Publications & Preprints

2020

Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortes-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Rippe K, Jones DTW, Brors B & Feuerbach L & PCAWG Consortium (2020) Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 11, 733. doi: 10.1038/s41467-019-13824-9 | Abstract | Reprint (2.2 MB) | Article metrics

Campbell, P.J., Getz, G., Korbel, J.O. et al. (2020) Pan-cancer analysis of whole genomes. Nature 578, 82-93. doi: 10.1038/s41586-020-1969-6 | Abstract | Reprint (23.6 MB) | Article metrics

Mallm JP, Windisch P, Biran A, Schumacher S, Glass R, Herold-Mende C, Meshorer E, Barbus M & Rippe K (2020) Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to loss of DNA repair capacity. Intl J Cancer 146, 1281-1292. doi: 10.1002/ijc.32649 | Abstract | Reprint (6.6 MB) | Article metrics

Hoflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Buscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, Konig R & Schroeder C (2020) Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Mol Oncol14, 129-138. doi: 10.1002/1878-0261.12597 | Abstract | Reprint (10.5 MB) | Article metrics

2019

Poos AM, Kordass T, Kolte A, Ast V, Oswald M, Rippe K & Konig R (2019) Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 20, 737. doi: 10.1186/s12859-019-3323-2

Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2019) GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation. Med Image Anal 56, 68-79. doi: 10.1016/j.media.2019.04.011 | Abstract | Reprint (2.1 MB) | Article metrics

Ritter C, Wollmann T, Bernhard P, Gunkel M, Braun DM, Lee JY, Meiners J, Simon R, Sauter G, Erfle H, Rippe K, Bartenschlager R & 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, 14, 1847-1857. doi: 10.1007/s11548-019-02010-3 | Abstract | Reprint (1.8 MB)

Feuerbach L, Sieverling L Deeg, KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Peter Lichter P, Fröhling S, Pfister SM, Jones DT, Rippe K & Brors B (2019). TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. BMC Bioinformatics 20, 272. doi: 10.1186/s12859-019-2851-0 | Abstract | Reprint (1.4 MB) | Article metrics

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D & Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: 10.15252/msb.20188339 | Abstract | Reprint (7.1 MB) | Appendix (6.8 MB) | Additional data | Article metrics

Wollmann T, Bernhard P, Gunkel M, Braun DM, Erfle H, Rippe K & Rohr K (2019) Black-box hyperparameter optimization for nuclei segmentation in prostate tissue images. In Bildverarbeitung für die Medizin 2019 (BVM 2019), Handels H, Deserno T, Maier A, Maier-Hein K, Palm C & Tolxdorff T, eds., Springer Vieweg, Wiesbaden, 345-350. doi: 10.1007/978-3-658-25326-4_75 | Reprint (0.7 MB) | Article metrics

Gao Q and Rohr K. (2019) A Global Method for Non-Rigid Registration of Cell Nuclei in Live Cell Time-Lapse Images, IEEE Transactions on Medical Imaging 38:10, 2259-2270

Minner S, Lutz J, Hube-Magg C, Kluth M, Simon R, Hoflmayer D, Burandt E, Tsourlakis MC, Sauter G, Buscheck 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, Konig R & 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. Prostate 79, 302-311. doi: 10.1002/pros.23736 | Abstract | Reprint (1.4 MB) | Article metrics

2018

Gao Q, Eck S, Matthias J, Chung I, Engelhardt J, Rippe K & Rohr K (2018) Bayesian joint super-resolution, deconvolution, and denoising of images with Poisson-Gaussian noise. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 938-942. doi: 10.1109/ISBI.2018.8363725 | Abstract | Reprint (0.4 MB)

Baltissen D, Wollmann T, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2018) Comparison of segmentation methods for tissue microscopy images of glioblastoma cells. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), 396-399. doi: 10.1109/ISBI.2018.8363601 | Abstract | Reprint (0.4 MB)

Braun DM, Chung I, Kepper N & Rippe K (2018). TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet 19, 32. doi: 10.1186/s12863-018-0617-8 | Abstract | Reprint (2.4 MB)

Wollmann T, Ivanova J, Gunkel M, Chung I, Erfle H, Rippe K & Rohr K (2018). Multi-channel deep transfer learning for nuclei segmentation in glioblastoma cell tissue images. In Bildverarbeitung für die Medizin 2018, Springer Berlin Heidelberg, 316-321. doi: 10.1007/978-3-662-56537-7_83 | Abstract | Reprint (0.6 MB)

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: 10.1016/j.diff.2018.02.002. Epub 2018 Feb 16.

Chudasama P, Mughal S, Sanders M, Hübschmann D, Chung I, Deeg KI, Wong SH, Rabe S, Hlevnjak M, Zapatka M, Ernst A, Kleinheinz K, Schlesner M, Sieverling L, Klink B, Schröck E, Hoogenboezem R, Kasper B, Heilig C, 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, 144. doi: 10.1038/s41467-017-02602-0 | Abstract | Reprint (3.1 MB) | Article metrics

Eberle JP, Muranyi W, Erfle H & Gunkel M (2018). Fully Automated Targeted Confocal and Single-Molecule Localization Microscopy. Methods Mol Biol 1663, 139-152. doi: 10.1007/978-1-4939-7265-4_12 | Abstract

2017

Graf M, Bonetti D, Lockhart A, Serha K, Kellner V, Maicher A, Jolivet P, Teixeira MT & Luke B (2017). Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle. Cell 170, 72-85. doi: 10.1016/j.cell.2017.06.006 | Abstract

Burdelski C, Borcherding L, Kluth M, Hube-Magg C, Melling N, Simon R, et al. (2017). Family with sequence similarity 13C (FAM13C) overexpression is an independent prognostic marker in prostate cancer. Oncotarget 8, 31494-508. | Abstract

Deeg KI, Chung I, Poos AM, Braun DM, Korshunov A, Oswald M, Keppe, N, Bender S, Castel D, Lichter P, Grill J, Pfister SM, König R, Jones DT & Rippe K (2017). Dissecting telomere maintenance mechanisms in pediatric glioblastoma. bioRxiv 129106. doi: 10.1101/129106

Gunkel M, Eberle JP & Erfle H (2017). Fluorescence-Based High-Throughput and Targeted Image Acquisition and Analysis for Phenotypic Screening. Methods Mol Biol 1563, 269-280. doi: 10.1007/978-1-4939-6810-7_17 | Abstract

Tektonidis M and 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: 10.1109/TIP.2017.2653360 | Abstract

Gunkel M, Chung I, Wörz S, Deeg KI, Simon R, Sauter G, Jones DT, Korshunov A, Rohr K, Erfle H & Rippe K (2017). Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Methods 114, 60-73. doi: 10.1016/j.ymeth.2016.09.014 | Abstract

Eberle JP, Muranyi W, Erfle H, Gunkel M (2017). Fully automated targeted confocal and single-molecule localization microscopy. Humana Press: Super-Resolution Microscopy, 139-152.

Eberle JP, Rapp A, Krufczik M, Eryilmaz M, Gunkel M, Erfle H, et al. (2017). Super-resolution microscopy techniques and their potential for applications in radiation biophysics. Humana Press: Super-Resolution Microscopy, 1-13.

Gunkel M, Eberle JP, Erfle H. (2017). Fluorescence-based high-throughput and targeted image acquisition and analysis for phenotypic screening. Humana Press: Light Microscopy, 269-280.

Wollmann T, Erfle H, Eils R, Rohr K, Gunkel M (2017). Workflows for microscopy image analysis and cellular phenotyping. J Biotechnol 261, 70-75.

Melling N, Rashed M, Schroeder C, Hube-Magg C, Kluth M, Lang D, et al. (2017). High-Level gamma-Glutamyl-Hydrolase (GGH) Expression is Linked to Poor Prognosis in ERG Negative Prostate Cancer. Int J Mol Sci 18, E286. doi: 10.3390/ijms18020286 | Abstract

Kluth M, Amschler NN, Galal R, Moller-Koop C, Barrow P, Tsourlakis MC, et al. (2017). Deletion of 8p is an independent prognostic parameter in prostate cancer. Oncotarget 8, 379-92. | Abstract

Wilczak W, Rashed S, Hube-Magg C, Kluth M, Simon R, Buscheck F, et al. (2017). Up-regulation of mismatch repair genes MSH6, PMS2 and MLH1 parallels development of genetic instability and is linked to tumor aggressiveness and early PSA recurrence in prostate cancer. Carcinogenesis 38, 19-27. doi: 10.1093/carcin/bgw116 | Abstract

2016

Bender S, Gronych J, Warnatz HJ, Hutter B, Gröbner S, Ryzhova M, Pfaff E, Hovestadt V, Weinberg F, Halbach S, et al. (2016). Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nat Med 22, 1-9. doi:10.1038/nm.4204 | Abstract

Dieckmann A, Babin V, Harari Y, Eils R, König R, Luke B & Kupiec M (2016) Role of ESCRT complexes in telomere biology. MBio 7, e01793-16. doi: 10.1128/mBio.01793-16 | Abstract

Deeg KI, 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: 10.3389/fonc.2016.00186 | Abstract

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: 10.1016/j.media.2016.03.001 | Abstract

Sharma AK, Eils R & König R (2016). Copy number alterartions in enzyme-coding and cancer-causing genes reprogram tumor metabolism. Cancer Res 76, 4058-4067. doi:10.1158/0008-5472.CAN-15-2350 | Abstract

Feuerbach L, Sieverling L Deeg, KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Lichter P, Pfister SM, Jones DT, Rippe K & Brors, B (2016). TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. bioRxiv 065532. doi: 10.1101/065532

Poos AM, Maicher A, Dieckmann A, 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 44, e93. doi: 10.1093/nar/gkw111 | Abstract .

Ernst A, Jones D., Maass KK, Rode A, Deeg KI, Jebaraj BM, Korshunov A, Hovestadt V, Tainsky MA, Pajtler KW, 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 SM, Zapatka M & Lichter P (2016). Telomere dysfunction and chromothripsis. Int J Cancer 138, 2905-2914. doi: 10.1002/ijc.30033 | Abstract.

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 Helth Technol Inform 228, 670-674. doi:10.3233/978-1-61499-678-1-670 | Abstract

Kluth M, Graunke M, Moller-Koop C, Hube-Magg C, Minner S, Michl U, et al. (2016) Deletion of 18q is a strong and independent prognostic feature in prostate cancer. Oncotarget 7, 86339-49. | Abstract

Kordaß T, Weber CEM, Oswald M, Ast V, Bernhardt M, Novak D, Utikal J, Eichmüller S & König R (2016). SOX5 is involved in balanced MITF regulation in human melanoma cells. BMC Med Genomics 9, 10. doi:10.1186/s12920-016-0170-0 | Abstract

2015

Rippe K & Luke B (2015). TERRA and the state of the telomere. Nat Struct Mol Biol 22, 853-858. doi: 10.1038/nsmb.3078 | Abstract.

Melling N, Thomsen E, Tsourlakis MC, 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:10.1093/carcin/bgv137 | Abstract

Mallm, JP & Rippe K (2015). Aurora kinase B regulates telomerase activity via a centromeric RNA in stem cells. Cell Rep 11, 1667-1678. doi: 10.1016/j.celrep.2015.05.015 | Abstract

Osterwald S, Deeg KI, Chung I, Parisotto D, Wörz S, Rohr K, Erfle H & Rippe K (2015). PML induces compaction, partial TRF2 depletion and DNA damage signaling at telomeres and promotes alternative lengthening of telomeres. J Cell Sci 128, 1887-1900. doi: 10.1242/jcs.148296 | Abstract.

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