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
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DISSECTING THE CELLULAR ARCHITECTURE OF BREAST CANCER BRAIN METASTASES REVEALS PROGNOSTICALLY DISTINCT IMMUNE LANDSCAPES Jassowicz, L.; Feng, F.; Warta, R.; Sor, F.; Soller, J.; Wollner, A.; Lotsch, C.; Wong, J. K.; Schlegel, J.; Frank, L.; Dao Trong, P.; Jungwirth, G.; Nohman, A.; Maass, K.; Barthel, M.; Unterberg, A.; Krieg, S. M.; Rippe, K.; Abdollahi, A.; von Deimling, A.; Malm, J.; Lichter, P.; Zapatka, M.; Seiffert, M.; Herold-Mende, C. Share Save
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Biopsy-derived organoids in personalised early breast cancer care: Challenges of tumour purity and normal cell overgrowth cap their practical utility Schwerd-Kleine, Paul; Wuerth, Roberto; Cheytan, Tasneem; Michel, Laura; Thewes, Verena; Gutjahr, Ewgenija; Seker-Cin, Huriye; Kazdal, Daniel; Neuberth, Sarah-Jane; Thiel, Vera; Schwickert, Jonas; Vorberg, Tim; Wischhusen, Jennifer; Stenzinger, Albrecht; Zapatka, Marc; Lichter, Peter; Schneeweiss, Andreas; Trumpp, Andreas; Sprick, Martin R. Share Save
COGNITION/-GUIDE - Implementation of Precision Oncology in Early High-Risk Breast Cancer Thewes, Verena; Strassl, Luise; Zapatka, Marc; Hlevnjak, Mario; Pixberg, Constantin; Maurer, Christian; Smetanay, Katharina; Fremd, Carlo; Michel, Laura; Heublein, Sabine; Wagner, Celina V.; Suppelna, Jan-Philip; Buschhorn, Lars; Stenzinger, Albrecht; Haidinger, Renate; Schumacher-Wulf, Eva; Loibl, Sibylle; Wimberger, Pauline; Blohmer, Jens-Uwe; Fasching, Peter A.; Janni, Wolfgang; Schlenk, Richard F.; Lichter, Peter; Schneeweiss, Andreas Share Save
B cell immunology predict response and survival in PD-1/PD-L1 targeting immune checkpoint inhibition of metastatic breast cancer Fremd, Carlo; Schulze, Markus; Cetin, Miray; Boehm, Hannah; Lenoire, Benedicte; Akilli-Oeztuerk, Oezlem; Zornig, Inka; Charoentong, Pornpimol; Lyu, Yanhong; Hubschmann, Daniel; Hubschmann, Daniel; Kommoss, Felix; Thewes, Verena; Schneeweiss, Andreas; Zapatka, Marc; Hartmann, Felix; Lichter, Peter Share Save
A composite biomarker for evaluation of homologous recombination repair deficiency in a pan-cancer cohort Ruebsam, M.; Rheinnecker, M.; Hutter, B.; Froehlich, M.; Heilig, C. E.; Paramasivam, N.; Oles, M.; Ball, C.; Glimm, H.; Hlevnjak, M.; Zapatka, M.; Lichter, P.; Froehling, S.; Schlenk, R. F.; Huebschmann, D. Share Save
The landscape of viral associations in human cancers (vol 52, pg 320, 2020) Zapatka, Marc; Borozan, Ivan; Brewer, Daniel S.; Iskar, Murat; Grundhoff, Adam; Alawi, Malik; Desai, Nikita; Sultmann, Holger; Moch, Holger; Cooper, Colin S.; Eils, Roland; Ferretti, Vincent; Lichter, Peter Share Save
COGNITION: a prospective precision oncology trial for patients with early breast cancer at high risk following neoadjuvant chemotherapy Pixberg, C.; Zapatka, M.; Hlevnjak, M.; Benedetto, S.; Suppelna, J. P.; Heil, J.; Smetanay, K.; Michel, L.; Fremd, C.; Koerber, V; Ruebsam, M.; Buschhorn, L.; Heublein, S.; Schaefgen, B.; Golatta, M.; Gomez, C.; von Au, A.; Wallwiener, M.; Wolf, S.; Dikow, N.; Schaaf, C.; Gutjahr, E.; Allgaeuer, M.; Stenzinger, A.; Pfuetze, K.; Kirsten, R.; Huebschmann, D.; Sinn, H-P; Jaeger, D.; Trumpp, A.; Schlenk, R.; Hoefer, T.; Thewes, V; Schneeweiss, A.; Lichter, P. Share Save
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia Herbst, Sophie A.; Vesterlund, Mattias; Helmboldt, Alexander J.; Jafari, Rozbeh; Siavelis, Ioannis; Stahl, Matthias; Schitter, Eva C.; Liebers, Nora; Brinkmann, Berit J.; Czernilofsky, Felix; Roider, Tobias; Bruch, Peter-Martin; Iskar, Murat; Kittai, Adam; Huang, Ying; Lu, Junyan; Richter, Sarah; Mermelekas, Georgios; Umer, Husen Muhammad; Knoll, Mareike; Kolb, Carolin; Lenze, Angela; Cao, Xiaofang; Osterholm, Cecilia; Wahnschaffe, Linus; Herling, Carmen; Scheinost, Sebastian; Ganzinger, Matthias; Mansouri, Larry; Kriegsmann, Katharina; Kriegsmann, Mark; Anders, Simon; Zapatka, Marc; Del Poeta, Giovanni; Zucchetto, Antonella; Bomben, Riccardo; Gattei, Valter; Dreger, Peter; Woyach, Jennifer; Herling, Marco; Muller-Tidow, Carsten; Rosenquist, Richard; Stilgenbauer, Stephan; Zenz, Thorsten; Huber, Wolfgang; Tausch, Eugen; Lehtioe, Janne; Dietrich, Sascha Share Save
Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly- informed therapies despite heterogeneity Moehrmann, Lino; Werner, Maximilian; Oles, Malgorzata; Mock, Andreas; Uhrig, Sebastian; Jahn, Arne; Kreutzfeldt, Simon; Froehlich, Martina; Hutter, Barbara; Paramasivam, Nagarajan; Richter, Daniela; Beck, Katja; Winter, Ulrike; Pfuetze, Katrin; Heilig, Christoph E.; Teleanu, Veronica; Lipka, Daniel B.; Zapatka, Marc; Hanf, Dorothea; List, Catrin; Allgaeuer, Michael; Penzel, Roland; Ruter, Gina; Jelas, Ivan; Hamacher, Rainer; Falkenhorst, Johanna; Wagner, Sebastian; Brandts, Christian H.; Boerries, Melanie; Illert, Anna L.; Metzeler, Klaus H.; Westphalen, C. Benedikt; Desuki, Alexander; Kindler, Thomas; Folprecht, Gunnar; Weichert, Wilko; Brors, Benedikt; Stenzinger, Albrecht; Schroeck, Evelin; Huebschmann, Daniel; Horak, Peter; Heining, Christoph; Froehling, Stefan; Glimm, Hanno Share Save
Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states Jaber, Mohammad; Radwan, Ahmed; Loyfer, Netanel; Abdeen, Mufeed; Sebban, Shulamit; Khatib, Areej; Yassen, Hazar; Kolb, Thorsten; Zapatka, Marc; Makedonski, Kirill; Ernst, Aurelie; Kaplan, Tommy; Buganim, Yosef Share Save
A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis Khalid, Umar; Simovic, Milena; Hammann, Linda A.; Iskar, Murat; Wong, John K. L.; Kumar, Rithu; Jugold, Manfred; Sill, Martin; Bolkestein, Michiel; Kolb, Thorsten; Hergt, Michaela; Devens, Frauke; Ecker, Jonas; Kool, Marcel; Milde, Till; Westermann, Frank; Benner, Axel; Lewis, Joe; Dietrich, Sascha; Pfister, Stefan M.; Lichter, Peter; Zapatka, Marc; Ernst, Aurelie Share Save
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Interleukin-10 receptor signaling promotes the maintenance of a PD-1int TCF-1+ CD8+ T cell population that sustains anti-tumor immunity Hanna, Bola S.; Llao-Cid, Laura; Iskar, Murat; Roessner, Philipp M.; Klett, Lara C.; Wong, John K. L.; Paul, Yashna; Ioannou, Nikolaos; Ozturk, Selcen; Mack, Norman; Kalter, Verena; Colomer, Dolors; Campo, Elias; Bloehdorn, Johannes; Stilgenbauer, Stephan; Dietrich, Sascha; Schmidt, Manfred; Gabriel, Richard; Rippe, Karsten; Feuerer, Markus; Ramsay, Alan G.; Lichter, Peter; Zapatka, Marc; Seiffert, Martina Share Save
Longitudinal analyses of CLL in mice identify leukemia-related clonal changes including a Myc gain predicting poor outcome in patients Oeztuerk, Selcen; Paul, Yashna; Afzal, Saira; Gil-Farina, Irene; Jauch, Anna; Bruch, Peter-Martin; Kalter, Verena; Hanna, Bola; Arseni, Lavinia; Roessner, Philipp M.; Schmidt, Manfred; Stilgenbauer, Stephan; Dietrich, Sascha; Lichter, Peter; Zapatka, Marc; Seiffert, Martina Share Save
Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model Simovic, Milena; Bolkestein, Michiel; Moustafa, Mahmoud; Wong, John K. L.; Koerber, Verena; Benedetto, Sarah; Khalid, Umar; Schreiber, Hannah Sophia; Jugold, Manfred; Korshunov, Andrey; Huebschmann, Daniel; Mack, Norman; Brons, Stephan; Wei, Pei-Chi; Breckwoldt, Michael O.; Heiland, Sabine; Bendszus, Martin; Debus, Jurgen; Hoefer, Thomas; Zapatka, Marc; Kool, Marcel; Pfister, Stefan M.; Abdollahi, Amir; Ernst, Aurelie Share Save
Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas Huebschmann, Daniel; Kleinheinz, Kortine; Wagener, Rabea; Bernhart, Stephan H.; Lopez, Cristina; Toprak, Umut H.; Sungalee, Stephanie; Ishaque, Naveed; Kretzmer, Helene; Kreuz, Markus; Waszak, Sebastian M.; Paramasivam, Nagarajan; Ammerpohl, Ole; Aukema, Sietse M.; Beekman, Renee; Bergmann, Anke K.; Bieg, Matthias; Binder, Hans; Borkhardt, Arndt; Borst, Christoph; Brors, Benedikt; Bruns, Philipp; Carrillo de Santa Pau, Enrique; Claviez, Alexander; Doose, Gero; Haake, Andrea; Karsch, Dennis; Haas, Siegfried; Hansmann, Martin-Leo; Hoell, Jessica I.; Hovestadt, Volker; Huang, Bingding; Hummel, Michael; Jaeger-Schmidt, Christina; Kerssemakers, Jules N. A.; Korbel, Jan O.; Kube, Dieter; Lawerenz, Chris; Lenze, Dido; Martens, Joost H. A.; Ott, German; Radlwimmer, Bernhard; Reisinger, Eva; Richter, Julia; Rico, Daniel; Rosenstiel, Philip; Rosenwald, Andreas; Schillhabel, Markus; Stilgenbauer, Stephan; Stadler, Peter F.; Martin-Subero, Jose I.; Szczepanowski, Monika; Warsow, Gregor; Weniger, Marc A.; Zapatka, Marc; Valencia, Alfonso; Stunnenberg, Hendrik G.; Lichter, Peter; Moller, Peter; Loeffler, Markus; Eils, Roland; Klapper, Wolfram; Hoffmann, Steve; Trumper, Lorenz; Kueppers, Ralf; Schlesner, Matthias; Siebert, Reiner Share Save
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