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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
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DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape Gehrs, Stephanie; Gu, Zuguang; Hey, Joschka; Weichenhan, Dieter; Buckwalter, Niklas; Jakab, Moritz; Hotz-Wagenblatt, Agnes; Breuer, Kersten; Prada, Maria Llamazares; Huebschmann, Daniel; Schlereth, Katharina; Plass, Christoph; Augustin, Hellmut Share Save
The spatial zonation of the murine placental vasculature is specified by epigenetic mechanisms Gehrs, Stephanie; Jakab, Moritz; Gutjahr, Ewgenija; Gu, Zuguang; Weichenhan, Dieter; Mallm, Jan-Philipp; Mogler, Carolin; Schlesner, Matthias; Plass, Christoph; Schlereth, Katharina; Augustin, Hellmut G. Share Save
Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) Weichenhan, Dieter; Riedel, Anna; Sollier, Etienne; Toprak, Umut H.; Hey, Joschka; Breuer, Kersten; Wierzbinska, Justyna A.; Touzart, Aurore; Lutsik, Pavlo; Baehr, Marion; Ostlund, Anders; Nilsson, Tina; Jacobsson, Susanna; Edler, Marcel; Waraky, Ahmed; Behrens, Yvonne Lisa; Goehring, Gudrun; Schlegelberger, Brigitte; Steinek, Clemens; Harz, Hartmann; Leonhardt, Heinrich; Dolnik, Anna; Reinhardt, Dirk; Bullinger, Lars; Palmqvist, Lars; Lipka, Daniel B.; Plass, Christoph Share Save
ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response Bakr, Ali; Della Corte, Giuditta; Veselinov, Olivera; Kelekci, Simge; Chen, Mei-Ju May; Lin, Yu-Yu; Sigismondo, Gianluca; Iacovone, Marika; Cross, Alice; Syed, Rabail; Jeong, Yunhee; Sollier, Etienne; Liu, Chun-Shan; Lutsik, Pavlo; Krijgsveld, Jeroen; Weichenhan, Dieter; Plass, Christoph; Popanda, Odilia; Schmezer, Peter Share Save
Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions Schoepf, Julia; Uhrig, Sebastian; Heilig, Christoph E.; Lee, Kwang-Seok; Walther, Tatjana; Carazzato, Alexander; Dobberkau, Anna Maria; Weichenhan, Dieter; Plass, Christoph; Hartmann, Mark; Diwan, Gaurav D.; Carrero, Zunamys, I; Ball, Claudia R.; Hohl, Tobias; Kindler, Thomas; Rudolph-Haehnel, Patricia; Helm, Dominic; Schneider, Martin; Nilsson, Anna; Ora, Ingrid; Imle, Roland; Banito, Ana; Russell, Robert B.; Jones, Barbara C.; Lipka, Daniel B.; Glimm, Hanno; Huebschmann, Daniel; Hartmann, Wolfgang; Froehling, Stefan; Scholl, Claudia Share Save
Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen Schmutz, Maximilian; Zucknick, Manuela; Schlenk, Richard F.; Mertens, Daniel; Benner, Axel; Weichenhan, Dieter; Muecke, Oliver; Doehner, Konstanze; Plass, Christoph; Bullinger, Lars; Claus, Rainer Share Save
High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD Schwartz, Uwe; Prada, Maria Llamazares; Pohl, Stephanie T.; Richter, Mandy; Tamas, Raluca; Schuler, Michael; Keller, Corinna; Mijosek, Vedrana; Muley, Thomas; Schneider, Marc A.; Quast, Karsten; Hey, Joschka; Heussel, Claus P.; Warth, Arne; Winter, Hauke; Sercin, Oezdemirhan; Karmouty-Quintana, Harry; Jyothula, Soma S. K.; Patel, Manish K.; Herth, Felix; Koch, Ina; Petrosino, Giuseppe; Titimeaua, Alexandru; Mardin, Balca R.; Weichenhan, Dieter; Jurkowski, Tomasz P.; Imbusch, Charles D.; Brors, Benedikt; Benes, Vladimir; Jung, Birgit; Wyatt, David; Stahl, Heiko F.; Plass, Christoph; Jurkowska, Renata Z. Share Save
Genomic, transcriptomic, functional, and mechanistic characterization of rhabdomyosarcoma with FUS-TFCP2 or EWSR1-TFCP2 fusions Schoepf, Julia; Uhrig, Sebastian; Heilig, Christoph E.; Lee, Kwang-Seok; Walther, Tatjana; Carazzato, Alexander; Dobberkau, Anna Maria; Weichenhan, Dieter; Plass, Christoph; Hartmann, Mark; Diwan, Gaurav; Carrero, Zunamys; Ball, Claudia R.; Hohl, Tobias; Kindler, Thomas; Rudolph-Hahnel, Patricia; Nilsson, Anna; Ora, Ingrid; Imle, Roland; Banito, Ana; Russell, Robert; Jones, Barbara C.; Lipka, Daniel B.; Glimm, Hanno; Hubschmann, Daniel; Hartmann, Wolfgang; Frohling, Stefan; Scholl, Claudia Share Save
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Translocation t(6;7) in AML-M4 cell line GDM-1 results in MNX1 activation through enhancer-hijacking Weichenhan, Dieter; Riedel, Anna; Meinen, Charlotte; Basic, Alisa; Toth, Reka; Baehr, Marion; Lutsik, Pavlo; Hey, Joschka; Sollier, Etienne; Toprak, Umut H.; Kelekci, Simge; Lin, Yu-Yu; Hakobyan, Mariam; Touzart, Aurore; Goyal, Ashish; Wierzbinska, Justyna A.; Schlesner, Matthias; Westermann, Frank; Lipka, Daniel B.; Plass, Christoph Share Save
Indirect epigenetic testing identifies a diagnostic signature of cardiomyocyte DNA methylation in heart failure Oeing, 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
Global hypomethylation in childhood asthma identified by genome-wide DNA-methylation sequencing preferentially affects enhancer regions Thuermann, Loreen; Kloes, Matthias; Mackowiak, Sebastian D.; Bieg, Matthias; Bauer, Tobias; Ishaque, Naveed; Messingschlager, Marey; Herrmann, Carl; Roeder, Stefan; Bauer, Mario; Schaeuble, Sascha; Faessler, Erik; Hahn, Udo; Weichenhan, Dieter; Muecke, Oliver; Plass, Christoph; Borte, Michael; von Mutius, Erika; Stangl, Gabriele I.; Lauener, Roger; Karvonen, Anne M.; Divaret-Chauveau, Amandine; Riedler, Josef; Heinrich, Joachim; Standl, Marie; von Berg, Andrea; Schaaf, Beate; Herberth, Gunda; Kabesch, Michael; Eils, Roland; Trump, Saskia; Lehmann, Irina Share Save
Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression Boonsanay, Boonsanay; Mosa, Mohammed H.; Looso, Mario; Weichenhan, Dieter; Ceteci, Fatih; Pudelko, Lorenz; Lechel, Andre; Michel, Christian S.; Kuenne, Carsten; Farin, Henner F.; Plass, Christoph; Greten, Florian R. Share Save
TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer Smith, Charlotte; Goyal, Ashish; Weichenhan, Dieter; Allemand, Eric; Mayakonda, Anand; Toprak, Umut; Riedel, Anna; Balducci, Estelle; Manojkumar, Manisha; Pejkovska, Anastasija; Muecke, Oliver; Sollier, Etienne; Bakr, Ali; Breuer, Kersten; Lutsik, Pavlo; Hermine, Olivier; Spicuglia, Salvatore; Asnafi, Vahid; Plass, Christoph; Touzart, Aurore Share Save
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