Not logged in 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
Intracellular HIV-1 Tat regulator induces epigenetic changes in the DNA methylation landscape Rodriguez-Agustin, Andrea; Ayala-Suarez, Ruben; Diez-Fuertes, Francisco; Maleno, Maria Jose; de Villasante, Izar; Merkel, Angelika; Coiras, Mayte; Casanova, Victor; Alcami, Jose; Climent, Nuria Share Save
Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation Arribas, Victor; Onetti, Yara; Ramiro-Pareta, Marina; Villacampa, Pilar; Beck, Heike; Alberola, Mariona; Esteve-Codina, Anna; Merkel, Angelika; Sperandio, Markus; Martinez-Estrada, Ofelia M.; Schmid, Bettina; Montanez, Eloi Share Save
METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer Garcia-Vilchez, Raquel; Anazco-Guenkova, Ana M. M.; Dietmann, Sabine; Lopez, Judith; Moron-Calvente, Virginia; D'Ambrosi, Silvia; Nombela, Paz; Zamacola, Kepa; Mendizabal, Isabel; Garcia-Longarte, Saioa; Zabala-Letona, Amaia; Astobiza, Ianire; Fernandez, Sonia; Paniagua, Alejandro; Miguel-Lopez, Borja; Marchand, Virginie; Alonso-Lopez, Diego; Merkel, Angelika; Garcia-Tunon, Ignacio; Ugalde-Olano, Aitziber; Loizaga-Iriarte, Ana; Lacasa-Viscasillas, Isabel; Unda, Miguel; Azkargorta, Mikel; Elortza, Felix; Barcena, Laura; Gonzalez-Lopez, Monika; Aransay, Ana M. M.; Di Domenico, Tomas; Sanchez-Martin, Manuel A. A.; De Las Rivas, Javier; Guil, Sonia; Motorin, Yuri; Helm, Mark; Pandolfi, Pier Paolo; Carracedo, Arkaitz; Blanco, Sandra Share Save
Novel Targeting of DNA Methyltransferase Activity Inhibits Ewing Sarcoma Cell Proliferation and Enhances Tumor Cell Sensitivity to DNA Damaging Drugs by Activating the DNA Damage Response Cristalli, Camilla; Manara, Maria Cristina; Valente, Sergio; Pellegrini, Evelin; Bavelloni, Alberto; De Feo, Alessandra; Blalock, William; Di Bello, Elisabetta; Pineyro, David; Merkel, Angelika; Esteller, Manel; Tirado, Oscar M.; Mai, Antonello; Scotlandi, Katia Share Save
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Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture Hernandez, Inmaculada; Dhiman, Heena; Klanert, Gerald; Jadhav, Vaibhav; Auer, Norbert; Hanscho, Michael; Baumann, Martina; Esteve-Codina, Anna; Dabad, Marc; Gomez, Jessica; Alioto, Tyler; Merkel, Angelika; Raineri, Emanuele; Heath, Simon; Rico, Daniel; Borth, Nicole Share Save
Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes Yi, Guoqiang; Wierenga, Albertus T. J.; Petraglia, Francesca; Narang, Pankaj; Janssen-Megens, Eva M.; Mandoli, Amit; Merkel, Angelika; Berentsen, Kim; Kim, Bowon; Matarese, Filomena; Singh, Abhishek A.; Habibi, Ehsan; Prange, Koen H. M.; Mulder, Andre B.; Jansen, Joop H.; Clarke, Laura; Heath, Simon; van der Reijden, Bert A.; Flicek, Paul; Yaspo, Marie-Laure; Gut, Ivo; Bock, Christoph; Schuringa, Jan Jacob; Altucci, Lucia; Vellenga, Edo; Stunnenberg, Hendrik G.; Martens, Joost H. A. Share Save
Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils Grassi, Luigi; Pourfarzad, Farzin; Ullrich, Sebastian; Merkel, Angelika; Were, Felipe; Carrillo-de-Santa-Pau, Enrique; Yi, Guoqiang; Hiemstra, Ida H.; Tool, Anton T. J.; Mul, Erik; Perner, Juliane; Janssen-Megens, Eva; Berentsen, Kim; Kerstens, Hinri; Habibi, Ehsan; Gut, Marta; Yaspo, Marie Laure; Linser, Matthias; Lowy, Ernesto; Datta, Avik; Clarke, Laura; Flicek, Paul; Vingron, Martin; Roos, Dirk; van den Berg, Timo K.; Heath, Simon; Rico, Daniel; Frontini, Mattia; Kostadima, Myrto; Gut, Ivo; Valencia, Alfonso; Ouwehand, Willem H.; Stunnenberg, Hendrik G.; Martens, Joost H. A.; Kuijpers, Taco W. Share Save
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia Beekman, Renee; Chapaprieta, Vicente; Russinol, Nuria; Vilarrasa-Blasi, Roser; Verdaguer-Dot, Nuria; Martens, Joost H. A.; Duran-Ferrer, Marti; Kulis, Marta; Serra, Francois; Javierre, Biola M.; Wingett, Steven W.; Clot, Guillem; Queiros, Ana C.; Castellano, Giancarlo; Blanc, Julie; Gut, Marta; Merkel, Angelika; Heath, Simon; Vlasova, Anna; Ullrich, Sebastian; Palumbo, Emilio; Enjuanes, Anna; Martin-Garcia, David; Bea, Silvia; Pinyol, Magda; Aymerich, Marta; Royo, Romina; Puiggros, Montserrat; Torrents, David; Datta, Avik; Lowy, Ernesto; Kostadima, Myrto; Roller, Masa; Clarke, Laura; Flicek, Paul; Agirre, Xabier; Prosper, Felipe; Baumann, Tycho; Delgado, Julio; Lopez-Guillermo, Armando; Fraser, Peter; Yaspo, Marie-Laure; Guigo, Roderic; Siebert, Reiner; Marti-Renom, Marc A.; Puente, Xose S.; Lopez-Otin, Carlos; Gut, Ivo; Stunnenberg, Hendrik G.; Campo, Elias; Martin-Subero, Jose I. Share Save
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types Ecker, Simone; Chen, Lu; Pancaldi, Vera; Bagger, Frederik O.; Maria Fernandez, Jose; de Santa Pau, Enrique Carrillo; Juan, David; Mann, Alice L.; Watt, Stephen; Casale, Francesco Paolo; Sidiropoulos, Nikos; Rapin, Nicolas; Merkel, Angelika; Stunnenberg, Hendrik G.; Stegle, Oliver; Frontini, Mattia; Downes, Kate; Pastinen, Tomi; Kuijpers, Taco W.; Rico, Daniel; Valencia, Alfonso; Beck, Stephan; Soranzo, Nicole; Paul, Dirk S. Share Save
Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems Schuyler, Ronald P.; Merkel, Angelika; Raineri, Emanuele; Altucci, Lucia; Vellenga, Edo; Martens, Joost H. A.; Pourfarzad, Farzin; Kuijpers, Taco W.; Burden, Frances; Farrow, Samantha; Downes, Kate; Ouwehand, Willem H.; Clarke, Laura; Datta, Avik; Lowy, Ernesto; Flicek, Paul; Frontini, Mattia; Stunnenberg, Hendrik G.; Martin-Subero, Jose I.; Gut, Ivo; Heath, Simon Share Save
Comprehensive Genome and Epigenome Characterization of CHO Cells in Response to Evolutionary Pressures and Over Time Feichtinger, Julia; Hernandez, Inmaculada; Fischer, Christoph; Hanscho, Michael; Auer, Norbert; Hackl, Matthias; Jadhav, Vaibhav; Baumann, Martina; Krempl, Peter M.; Schmidl, Christian; Farlik, Matthias; Schuster, Michael; Merkel, Angelika; Sommer, Andreas; Heath, Simon; Rico, Daniel; Bock, Christoph; Thallinger, Gerhard G.; Borth, Nicole Share Save
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers Agirre, Xabier; Castellano, Giancarlo; Pascual, Marien; Heath, Simon; Kulis, Marta; Segura, Victor; Bergmann, Anke; Esteve, Anna; Merkel, Angelika; Raineri, Emanuele; Agueda, Lidia; Blanc, Julie; Richardson, David; Clarke, Laura; Datta, Avik; Russinol, Nuria; Queiros, Ana C.; Beekman, Renee; Rodriguez-Madoz, Juan R.; San Jose-Eneriz, Edurne; Fang, Fang; Gutierrez, Norma C.; Garcia-Verdugo, Jose M.; Robson, Michael I.; Schirmer, Eric C.; Guruceaga, Elisabeth; Martens, Joost H. A.; Gut, Marta; Calasanz, Maria J.; Flicek, Paul; Siebert, Reiner; Campo, Elias; San Miguel, Jesus F.; Melnick, Ari; Stunnenberg, Hendrik G.; Gut, Ivo G.; Prosper, Felipe; Martin-Subero, Jose I. Share Save
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; Gonzalez, Jose M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigo, Roderic Share Save
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