Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling by Marc Pagès-Gallego, Jeroen de Ridder

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Evrim Teorisinin Epistemik Statüsü by Gülay Parlak, Gijberk Van den Brink, Jeroen De Ridder, René Van Woudenberg

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Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex. by Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P F Lelieveldt, Jeroen de Ridder, Marcel Reinders

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sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data by Arnold Kuzniar, Jason Maassen, Stefan Verhoeven, Luca Santuari, Carl Shneider, Wigard P. Kloosterman, Jeroen de Ridder

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The genome-wide mutational consequences of DNA hypomethylation by Nicolle Besselink, Janneke Keijer, Carlo Vermeulen, Sander Boymans, Jeroen de Ridder, Arne van Hoeck, Edwin Cuppen, Ewart Kuijk

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Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning by Anouk C. de Jong, Alexandra Danyi, Job van Riet, Ronald de Wit, Martin Sjöström, Felix Feng, Jeroen de Ridder, Martijn P. Lolkema

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Evidence of survival bias in the association between APOE-Є4 and age at ischemic stroke onset by Joanna von Berg, Joanna von Berg, Patrick F. McArdle, Paavo Häppölä, Jeffrey Haessler, Charles Kooperberg, Robin Lemmens, Robin Lemmens, Alessandro Pezzini, Alessandro Pezzini, Vincent Thijs, Vincent Thijs, Vincent Thijs, Sara L. Pulit, Steven J. Kittner, Steven J. Kittner, Braxton D. Mitchell, Braxton D. Mitchell, Jeroen de Ridder, Jeroen de Ridder, Sander W. van der Laan, Sander W. van der Laan

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Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution by Lennart Kester, Buys de Barbanson, Anna Lyubimova, Li-Ting Chen, Valérie van der Schrier, Anna Alemany, Dylan Mooijman, Josi Peterson-Maduro, Jarno Drost, Jeroen de Ridder, Alexander van Oudenaarden

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Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes by Carlos G. Urzúa-Traslaviña, Tijs van Lieshout, Floranne Boulogne, Kevin Domanegg, Mahmoud Zidan, Olivier B. Bakker, Annique Claringbould, Jeroen de Ridder, Wilbert Zwart, Harm-Jan Westra, Patrick Deelen, Lude Franke

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A Single Complex Agpat2 Allele in a Patient With Partial Lipodystrophy by Marjoleine F. Broekema, Maarten P. G. Massink, Joep De Ligt, Edwin C. A. Stigter, Houshang Monajemi, Houshang Monajemi, Jeroen De Ridder, Boudewijn M. T. Burgering, Gijs W. van Haaften, Eric Kalkhoven

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Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis. by Camille A Huser, Kathryn L Gilroy, Jeroen de Ridder, Anna Kilbey, Gillian Borland, Nancy Mackay, Alma Jenkins, Margaret Bell, Pawel Herzyk, Louise van der Weyden, David J Adams, Alistair G Rust, Ewan Cameron, James C Neil

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Accurate detection of circulating tumor DNA using nanopore consensus sequencing by Alessio Marcozzi, Myrthe Jager, Martin Elferink, Roy Straver, Joost H. van Ginkel, Boris Peltenburg, Li-Ting Chen, Ivo Renkens, Joyce van Kuik, Chris Terhaard, Remco de Bree, Lot A. Devriese, Stefan M. Willems, Wigard P. Kloosterman, Jeroen de Ridder

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Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing by Alessio Marcozzi, Myrthe Jager, Martin Elferink, Roy Straver, Joost H. van Ginkel, Boris Peltenburg, Li-Ting Chen, Ivo Renkens, Joyce van Kuik, Chris Terhaard, Remco de Bree, Lot A. Devriese, Stefan M. Willems, Wigard P. Kloosterman, Jeroen de Ridder

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Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns by Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P. Lolkema, Neeltje Steeghs, Gad Getz, Quaid D. Morris, Lincoln D. Stein, PCAWG Consortium

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Eleven grand challenges in single-cell data science by David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Alicja Rączkowska, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

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