Markowetz, I. Martincorena, A. Martinez-Fundichely, M. Meyerson, S. Miyano, H. Nakagawa, F. C. P. Navarro, S. Ossowski, P. J. Park, J. V. Pearson, M. Puiggròs, K. Rippe, N. D. Roberts, S. A. Roberts, B. Rodriguez-Martin, S. E. Schumacher, R. Scully, M. Shackleton, N. Sidiropoulos, L. Sieverling, C. Stewart, D. Torrents, J. M. C. Tubio, I. Villasante, N. Waddell, J. A. Wala, J. Weischenfeldt, L. Yang, X. Yao, S.-S. Yoon, J. Zamora, and C.-Z. Zhang (2020). "Genomic footprints of activated telomere maintenance mechanisms in cancer." Nat Commun 11(1): 733. doi.org/10.1038/s41467-019-13824-9.

2019

Feuerbach, L., Sieverling, L., Deeg, K. I., Ginsbach, P., Hutter, B., Buchhalter, I., Northcott, P. A., Mughal, S. S., Chudasama, P., Glimm, H., Scholl, C., Lichter, P., Frohling, S., Pfister, S. M., Jones, D. T. W., Rippe, K. and Brors, B. (2019). "TelomereHunter - in silico estimation of telomere content and composition from cancer genomes." BMC Bioinformatics 20(1): 272. www.ncbi.nlm.nih.gov/pubmed/31138115.

Gao, Q. and Rohr, K. (2019). "A Global Method for Non-Rigid Registration of Cell Nuclei in Live Cell Time-Lapse Images." IEEE Trans Med Imaging 38(10): 2259-2270. www.ncbi.nlm.nih.gov/pubmed/30835217.

Jolivet, P., Serhal, K., Graf, M., Eberhard, S., Xu, Z., Luke, B. and Teixeira, M. T. (2019). "A subtelomeric region affects telomerase-negative replicative senescence in Saccharomyces cerevisiae." Sci Rep 9(1): 1845. www.ncbi.nlm.nih.gov/pubmed/30755624.

Kolte, A. and Konig, R. (2019). "Temporal progression of gene regulation of peripheral white blood cells explains gender dimorphism of critically ill patients after trauma." Mol Med 25(1): 19. www.ncbi.nlm.nih.gov/pubmed/31096912.

König, R., Cao, X., Oswald, M., Forstner, C., Rohde, G., Rupp, J., Witzenrath, M., Welte, T., Kolditz, M. and Pletz, M. (2019). "Macrolide combination therapy for patients hospitalised with community-acquired pneumonia? An individualised approach supported by machine learning." European Respiratory Journal 54: 6. www.ncbi.nlm.nih.gov/pubmed/31537702.

Kresinsky, A., Schnoder, T. M., Jacobsen, I. D., Rauner, M., Hofbauer, L. C., Ast, V., Konig, R., Hoffmann, B., Svensson, C. M., Figge, M. T., Hilger, I., Heidel, F. H., Bohmer, F. D. and Muller, J. P. (2019). "Lack of CD45 in FLT3-ITD mice results in a myeloproliferative phenotype, cortical porosity, and ectopic bone formation." Oncogene 38(24): 4773-4787. www.ncbi.nlm.nih.gov/pubmed/30820040.

Mallm, J. P., Iskar, M., Ishaque, N., Klett, L. C., Kugler, S. J., Muino, J. M., Teif, V. B., Poos, A. M., Grossmann, S., Erdel, F., Tavernari, D., Koser, S. D., Schumacher, S., Brors, B., Konig, R., Remondini, D., Vingron, M., Stilgenbauer, S., Lichter, P., Zapatka, M., Mertens, D. and Rippe, K. (2019). "Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks." Mol Syst Biol 15(5): e8339. www.ncbi.nlm.nih.gov/pubmed/31118277.

Minner, S., Lutz, J., Hube-Magg, C., Kluth, M., Simon, R., Höflmayer, D., Burandt, E., Tsourlakis, M. C., Sauter, G., Büscheck, F., Wilczak, W., Steurer, S., Schlomm, T., Huland, H., Graefen, M., Haese, A., Heinzer, H., Jacobsen, F., Hinsch, A., Poos, A., Oswald, M., Rippe, K., König, R. and Schroeder, C. (2019). "Loss of CCAAT-enhancer-binding protein alpha (CEBPA) is linked to poor prognosis in PTEN deleted and TMPRSS2:ERG fusion type prostate cancers." The Prostate 79(3): 302-311. www.ncbi.nlm.nih.gov/pubmed/30430607.

Poos, A. M., Kordass, T., Kolte, A., Ast, V., Oswald, M., Rippe, K. and Konig, R. (2019). "Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach." Bmc Bioinformatics 20(1): 12. www.ncbi.nlm.nih.gov/pubmed/31888467.

Ritter, C., Wollmann, T., Bernhard, P., Gunkel, M., Braun, D. M., Lee, J. Y., Meiners, J., Simon, R., Sauter, G., Erfle, H., Rippe, K., Bartenschlager, R. and Rohr, K. (2019). "Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells." Int J Comput Assist Radiol Surg. www.ncbi.nlm.nih.gov/pubmed/31177423.

Wollmann, T., Gunkel, M., Chung, I., Erfle, H., Rippe, K. and Rohr, K. (2019). "GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation." Med Image Anal 56: 68-79. www.ncbi.nlm.nih.gov/pubmed/31200289.

2018

Ansari, S. S., Sharma, A. K., Soni, H., Ali, D. M., Tews, B., König, R., Eibl, H.Berger, M. R., 2018. Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells. Cell Death Dis, 9(3), 296. doi.org/10.1038/s41419-018-0342-2

Bonetti, D.Longhese, M. P., 2018. Analysis of De Novo Telomere Addition by Southern Blot. Methods Mol. Biol., 1672, 363-373. doi.org/10.1007/978-1-4939-7306-4_25

Braun, D. M., Chung, I., Kepper, N., Deeg, K. I.Rippe, K., 2018. TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet., 19(1), 32. doi.org/10.1186/s12863-018-0617-8

Chudasama, P., Mughal, S. S., Sanders, M. A., Hübschmann, D., Chung, I., Deeg, K. I., Wong, S.-H., Rabe, S., Hlevnjak, M., Zapatka, M., Ernst, A., Kleinheinz, K., Schlesner, M., Sieverling, L., Klink, B., Schröck, E., Hoogenboezem, R. M., Kasper, B., Heilig, C. E., Egerer, G., Wolf, S., von Kalle, C., Eils, R., Stenzinger, A., Weichert, W., Glimm, H., Gröschel, S., Kopp, H.-G., Omlor, G., Lehner, B., Bauer, S., Schimmack, S., Ulrich, A., Mechtersheimer, G., Rippe, K., Brors, B., Hutter, B., Renner, M., Hohenberger, P., Scholl, C.Fröhling, S., 2018. Integrative genomic and transcriptomic analysis of leiomyosarcoma. Nat Commun, 9(1), 144. doi.org/10.1038/s41467-017-02602-0

Kluth, M., Scherzai, S., Büschek, F., Fraune, C., Möller, K., Höflmayer, D., Minner, S., Göbel, C., Möller-Koop, C., Hinsch, A., Neubauer, E., Tsourlakis, M. C., Sauter, G., Heinzer, H., Graefen, M., Wilczak, W., Luebke, A. M., Burandt, E., Steurer, S., Schlomm, T.Simon, R., 2018. 13q deletion is linked to an adverse phenotype and poor prognosis in prostate cancer. Genes Chromosomes Cancer, 57(10), 504-512. doi.org/10.1002/gcc.22645

Kluth, M., Volta, H., Hussein, M., Taskin, B., Frogh, S., Möller-Koop, C., Büscheck, F., Jacobsen, F., Tsourlakis, M. C., Lübke, A. M., Hinsch, A., Clauditz, T., Graefen, M., Heinzer, H., Huland, H., Minner, S., Sauter, G., Wilczak, W., Schlomm, T.Simon, R., 2018. Deletion of 3p13 is a late event linked to progression of TMPRSS2:ERG fusion prostate cancer. Cancer Manag Res, 10, 5909-5917. doi.org/10.2147/CMAR.S172637

Kresinsky, A., Bauer, R., Schnöder, T. M., Berg, T., Meyer, D., Ast, V., König, R., Serve, H., Heidel, F. H., Böhmer, F.-D.Müller, J. P., 2018. Loss of DEP-1 (Ptprj) promotes myeloproliferative disease in FLT3-ITD acute myeloid leukemia. Haematologica, 103(11), e505-e509. doi.org/10.3324/haematol.2017.185306

Luke, B., 2018. Telomere regulation. Differentiation, 102, 27-29. doi.org/10.1016/j.diff.2018.06.002

Michelini, F., Jalihal, A. P., Francia, S., Meers, C., Neeb, Z. T., Rossiello, F., Gioia, U., Aguado, J., Jones-Weinert, C., Luke, B., Biamonti, G., Nowacki, M., Storici, F., Carninci, P., Walter, N. G.Fagagna, F. d. A. d., 2018. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem. Rev., 118(8), 4365-4403. doi.org/10.1021/acs.chemrev.7b00487

Misino, S., Bonetti, D., Luke-Glaser, S.Luke, B., 2018. Increased TERRA levels and RNase H sensitivity are conserved hallmarks of post-senescent survivors in budding yeast. Differentiation, 100, 37-45. doi.org/10.1016/j.diff.2018.02.002

Sorokin, D. V., Peterlik, I., Tektonidis, M., Rohr, K.Matula, P., 2018. Non-Rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model. IEEE Trans Med Imaging, 37(1), 173-184. doi.org/10.1109/TMI.2017.2734169

 

2017

Braun, D.M., Chung, I., Kepper, N., Rippe, K., 2017. TelNet - a database for human and yeast genes involved in telomere maintenance. bioRxiv 130153. doi.org/10.1101/130153

Graf, M., Bonetti, D., Lockhart, A., Serhal, K., Kellner, V., Maicher, A., Jolivet, P., Teixeira, M.T., Luke, B., 2017. Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle. Cell 170, 72–85.e14. doi.org/10.1016/j.cell.2017.06.006

Gunkel, M., Chung, I., Wörz, S., Deeg, K.I., Simon, R., Sauter, G., Jones, D.T.W., Korshunov, A., Rohr, K., Erfle, H., Rippe, K., 2017a. Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Methods 114, 60–73. doi.org/10.1016/j.ymeth.2016.09.014

Gunkel, M., Eberle, J.P., Erfle, H., 2017b. Fluorescence-Based High-Throughput and Targeted Image Acquisition and Analysis for Phenotypic Screening. Methods Mol. Biol. 1563, 269–280. doi.org/10.1007/978-1-4939-6810-7_17

Kluth, M., Jung, S., Habib, O., Eshagzaiy, M., Heinl, A., Amschler, N., Masser, S., Mader, M., Runte, F., Barow, P., Frogh, S., Omari, J., Möller-Koop, C., Hube-Magg, C., Weischenfeldt, J., Korbel, J., Steurer, S., Krech, T., Huland, H., Graefen, M., Minner, S., Sauter, G., Schlomm, T., Simon, R., 2017. Deletion lengthening at chromosomes 6q and 16q targets multiple tumor suppressor genes and is associated with an increasingly poor prognosis in prostate cancer. Oncotarget 8, 108923–108935. doi.org/10.18632/oncotarget.22408

Lafuente-Barquero, J., Luke-Glaser, S., Graf, M., Silva, S., Gómez-González, B., Lockhart, A., Lisby, M., Aguilera, A., Luke, B., 2017. The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage. PLoS Genet. 13, e1007136. doi.org/10.1371/journal.pgen.1007136

Saraiva, J.P., Oswald, M., Biering, A., Röll, D., Assmann, C., Klassert, T., Blaess, M., Czakai, K., Claus, R., Löffler, J., Slevogt, H., König, R., 2017. Fungal biomarker discovery by integration of classifiers. BMC Genomics 18, 601. doi.org/10.1186/s12864-017-4006-x

Saraiva, L.F., P, J., Zubiria-Barrera, C., Klassert, T.E., Lautenbach, M.J., Blaess, M., Claus, R.A., Slevogt, H., König, R., 2017. Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes. Front. Microbiol. 8. doi.org/10.3389/fmicb.2017.02366

Tektonidis, M., Rohr, K., 2017. Diffeomorphic Multi-Frame Non-Rigid Registration of Cell Nuclei in 2D and 3D Live Cell Images. IEEE Trans Image Process 26, 1405–1417. doi.org/10.1109/TIP.2017.2653360

2016

Deeg, K.I., Chung, I., Bauer, C., Rippe, K., 2016. Cancer Cells with Alternative Lengthening of Telomeres Do Not Display a General Hypersensitivity to ATR Inhibition. Front Oncol 6, 186. doi.org/10.3389/fonc.2016.00186

Dieckmann, A.K., Babin, V., Harari, Y., Eils, R., König, R., Luke, B., Kupiec, M., 2016. Role of the ESCRT Complexes in Telomere Biology. MBio 7. doi.org/10.1128/mBio.01793-16

Eck, S., Wörz, S., Müller-Ott, K., Hahn, M., Biesdorf, A., Schotta, G., Rippe, K., Rohr, K., 2016. A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci. Med Image Anal 32, 18–31. doi.org/10.1016/j.media.2016.03.001

Ernst, A., Jones, D.T.W., Maass, K.K., Rode, A., Deeg, K.I., Jebaraj, B.M.C., Korshunov, A., Hovestadt, V., Tainsky, M.A., Pajtler, K.W., Bender, S., Brabetz, S., Gröbner, S., Kool, M., Devens, F., Edelmann, J., Zhang, C., Castelo-Branco, P., Tabori, U., Malkin, D., Rippe, K., Stilgenbauer, S., Pfister, S.M., Zapatka, M., Lichter, P., 2016. Telomere dysfunction and chromothripsis. Int. J. Cancer 138, 2905–2914. doi.org/10.1002/ijc.30033

Gietzelt, M., Höfer, T., Knaup-Gregori, P., König, R., Löpprich, M., Poos, A., Ganzinger, M., 2016. The Use of Tools, Modelling Methods, Data Types, and Endpoints in Systems Medicine: A Survey on Projects of the German e:Med-Programme. Stud Health Technol Inform 228, 670–674. doi.org/10.3233/978-1-61499-678-1-670

International Cancer Genome Consortium PedBrain Tumor Project, 2016. Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nat. Med. 22, 1314–1320. doi.org/10.1038/nm.4204

Kordaß, T., Weber, C.E.M., Oswald, M., Ast, V., Bernhardt, M., Novak, D., Utikal, J., Eichmüller, S.B., König, R., 2016. SOX5 is involved in balanced MITF regulation in human melanoma cells. BMC Med Genomics 9, 10. doi.org/10.1186/s12920-016-0170-0

Poos, A.M., Maicher, A., Dieckmann, A.K., Oswald, M., Eils, R., Kupiec, M., Luke, B., König, R., 2016. Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast. Nucleic Acids Res. doi.org/10.1093/nar/gkw111

Sharma, A.K., Eils, R., König, R., 2016. Copy Number Alterations in Enzyme-Coding and Cancer-Causing Genes Reprogram Tumor Metabolism. Cancer Res. 76, 4058–4067. http://doi.org/10.1158/0008-5472.CAN-15-2350

2015

Mallm, J.-P., Rippe, K., 2015. Aurora Kinase B Regulates Telomerase Activity via a Centromeric RNA in Stem Cells. Cell Rep 11, 1667–1678. doi.org/10.1016/j.celrep.2015.05.015

Melling, N., Thomsen, E., Tsourlakis, M.C., Kluth, M., Hube-Magg, C., Minner, S., Koop, C., Graefen, M., Heinzer, H., Wittmer, C., Sauter, G., Wilczak, W., Huland, H., Simon, R., Schlomm, T., Steurer, S., Krech, T., 2015. Overexpression of enhancer of zeste homolog 2 (EZH2) characterizes an aggressive subset of prostate cancers and predicts patient prognosis independently from pre- and postoperatively assessed clinicopathological parameters. Carcinogenesis 36, 1333–1340. doi.org/10.1093/carcin/bgv137

Osterwald, S., Deeg, K.I., Chung, I., Parisotto, D., Wörz, S., Rohr, K., Erfle, H., Rippe, K., 2015. PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening. J. Cell. Sci. 128, 1887–1900. doi.org/10.1242/jcs.148296

Rippe, K., Luke, B., 2015. TERRA and the state of the telomere. Nat. Struct. Mol. Biol. 22, 853–858. http://doi.org/10.1038/nsmb.3078

2014

Schacht, T., Oswald, M., Eils, R., Eichmüller, S.B., König, R., 2014. Estimating the activity of transcription factors by the effect on their target genes. Bioinformatics 30, i401-407. doi.org/10.1093/bioinformatics/btu446