Not logged inPipeline 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 .png)
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SaveIndirect epigenetic testing identifies a diagnostic signature of cardiomyocyte DNA methylation in heart failureOeing, Christian U.; Pepin, Mark E.; Saul, Kerstin B.; Agircan, Ayca Seyhan; Assenov, Yassen; Merkel, Tobias S.; Sedaghat-Hamedani, Farbod; Weis, Tanja; Meder, Benjamin; Guan, Kaomei; Plass, Christoph; Weichenhan, Dieter; Siede, Dominik; Backs, Johannes Share Save DNA methylation biomarkers for noninvasive detection of triple-negative breast cancer using liquid biopsyManoochehri, 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 Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolutionRichter-Pechanska, Paulina; Kunz, Joachim B.; Rausch, Tobias; Erarslan-Uysal, Busra; Bornhauser, Beat; Frismantas, Viktoras; Assenov, Yassen; Zimmermann, Martin; Happich, Margit; von Knebel-Doeberitz, Caroline; von Neuhoff, Nils; Kohler, Rolf; Stanulla, Martin; Schrappe, Martin; Cario, Gunnar; Escherich, Gabriele; Kirschner-Schwabe, Renate; Eckert, Cornelia; Avigad, Smadar; Pfister, Stefan M.; Muckenthaler, Martina U.; Bourquin, Jean-Pierre; Korbel, Jan O.; Kulozik, Andreas E. Share Save Immunotyping of clinically divergent p.Phe508del homozygous monozygous cystic fibrosis twinsSchamschula, Esther; Hagmann, Wolfgang; Assenov, Yassen; Hedtfeld, Silke; Farag, Ahmed K.; Roesner, Lennart M.; Wiehlmann, Lutz; Stanke, Frauke; Fischer, Sebastian; Risch, Angela; Tuemmler, Burkhard Share Save Random forest-based modelling to detect biomarkers for prostate cancer progressionToth, 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 Histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic targetOrouji, Elias; Federico, Aniello; Larribere, Lionel; Novak, Daniel; Lipka, Daniel B.; Assenov, Yassen; Sachindra, Sachindra; Hueser, Laura; Granados, Karol; Gebhardt, Christoffer; Plass, Christoph; Umansky, Viktor; Utikal, Jochen Share Save DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancerWeigel, Christoph; Chaisaingmongkol, Jittiporn; Assenov, Yassen; Kuhmann, Christine; Winkler, Volker; Santi, Irene; Bogatyrova, Olga; Kaucher, Simone; Bermejo, Justo L.; Leung, Suet Y.; Chan, Tsun L.; Lasitschka, Felix; Bohrer, Manfred H.; Marx, Alexander; Heyny-von Haussen, Roland; Herold-Mende, Christel; Dyckhoff, Gerhard; Boukamp, Petra; Delank, Klaus W.; Hoermann, Karl; Lippert, Burkhard M.; Baier, Gerald; Dietz, Andreas; Oakes, Christopher C.; Plass, Christoph; Becher, Heiko; Schmezer, Peter; Ramroth, Heribert; Popanda, Odilia Share Save Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic CholangiocarcinomaGoeppert, Benjamin; Toth, Reka; Singer, Stephan; Albrecht, Thomas; Lipka, Daniel B.; Lutsik, Pavlo; Brocks, David; Baehr, Marion; Muecke, Oliver; Assenov, Yassen; Gu, Lei; Endris, Volker; Stenzinger, Albrecht; Mehrabi, Arianeb; Schirmacher, Peter; Plass, Christoph; Weichcnhan, Dieter; Roessler, Stephanie Share Save Share Save Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood CellsThier, Marc Christian; Hommerding, Oliver; Panten, Jasper; Pinna, Roberta; Garcia-Gonzalez, Diego; Berger, Thomas; Woersdoefer, Philipp; Assenov, Yassen; Scognamiglio, Roberta; Przybylla, Adriana; Kaschutnig, Paul; Becker, Lisa; Milsom, Michael D.; Jauch, Anna; Utikal, Jochen; Herrmann, Carl; Monyer, Hannah; Edenhofer, Frank; Trumpp, Andreas Share Save PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemiaRichter-Pechanska, Paulina; Kunz, Joachim B.; Bornhauser, Beat; Doeberitz, Caroline von Knebel; Rausch, Tobias; Erarslan-Uysal, Buesra; Assenov, Yassen; Frismantas, Viktoras; Marovca, Blerim; Waszak, Sebastian M.; Zimmermann, Martin; Seemann, Julia; Happich, Margit; Stanulla, Martin; Schrappe, Martin; Cario, Gunnar; Escherich, Gabriele; Bakharevich, Kseniya; Kirschner-Schwabe, Renate; Eckert, Cornelia; Muckenthaler, Martina U.; Korbel, Jan O.; Bourquin, Jean-Pierre; Kulozik, Andreas E. Share Save Share Save Share Save Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitorsDaskalakis, Michael; Brocks, David; Sheng, Yi-Hua; Islam, Md Saiful; Ressnerova, Alzbeta; Assenov, Yassen; Milde, Till; Oehme, Ina; Witt, Olaf; Goyal, Ashish; Kuehn, Alexander; Hartmann, Mark; Weichenhan, Dieter; Jung, Manfred; Plass, Christoph Share Save RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemiaLipka, Daniel B.; Witte, Tania; Toth, Reka; Yang, Jing; Wiesenfarth, Manuel; Noellke, Peter; Fischer, Alexandra; Brocks, David; Gu, Zuguang; Park, Jeongbin; Strahm, Brigitte; Wlodarski, Marcin; Yoshimi, Ayami; Claus, Rainer; Luebbert, Michael; Busch, Hauke; Boerries, Melanie; Hartmann, Mark; Schoenung, Maximilian; Kilik, Umut; Langstein, Jens; Wierzbinska, Justyna A.; Pabst, Caroline; Garg, Swati; Catala, Albert; De Moerloose, Barbara; Dworzak, Michael; Hasle, Henrik; Locatelli, Franco; Masetti, Riccardo; Schmugge, Markus; Smith, Owen; Stary, Jan; Ussowicz, Marek; van den Heuvel-Eibrink, Marry M.; Assenov, Yassen; Schlesner, Matthias; Niemeyer, Charlotte; Flotho, Christian; Plass, Christoph Share Save Genome-wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stabilityJaekel, Cornelia; Bergmann, Frank; Toth, Reka; Assenov, Yassen; van der Duin, Daniel; Strobel, Oliver; Hank, Thomas; Kloeppel, Guenter; Dorrell, Craig; Grompe, Markus; Moss, Joshua; Dor, Yuval; Schirmacher, Peter; Plass, Christoph; Popanda, Odilia; Schmezer, Peter Share Save Share Save 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 Share Save 
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