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

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Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration por Alexandra Danyi, Myrthe Jager, Jeroen de Ridder

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A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. por Amin Allahyar, Joske Ubels, Jeroen de Ridder

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Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning por Marleen M. Nieboer, Luan Nguyen, Jeroen de Ridder

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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy por Franka J. Rang, Wigard P. Kloosterman, Jeroen de Ridder

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Value pluralism in research integrity por Rik Peels, Jeroen de Ridder, Tamarinde Haven, Lex Bouter

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Academia’s Big Five: a normative taxonomy for the epistemic responsibilities of universities [version 2; peer review: 2 approved] por Rik Peels, René van Woudenberg, Jeroen de Ridder, Lex Bouter

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Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. por Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel Reinders, Lodewyk Wessels

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Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator. por Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg

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Evrim Teorisinin Epistemik Statüsü por 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. por Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P F Lelieveldt, Jeroen de Ridder, Marcel Reinders

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Three-dimensional analysis of single molecule FISH in human colon organoids por Manja Omerzu, Nicola Fenderico, Buys de Barbanson, Joep Sprangers, Jeroen de Ridder, Madelon M. Maurice

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

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TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors. por Marleen M Nieboer, Lambert C J Dorssers, Roy Straver, Leendert H J Looijenga, Jeroen de Ridder

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Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects por Joske Ubels, Pieter Sonneveld, Erik H. van Beers, Annemiek Broijl, Martin H. van Vliet, Jeroen de Ridder

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The genome-wide mutational consequences of DNA hypomethylation por 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 por 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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Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors. por Martin A Rijlaarsdam, David M J Tax, Ad J M Gillis, Lambert C J Dorssers, Devin C Koestler, Jeroen de Ridder, Leendert H J Looijenga

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Evidence of survival bias in the association between APOE-Є4 and age at ischemic stroke onset por 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 por 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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