Search Results - "van de Werken, Harmen J G"

Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons by 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

“…Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for…”
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The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact by 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.

“…Metastatic castration-resistant prostate cancer (mCRPC) has a highly complex genomic landscape. With the recent development of novel treatments, accurate…”
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The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets by 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

“…Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) form clinically and genetically heterogeneous malignancies, characterized by distinct prognoses…”
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Patient-Derived Xenografts and Organoids Recapitulate Castration-Resistant Prostate Cancer with Sustained Androgen Receptor Signaling by 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

“…Castration-resistant prostate cancer (CRPC) remains an incurable and lethal malignancy. The development of new CRPC treatment strategies is strongly impeded by…”
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FASTAFS: file system virtualisation of random access compressed FASTA files by Hoogstrate, Youri, Jenster, Guido W., van de Werken, Harmen J. G.

“…Background The FASTA file format, used to store polymeric sequence data, has become a bioinformatics file standard used for decades. The relatively large files…”
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Tumor organoids improve mutation detection of pancreatic ductal adenocarcinoma by 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.

“…Pancreatic ductal adenocarcinoma (PDAC) presents challenges in detecting somatic mutations due to its complex cellular composition. This study investigated the…”
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Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo by 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

“…Hematopoietic stem cells (HSCs) produce all essential cellular components of the blood. Stromal cell lines supporting HSCs follow a vascular smooth muscle cell…”
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The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes by 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

“…The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of…”
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Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development by 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.

“…Background Testicular germ cell cancer (TGCC), being the most frequent malignancy in young Caucasian males, is initiated from an embryonic germ cell. This…”
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Evaluation of AXIN1 and AXIN2 as targets of tankyrase inhibition in hepatocellular carcinoma cell lines by 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

“…AXIN1 mutations are observed in 8–10% of hepatocellular carcinomas (HCCs) and originally were considered to support tumor growth by aberrantly enhancing…”
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Overcoming immune checkpoint blockade resistance in solid tumors with intermittent ITK inhibition by 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.

“…Cytotoxic CD8 + T cell (CTL) exhaustion is driven by chronic antigen stimulation. Reversing CTL exhaustion with immune checkpoint blockade (ICB) has provided…”
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The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder by 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.

“…The risk of developing urothelial carcinoma of the bladder (UCB) in patients treated by radical nephroureterectomy (RNU) for an upper urinary tract urothelial…”
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Evaluation of pre-processing methods for tear fluid proteomics using proximity extension assays by 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

“…Tear fluid forms a potential source for biomarker identification, and can be minimal invasively collected via Schirmer strips. The lack of knowledge on the…”
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Transcriptome Analysis of Infection of the Archaeon Sulfolobus solfataricus with Sulfolobus Turreted Icosahedral Virus by 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

“…Erratum ( vol. 82 , p. 6784 ) Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious…”
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Identification of a regulatory domain controlling the Nppa-Nppb gene cluster during heart development and stress by 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

“…The paralogous genes Nppa and Nppb are organized in an evolutionarily conserved cluster and provide a valuable model for studying co-regulation and regulatory…”
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The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation by 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

“…Krüppel-like factor 1 (KLF1) is an essential transcription factor for erythroid development, as demonstrated by Klf1 knockout mice which die around E14 due to…”
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Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection by Hazelaar, Daan M, van Riet, Job, Hoogstrate, Youri, van de Werken, Harmen J G

“…Abstract Background Kataegis refers to the occurrence of regional genomic hypermutation in cancer and is a phenomenon that has been observed in a wide range of…”
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A reported 20-gene expression signature to predict lymph node-positive disease at radical cystectomy for muscle-invasive bladder cancer is clinically not applicable by van Kessel, Kim E M, van de Werken, Harmen J G, Lurkin, Irene, Ziel-van der Made, Angelique C J, Zwarthoff, Ellen C, Boormans, Joost L

“…Neoadjuvant chemotherapy (NAC) for muscle-invasive bladder cancer (MIBC) provides a small but significant survival benefit. Nevertheless, controversies on…”
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Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data by Hoogstrate, Youri, Komor, Malgorzata A, Böttcher, René, van Riet, Job, van de Werken, Harmen J G, van Lieshout, Stef, Hoffmann, Ralf, van den Broek, Evert, Bolijn, Anne S, Dits, Natasja, Sie, Daoud, van der Meer, David, Pepers, Floor, Bangma, Chris H, van Leenders, Geert J L H, Smid, Marcel, French, Pim J, Martens, John W M, van Workum, Wilbert, van der Spek, Peter J, Janssen, Bart, Caldenhoven, Eric, Rausch, Christian, de Jong, Mark, Stubbs, Andrew P, Meijer, Gerrit A, Fijneman, Remond J A, Jenster, Guido W

“…Abstract Background Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However,…”
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Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells by 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.

“…Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The…”
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