Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons von Smid, Marcel, Coebergh van den Braak, Robert R J, van de Werken, Harmen J G, van Riet, Job, van Galen, Anne, de Weerd, Vanja, van der Vlugt-Daane, Michelle, Bril, Sandra I, Lalmahomed, Zarina S, Kloosterman, Wigard P, Wilting, Saskia M, Foekens, John A, IJzermans, Jan N M, Martens, John W M, Sieuwerts, Anieta M

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The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact von van Dessel, Lisanne F., van Riet, Job, Smits, Minke, Zhu, Yanyun, Hamberg, Paul, van der Heijden, Michiel S., Bergman, Andries M., van Oort, Inge M., de Wit, Ronald, Voest, Emile E., Steeghs, Neeltje, Yamaguchi, Takafumi N., Livingstone, Julie, Boutros, Paul C., Martens, John W. M., Sleijfer, Stefan, Cuppen, Edwin, Zwart, Wilbert, van de Werken, Harmen J. G., Mehra, Niven, Lolkema, Martijn P.

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The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets von van Riet, Job, van de Werken, Harmen J. G., Cuppen, Edwin, Eskens, Ferry A. L. M., Tesselaar, Margot, van Veenendaal, Linde M., Klümpen, Heinz-Josef, Dercksen, Marcus W., Valk, Gerlof D., Lolkema, Martijn P., Sleijfer, Stefan, Mostert, Bianca

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The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder von Doeveren, Thomas, Nakauma‐Gonzalez, Jose A., Mason, Andrew S., Leenders, Geert J. L. H., Zuiverloon, Tahlita C. M., Zwarthoff, Ellen C., Meijssen, Isabelle C., Made, Angelique C., Heijden, Antoine G., Hendricksen, Kees, Rhijn, Bas W. G., Voskuilen, Charlotte S., Riet, Job, Dinjens, Winand N. M., Dubbink, Hendrikus J., Werken, Harmen J. G., Boormans, Joost L.

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Patient-Derived Xenografts and Organoids Recapitulate Castration-Resistant Prostate Cancer with Sustained Androgen Receptor Signaling von Van Hemelryk, Annelies, Tomljanovic, Ingrid, de Ridder, Corrina M A, Stuurman, Debra C, Teubel, Wilma J, Erkens-Schulze, Sigrun, Verhoef, Esther I, Remmers, Sebastiaan, Mahes, Amrish J, van Leenders, Geert J L H, van Royen, Martin E, van de Werken, Harmen J G, Grudniewska, Magda, Jenster, Guido W, van Weerden, Wytske M

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FASTAFS: file system virtualisation of random access compressed FASTA files von Hoogstrate, Youri, Jenster, Guido W., van de Werken, Harmen J. G.

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Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo von Gonzalez Galofre, Zaniah N., Kilpatrick, Alastair M., Marques, Madalena, Sá da Bandeira, Diana, Ventura, Telma, Gomez Salazar, Mario, Bouilleau, Léa, Marc, Yvan, Barbosa, Ana B., Rossi, Fiona, Beltran, Mariana, van de Werken, Harmen J. G., van IJcken, Wilfred F. J., Henderson, Neil C., Forbes, Stuart J., Crisan, Mihaela

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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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Tumor organoids improve mutation detection of pancreatic ductal adenocarcinoma von Farshadi, Elham Aida, Wang, Wenya, Mohammad, Farzana, van der Oost, Elise, Doukas, Michail, van Eijck, Casper H. J., van de Werken, Harmen J. G., Katsikis, Peter D.

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The genomic and transcriptomic landscape of advanced renal cell cancer for individualized treatment strategies von de Joode, K., van de Geer, W. S., van Leenders, G. J. L. H., Hamberg, P., Westgeest, H. M., Beeker, A., Oosting, S. F., van Rooijen, J. M., Beerepoot, L. V., Labots, M., Mathijssen, R. H. J., Lolkema, M. P., Cuppen, E., Sleijfer, S., van de Werken, H. J. G., van der Veldt, A. A. M.

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Evaluation of AXIN1 and AXIN2 as targets of tankyrase inhibition in hepatocellular carcinoma cell lines von Wang, Wenhui, Liu, Pengyu, Lavrijsen, Marla, Li, Shan, Zhang, Ruyi, Li, Shanshan, van de Geer, Wesley S., van de Werken, Harmen J. G., Peppelenbosch, Maikel P., Smits, Ron

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The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes von Knoch, Tobias A, Wachsmuth, Malte, Kepper, Nick, Lesnussa, Michael, Abuseiris, Anis, Ali Imam, A M, Kolovos, Petros, Zuin, Jessica, Kockx, Christel E M, Brouwer, Rutger W W, van de Werken, Harmen J G, van IJcken, Wilfred F J, Wendt, Kerstin S, Grosveld, Frank G

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Overcoming immune checkpoint blockade resistance in solid tumors with intermittent ITK inhibition von Zhao, Manzhi, Li, Ling, Kiernan, Caoimhe H., Castro Eiro, Melisa D., Dammeijer, Floris, van Meurs, Marjan, Brouwers-Haspels, Inge, Wilmsen, Merel E. P., Grashof, Dwin G. B., van de Werken, Harmen J. G., Hendriks, Rudi W., Aerts, Joachim G., Mueller, Yvonne M., Katsikis, Peter D.

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Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells von Zuin, Jessica, Dixon, Jesse R., van der Reijden, Michael I. J. A., Ye, Zhen, Kolovos, Petros, Brouwer, Rutger W. W., van de Corput, Mariëtte P. C., van de Werken, Harmen J. G., Knoch, Tobias A., van IJcken, Wilfred F. J., Grosveld, Frank G., Ren, Bing, Wendt, Kerstin S.

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Evaluation of pre-processing methods for tear fluid proteomics using proximity extension assays von Vergouwen, Daphne P. C., Schotting, Amber J., Endermann, Tanja, van de Werken, Harmen J. G., Grashof, Dwin G. B., Arumugam, Sinthuja, Nuijts, Rudy M. M. A., ten Berge, Josianne C., Rothova, Aniki, Schreurs, Marco W. J., Gijs, Marlies

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Identification of a regulatory domain controlling the Nppa-Nppb gene cluster during heart development and stress von Sergeeva, Irina A, Hooijkaas, Ingeborg B, Ruijter, Jan M, van der Made, Ingeborg, de Groot, Nina E, van de Werken, Harmen J G, Creemers, Esther E, Christoffels, Vincent M

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The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation von Cantú, Ileana, van de Werken, Harmen J G, Gillemans, Nynke, Stadhouders, Ralph, Heshusius, Steven, Maas, Alex, Esteghamat, Fatemehsadat, Ozgur, Zeliha, van IJcken, Wilfred F J, Grosveld, Frank, von Lindern, Marieke, Philipsen, Sjaak, van Dijk, Thamar B

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Transcriptome Analysis of Infection of the Archaeon Sulfolobus solfataricus with Sulfolobus Turreted Icosahedral Virus von ORTMANN, Alice C, BRUMFIELD, Susan K, WALTHER, Jasper, MCLNNERNEY, Kathleen, BROUNS, Stan J. J, VAN DE WERKEN, Harmen J. G, BOTHNER, Brian, DOUGLAS, Trevor, VAN DE OOST, John, YOUNG, Mark J

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Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection von Hazelaar, Daan M, van Riet, Job, Hoogstrate, Youri, van de Werken, Harmen J G

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Robust 4C-seq data analysis to screen for regulatory DNA interactions von van de Werken, Harmen J G, Landan, Gilad, Holwerda, Sjoerd J B, Hoichman, Michael, Klous, Petra, Chachik, Ran, Splinter, Erik, Valdes-Quezada, Christian, Öz, Yuva, Bouwman, Britta A M, Verstegen, Marjon J A M, de Wit, Elzo, Tanay, Amos, de Laat, Wouter

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