Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel von Akhtar, Waseem, de Jong, Johann, Pindyurin, Alexey V., Pagie, Ludo, Meuleman, Wouter, de Ridder, Jeroen, Berns, Anton, Wessels, Lodewyk F.A., van Lohuizen, Maarten, van Steensel, Bas

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

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Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development von Dorssers, Lambert C. J., Gillis, Ad J. M., Stoop, Hans, van Marion, Ronald, Nieboer, Marleen M., van Riet, Job, van de Werken, Harmen J. G., Oosterhuis, J. Wolter, de Ridder, Jeroen, Looijenga, Leendert H. J.

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

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

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

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Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics von Gilroy, Kathryn L, Terry, Anne, Naseer, Asif, de Ridder, Jeroen, Allahyar, Amin, Wang, Weiwei, Carpenter, Eric, Mason, Andrew, Wong, Gane K-S, Cameron, Ewan R, Kilbey, Anna, Neil, James C

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Enhancer hubs and loop collisions identified from single-allele topologies von Allahyar, Amin, Vermeulen, Carlo, Bouwman, Britta A. M., Krijger, Peter H. L., Verstegen, Marjon J. A. M., Geeven, Geert, van Kranenburg, Melissa, Pieterse, Mark, Straver, Roy, Haarhuis, Judith H. I., Jalink, Kees, Teunissen, Hans, Renkens, Ivo J., Kloosterman, Wigard P., Rowland, Benjamin D., de Wit, Elzo, de Ridder, Jeroen, de Laat, Wouter

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

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Enthalpy and Entropy Barriers Explain the Effects of Topology on the Kinetics of Zeolite-Catalyzed Reactions von Van der Mynsbrugge, Jeroen, De Ridder, Jeroen, Hemelsoet, Karen, Waroquier, Michel, Van Speybroeck, Veronique

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Online and Offline Battles: Usage of Different Political Conflict Frames von van der Goot, Emma, Kruikemeier, Sanne, de Ridder, Jeroen, Vliegenthart, Rens

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

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PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia von Dang, Jinjun, Wei, Lei, de Ridder, Jeroen, Su, Xiaoping, Rust, Alistair G., Roberts, Kathryn G., Payne-Turner, Debbie, Cheng, Jinjun, Ma, Jing, Qu, Chunxu, Wu, Gang, Song, Guangchun, Huether, Robert G., Schulman, Brenda, Janke, Laura, Zhang, Jinghui, Downing, James R., van der Weyden, Louise, Adams, David J., Mullighan, Charles G.

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

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

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Scale-space measures for graph topology link protein network architecture to function von Hulsman, Marc, Dimitrakopoulos, Christos, de Ridder, Jeroen

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

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

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Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia von Taskesen, Erdogan, Babaei, Sepideh, Reinders, Marcel M J, de Ridder, Jeroen

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

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