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
Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology (vol 29, pg 917, 2023) Sturm, Dominik; Capper, David; Andreiuolo, Felipe; Gessi, Marco; Koelsche, Christian; Reinhardt, Annekathrin; Sievers, Philipp; Wefers, Annika K.; Ebrahimi, Azadeh; Suwala, Abigail K.; Gielen, Gerrit H.; Sill, Martin; Schrimpf, Daniel; Stichel, Damian; Hovestadt, Volker; Daenekas, Bjarne; Rode, Agata; Hamelmann, Stefan; Previti, Christopher; Jaeger, Natalie; Buchhalter, Ivo; Blattner-Johnson, Mirjam; Jones, Barbara C.; Warmuth-Metz, Monika; Bison, Brigitte; Grund, Kerstin; Sutter, Christian; Hirsch, Steffen; Dikow, Nicola; Hasselblatt, Martin; Schueller, Ulrich; Koch, Arend; Gerber, Nicolas U.; White, Christine L.; Buntine, Molly K.; Kinross, Kathryn; Algar, Elizabeth M.; Hansford, Jordan R.; Gottardo, Nicholas G.; Schuhmann, Martin U.; Thomale, Ulrich W.; Driever, Pablo; Gnekow, Astrid; Witt, Olaf; Mueller, Hermann L.; Calaminus, Gabriele; Fleischhack, Gudrun; Kordes, Uwe; Mynarek, Martin; Rutkowski, Stefan; Fruehwald, Michael C.; Kramm, Christof M.; von Deimling, Andreas; Pietsch, Torsten; Sahm, Felix; Pfister, Stefan M.; Jones, David. T. W. Share Save
ITCC-P4: Genomic profiling and analyses of pediatric patient tumor and patient-derived xenograft (PDX) models for high throughput in vivo testing Gopisetty, Apurva; Federico, Aniello; Surdez, Didier; Iddir, Yasmine; Zaidi, Sakina; Saint-Charles, Alexandra; Waterfall, Joshua; Saberi-Ansari, Elnaz; Wierzbinska, Justyna; Schlicker, Andreas; Mack, Norman; Schwalm, Benjamin; Previti, Christopher; Weiser, Lena; Buchhalter, Ivo; Bottcher, Anna-Lisa; Sill, Martin; Autry, Robert; Estermann, Frank; Jones, David; Volckmann, Richard; Zwijnenburg, Danny; Eggert, Angelika; Heidenreich, Olaf; Iradier, Fatima; Jeremias, Irmela; Kovar, Heinrich; Klusmann, Jan-Henning; Debatin, Klaus-Michael; Bomken, Simon; Hamerlik, Petra; Hattersley, Maureen; Witt, Olaf; Chesler, Louis; Mackay, Alan; Gojo, Johannes; Cairo, Stefano; Schueler, Julia; Schulte, Johannes; Geoerger, Birgit; Molenaar, Jan J.; Shields, David J.; Caron, Hubert N.; Vassal, Gilles; Stancato, Louis F.; Pfister, Stefan M.; Jaeger, Natalie; Koster, Jan; Kool, Marcel; Schleiermacher, Gudrun Share Save
Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology Sturm, Dominik; Capper, David; Andreiuolo, Felipe; Gessi, Marco; Koelsche, Christian; Reinhardt, Annekathrin; Sievers, Philipp; Wefers, Annika K.; Ebrahimi, Azadeh; Suwala, Abigail K.; Gielen, Gerrit H.; Sill, Martin; Schrimpf, Daniel; Stichel, Damian; Hovestadt, Volker; Daenekas, Bjarne; Rode, Agata; Hamelmann, Stefan; Previti, Christopher; Jaeger, Natalie; Buchhalter, Ivo; Blattner-Johnson, Mirjam; Jones, Barbara C.; Warmuth-Metz, Monika; Bison, Brigitte; Grund, Kerstin; Sutter, Christian; Hirsch, Steffen; Dikow, Nicola; Hasselblatt, Martin; Schueller, Ulrich; Gerber, Nicolas U.; White, Christine L.; Buntine, Molly K.; Kinross, Kathryn; Algar, Elizabeth M.; Hansford, Jordan R.; Gottardo, Nicholas G.; Driever, Pablo Hernaiz; Gnekow, Astrid; Witt, Olaf; Mueller, Hermann L.; Calaminus, Gabriele; Fleischhack, Gudrun; Kordes, Uwe; Mynarek, Martin; Rutkowski, Stefan; Fruehwald, Michael C.; Kramm, Christof M.; von Deimling, Andreas; Pietsch, Torsten; Sahm, Felix; Pfister, Stefan M.; Jones, David. T. W. Share Save
Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers Jahn, A.; Rump, A.; Widmann, T. J.; Heining, C.; Horak, P.; Hutter, B.; Paramasivam, N.; Uhrig, S.; Gieldon, L.; Drukewitz, S.; Kuebler, A.; Bermudez, M.; Hackmann, K.; Porrmann, J.; Wagner, J.; Arlt, M.; Franke, M.; Fischer, J.; Kowalzyk, Z.; William, D.; Weth, V.; Oster, S.; Froehlich, M.; Huellein, J.; Gonzalez, C. Valle; Kreutzfeldt, S.; Mock, A.; Heilig, C. E.; Lipka, D. B.; Moehrmann, L.; Hanf, D.; Oles, M.; Teleanu, V.; Allgaeuer, M.; Ruhnke, L.; Kutz, O.; Knurr, A.; Lassmann, A.; Endris, V.; Neumann, O.; Penzel, R.; Beck, K.; Richter, D.; Winter, U.; Wolf, S.; Pfuetze, K.; Geoerg, C.; Meissburger, B.; Buchhalter, I.; Augustin, M.; Aulitzky, W. E.; Hohenberger, P.; Kroiss, M.; Schirmacher, P.; Schlenk, R. F.; Keilholz, U.; Klauschen, F.; Folprecht, G.; Bauer, S.; Siveke, J. T.; Brandts, C. H.; Kindler, T.; Boerries, M.; Illert, A. L.; von Bubnoff, N.; Jost, P. J.; Metzeler, K. H.; Bitzer, M.; Schulze-Osthoff, K.; von Kalle, C.; Brors, B.; Stenzinger, A.; Weichert, W.; Huebschmann, D.; Froehling, S.; Glimm, H.; Schroeck, E.; Klink, B. Share Save
Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers Horak, Peter; Heining, Christoph; Kreutzfeldt, Simon; Hutter, Barbara; Mock, Andreas; Huellein, Jennifer; Froehlich, Martina; Uhrig, Sebastian; Jahn, Arne; Rump, Andreas; Gieldon, Laura; Moehrmann, Lino; Hanf, Dorothea; Teleanu, Veronica; Heilig, Christoph E.; Lipka, Daniel B.; Allgaeuer, Michael; Ruhnke, Leo; Lassmann, Andreas; Endris, Volker; Neumann, Olaf; Penzel, Roland; Beck, Katja; Richter, Daniela; Winter, Ulrike; Wolf, Stephan; Pfuetze, Katrin; Geoerg, Christina; Meissburger, Bettina; Buchhalter, Ivo; Augustin, Marinela; Aulitzky, Walter E.; Hohenberger, Peter; Kroiss, Matthias; Schirmacher, Peter; Schlenk, Richard F.; Keilholz, Ulrich; Klauschen, Frederick; Folprecht, Gunnar; Bauer, Sebastian; Siveke, Jens Thomas; Brandts, Christian H.; Kindler, Thomas; Boerries, Melanie; Illert, Anna L.; von Bubnoff, Nikolas; Jost, Philipp J.; Spiekermann, Karsten; Bitzer, Michael; Schulze-Osthoff, Klaus; von Kalle, Christof; Klink, Barbara; Brors, Benedikt; Stenzinger, Albrecht; Schroeck, Evelin; Huebschmann, Daniel; Weichert, Wilko; Glimm, Hanno; Froehling, Stefan Share Save
Framework for quality assessment of whole genome cancer sequences Whalley, Justin P.; Buchhalter, Ivo; Rheinbay, Esther; Raine, Keiran M.; Stobbe, Miranda D.; Kleinheinz, Kortine; Werner, Johannes; Beltran, Sergi; Gut, Marta; Huebschmann, Daniel; Hutter, Barbara; Livitz, Dimitri; Perry, Marc D.; Rosenberg, Mara; Saksena, Gordon; Trotta, Jean-Remi; Eils, Roland; Gerhard, Daniela S.; Campbell, Peter J.; Schlesner, Matthias; Gut, Ivo G. Share Save
Genomic Characterization of Cholangiocarcinoma in Primary Sclerosing Cholangitis Reveals Therapeutic Opportunities Goeppert, Benjamin; Folseraas, Trine; Roessler, Stephanie; Kloor, Matthias; Volckmar, Anna-Lena; Endris, Volker; Buchhalter, Ivo; Stenzinger, Albrecht; Grzyb, Krzysztof; Grimsrud, Marit M.; Gornicka, Barbara; von Seth, Erik; Reynolds, Gary M.; Franke, Andre; Gotthardt, Daniel N.; Mehrabi, Arianeb; Cheung, Angela; Verheij, Joanne; Arola, Johanna; Makisalo, Heikki; Eide, Tor J.; Weidemann, Soren; Cheville, John C.; Mazza, Giuseppe; Hirschfield, Gideon M.; Ponsioen, Cyriel Y.; Bergquist, Annika; Milkiewicz, Piotr; Lazaridis, Konstantinos N.; Schramm, Christoph; Manns, Michael P.; Farkkila, Martti; Vogel, Arndt; Boberg, Kirsten M.; Schirmacher, Peter; Karlsen, Tom H. Share Save
Butler enables rapid cloud-based analysis of thousands of human genomes (vol 79, pg 134, 2019) Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll.; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Hubschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Ratsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon I.; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Waszak, Sebastian M.; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun; Korbel, Jan O. Share Save
Butler enables rapid cloud-based analysis of thousands of human genomes Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Huebschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Raetsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon, I; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun Share Save
Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics: Analysis of the first 3,000 Heidelberg cases Volckmar, Anna-Lena; Leichsenring, Jonas; Kirchner, Martina; Christopoulos, Petros; Neumann, Olaf; Budczies, Jan; de Oliveira, Cristiano Manuel Morais; Rempel, Eugen; Buchhalter, Ivo; Brandt, Regine; Allgaeuer, Michael; Talla, Suranand Babu; von Winterfeld, Moritz; Herpel, Esther; Goeppert, Benjamin; Lier, Amelie; Winter, Hauke; Brummer, Tilman; Froehling, Stefan; Faehling, Martin; Fischer, Juergen R.; Heussel, Claus Peter; Herth, Felix; Lasitschka, Felix; Schirmacher, Peter; Thomas, Michael; Endris, Volker; Penzel, Roland; Stenzinger, Albrecht Share Save
Measurement of tumor mutational burden (TMB) in routine molecular diagnostics: in silico and real-life analysis of three larger gene panels Endris, Volker; Buchhalter, Ivo; Allgaeuer, Michael; Rempel, Eugen; Lier, Amelie; Volckmar, Anna-Lena; Kirchner, Martina; von Winterfeld, Moritz; Leichsenring, Jonas; Neumann, Olaf; Penzel, Roland; Weichert, Wilko; Glimm, Hanno; Froehling, Stefan; Winter, Hauke; Herth, Felix; Thomas, Michael; Schirmacher, Peter; Budczies, Jan; Stenzinger, Albrecht Share Save
Size matters: Dissecting key parameters for panel-based tumor mutational burden analysis Buchhalter, Ivo; Rempel, Eugen; Endris, Volker; Allgaeuer, Michael; Neumann, Olaf; Volckmar, Anna-Lena; Kirchner, Martina; Leichsenring, Jonas; Lier, Amelie; von Winterfeld, Moritz; Penzel, Roland; Christopoulos, Petros; Thomas, Michael; Froehling, Stefan; Schirmacher, Peter; Budczies, Jan; Stenzinger, Albrecht Share Save
Genetic profiling of melanoma in routine diagnostics: assay performance and molecular characteristics in a consecutive series of 274 cases Leichsenring, Jonas; Stoegbauer, Fabian; Volckmar, Anna-Lena; Buchhalter, Ivo; Oliveira, Cristiano; Kirchner, Martina; Froehling, Stefan; Hassel, Jessica; Enk, Alexander; Schirmacher, Peter; Endris, Volker; Penzel, Roland; Stenzinger, Albrecht Share Save
Targeted molecular profiling reveals genetic heterogeneity of poromas and porocarcinomas Bosic, Martina; Kirchner, Martina; Brasanac, Dimitrije; Leichsenring, Jonas; Lier, Amelie; Volckmar, Anna-Lena; Oliveira, Cristiano; Buchhalter, Ivo; Stoegbauer, Fabian; Zivkovic-Perisic, Snezana; Goeppert, Benjamin; Schirmacher, Peter; Penzel, Roland; Endris, Volker; Stenzinger, Albrecht Share Save
EML4-ALK fusion variant V3 is a high-risk feature conferring accelerated metastatic spread, early treatment failure and worse overall survival in ALK+ non-small cell lung cancer Christopoulos, Petros; Endris, Volker; Bozorgmehr, Farastuk; Elsayed, Mei; Kirchner, Martina; Ristau, Jonas; Buchhalter, Ivo; Penzel, Roland; Herth, Felix J.; Heussel, Claus P.; Eichhorn, Martin; Muley, Thomas; Meister, Michael; Fischer, Juergen R.; Rieken, Stefan; Warth, Arne; Bischoff, Helge; Schirmacher, Peter; Stenzinger, Albrecht; Thomas, Michael Share Save
Deep sequencing of WNT-activated medulloblastomas reveals secondary SHH pathway activation Iorgulescu, J. Bryan; Van Ziffle, Jessica; Stevers, Meredith; Grenert, James P.; Bastian, Boris C.; Chavez, Lukas; Stichel, Damian; Buchhalter, Ivo; Samuel, David; Nicolaides, Theodore; Banerjee, Anuradha; Mueller, Sabine; Gupta, Nalin; Tihan, Tarik; Bollen, Andrew W.; Northcott, Paul A.; Kool, Marcel; Pfister, Stefan; Korshunov, Andrey; Perry, Arie; Solomon, David A. Share Save
Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer Giessler, Klara M.; Kleinheinz, Kortine; Huebschmann, Daniel; Balasubramanian, Gnana Prakash; Dubash, Taronish D.; Dieter, Sebastian M.; Siegl, Christine; Herbst, Friederike; Weber, Sarah; Hoffmann, Christopher M.; Fronza, Raffaele; Buchhalter, Ivo; Paramasivam, Nagarajan; Eils, Roland; Schmidt, Manfred; von Kalle, Christof; Schneider, Martin; Ulrich, Alexis; Scholl, Claudia; Froehling, Stefan; Weichert, Wilko; Brors, Benedikt; Schlesner, Matthias; Ball, Claudia R.; Glimm, Hanno Share Save
Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature Sahm, Felix; Toprak, Umut H.; Huebschmann, Daniel; Kleinheinz, Kortine; Buchhalter, Ivo; Sill, Martin; Stichel, Damian; Schick, Matthias; Bewerunge-Hudler, Melanie; Schrimpf, Daniel; Zadeh, Gelareh; Aldape, Ken; Herold-Mende, Christel; Beck, Katja; Staszewski, Ori; Prinz, Marco; Ben Harosh, Carmit; Eils, Roland; Sturm, Dominik; Jones, David T. W.; Pfister, Stefan M.; Paulus, Werner; Ram, Zvi; Schlesner, Matthias; Grossman, Rachel; von Deimling, Andreas Share Save
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