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Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard Lin, Yu-Yu; Breuer, Kersten; Weichenhan, Dieter; Lafrenz, Pascal; Sarnataro, Antonella; Wilk, Agata; Chepeleva, Maryna; Mucke, Oliver; Schonung, Maximilian; Petermann, Franziska; Kensche, Philip Reiner; Weiser, Lena; Thommen, Frank; Giacomelli, Gideon; Nordstroem, Karl; Gonzalez-Avalos, Edahi; Merkel, Angelika; Kretzmer, Helene; Fischer, Jonas; Kramer, Stephen; Iskar, Murat; Wolf, Stephan; Buchhalter, Ivo; Esteller, Manel; Lawerenz, Christian; Twardziok, Sven; Zapatka, Marc; Hovestadt, Volker; Schlesner, Matthias; Schulz, Marcel H.; Hoffmann, Steve; Gerhauser, Clarissa; Walter, Jorn; Hartmann, Mark; Lipka, Daniel B.; Assenov, Yassen; Bock, Christoph; Plass, Christoph; Toth, Reka; Lutsik, Pavlo Share Save
A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders Zhang, Guokun; Jurinovic, Vindi; Bartels, Stephan; Christgen, Matthias; Christgen, Henriette; Kandt, Leonie Donata; Mishieva, Lidiya; Ni, Hua; Raap, Mieke; Klein, Janin; Katzke, Anna-Lena; Hofmann, Winfried; Steinemann, Doris; Kates, Ronald E.; Gluz, Oleg; Graeser, Monika; Kummel, Sherko; Nitz, Ulrike; Plass, Christoph; Lehmann, Ulrich; Eulenburg, Christine zu; Mansmann, Ulrich; Gerhauser, Clarissa; Harbeck, Nadia; Kreipe, Hans H. Share Save
EpiCRISPR targeted methylation of Arx gene initiates transient switch of mouse pancreatic alpha to insulin-producing cells Dordevic, Marija; Stepper, Peter; Feuerstein-Akgoz, Clarissa; Gerhauser, Clarissa; Paunovic, Verica; Tolic, Anja; Rajic, Jovana; Dinic, Svetlana; Uskokovic, Aleksandra; Grdovic, Nevena; Mihailovic, Mirjana; Jurkowska, Renata Z.; Jurkowski, Tomasz P.; Jovanovic, Jelena Arambasic; Vidakovic, Melita Share Save
DNA methylation biomarkers for noninvasive detection of triple-negative breast cancer using liquid biopsy Manoochehri, Mehdi; Borhani, Nasim; Gerhaeuser, Clarissa; Assenov, Yassen; Schoenung, Maximilian; Hielscher, Thomas; Christensen, Brock C.; Lee, Min Kyung; Grone, Hermann-Josef; Lipka, Daniel B.; Bruening, Thomas; Brauch, Hiltrud; Ko, Yon-Dschun; Hamann, Ute Share Save
A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation Llimos, Gerard; Gardeux, Vincent; Koch, Ute; Kribelbauer, Judith F.; Hafner, Antonina; Alpern, Daniel; Pezoldt, Joern; Litovchenko, Maria; Russeil, Julie; Dainese, Riccardo; Moia, Riccardo; Mahmoud, Abdurraouf Mokhtar; Rossi, Davide; Gaidano, Gianluca; Plass, Christoph; Lutsik, Pavlo; Gerhauser, Clarissa; Waszak, Sebastian M.; Boettiger, Alistair; Radtke, Freddy; Deplancke, Bart Share Save
Epigenetic quantification of circulating immune cells in peripheral blood of triple-negative breast cancer patients Manoochehri, Mehdi; Hielscher, Thomas; Borhani, Nasim; Gerhaeuser, Clarissa; Fletcher, Olivia; Swerdlow, Anthony J.; Ko, Yon-Dschun; Brauch, Hiltrud; Bruening, Thomas; Hamann, Ute Share Save
Random forest-based modelling to detect biomarkers for prostate cancer progression Toth, Reka; Schiffmann, Heiko; Hube-Magg, Claudia; Buescheck, Franziska; Hoeflmayer, Doris; Weidemann, Soeren; Lebok, Patrick; Fraune, Christoph; Minner, Sarah; Schlomm, Thorsten; Sauter, Guido; Plass, Christoph; Assenov, Yassen; Simon, Ronald; Meiners, Jan; Gerhaeuser, Clarissa Share Save
A systems biology network analysis of nutri(epi)genomic changes in endothelial cells exposed to epicatechin metabolites Milenkovic, Dragan; Vanden Berghe, Wim; Morand, Christine; Claude, Sylvain; van de Sandt, Annette; Gorressen, Simone; Monfoulet, Laurent-Emmanuel; Chirumamilla, Chandra S.; Declerck, Ken; Szic, Katarzyna Szarc Vel; Lahtela-Kakkonen, Maija; Gerhauser, Clarissa; Merx, Marc W.; Kelm, Malte Share Save
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DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats (vol 49, pg 1052, 2017) Brocks, David; Schmidt, Christopher R.; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M.; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B.; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Islam, Md Saiful; Lindroth, Anders M.; Haas, Simon; Essers, Marieke; Imbusch, Charles D.; Brors, Benedikt; Oehme, Ina; Witt, Olaf; Lubbert, Michael; Mallm, Jan-Philipp; Rippe, Karsten; Will, Rainer; Weichenhan, Dieter; Stoecklin, Georg; Gerhauser, Clarissa; Oakes, Christopher C.; Wang, Ting; Plass, Christoph Share Save
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Identification of differentially methylated BRCA1 and CRISP2 DNA regions as blood surrogate markers for cardiovascular disease Istas, Geoffrey; Declerck, Ken; Pudenz, Maria; Szic, Katarzyna Szarc Vel; Lendinez-Tortajada, Veronica; Leon-Latre, Montserrat; Heyninck, Karen; Haegeman, Guy; Casasnovas, Jose A.; Tellez-Plaza, Maria; Gerhauser, Clarissa; Heiss, Christian; Rodriguez-Mateos, Ana; Vanden Berghe, Wim Share Save
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats Brocks, David; Schmidt, Christopher R.; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M.; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B.; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Islam, Md Saiful; Lindroth, Anders M.; Haas, Simon; Essers, Marieke; Imbusch, Charles D.; Brors, Benedikt; Oehme, Ina; Witt, Olaf; Luebbert, Michael; Mallm, Jan-Philipp; Rippe, Karsten; Will, Rainer; Weichenhan, Dieter; Stoecklin, Georg; Gerhaeuser, Clarissa; Oakes, Christopher C.; Wang, Ting; Plass, Christoph Share Save
Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer Dewi, Dyah L.; Mohapatra, Soumya R.; Cabanes, Saioa Blanco; Adam, Isabell; Patterson, Luis F. Somarribas; Berdel, Bianca; Kahloon, Masroor; Thuemann, Loreen; Loth, Stefanie; Heilmann, Katharina; Weichenhan, Dieter; Muecke, Oliver; Heiland, Ines; Wimberger, Pauline; Kuhlmann, Jan Dominik; Kellner, Karl-Heinz; Schott, Sarah; Plass, Christoph; Platten, Michael; Gerhaeuser, Clarissa; Trump, Saskia; Opitz, Christiane A. Share Save
Quantitative comparison of DNA methylation assays for biomarker development and clinical applications Bock, Christoph; Halbritter, Florian; Carmona, Francisco J.; Tierling, Sascha; Datlinger, Paul; Assenov, Yassen; Berdasco, Maria; Bergmann, Anke K.; Booher, Keith; Busato, Florence; Campan, Mihaela; Dahl, Christina; Dahmcke, Christina M.; Diep, Dinh; Fernandez, Agustin F.; Gerhauser, Clarissa; Haake, Andrea; Heilmann, Katharina; Holcomb, Thomas; Hussmann, Dianna; Ito, Mitsuteru; Klaever, Ruth; Kreutz, Martin; Kulis, Marta; Lopez, Virginia; Nair, Shalima S.; Paul, Dirk S.; Plongthongkum, Nongluk; Qu, Wenjia; Queiros, Ana C.; Reinicke, Frank; Sauter, Guido; Schlomm, Thorsten; Statham, Aaron; Stirzaker, Clare; Strogantsev, Ruslan; Urdinguio, Rocio G.; Walter, Kimberly; Weichenhan, Dieter; Weisenberger, Daniel J.; Beck, Stephan; Clark, Susan J.; Esteller, Manel; Ferguson-Smith, Anne C.; Fraga, Mario F.; Guldberg, Per; Hansen, Lise Lotte; Laird, Peter W.; Martin-Subero, Jose I.; Nygren, Anders O. H.; Peist, Ralf; Plass, Christoph; Shames, David S.; Siebert, Reiner; Sun, Xueguang; Tost, Jorg; Walter, Joern; Zhang, Kun Share Save
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