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Development of a Personalized Tumor Neoantigen Based Vaccine Formulation (FRAME-001) for Use in a Phase II Trial for the Treatment of Advanced Non-Small Cell Lung Cancer.
Published in:
Pharmaceutics, 2022, v. 14, n. 7, p. N.PAG, doi. 10.3390/pharmaceutics14071515
By:
- Oosting, Linette T.;
- Franke, Katka;
- Martin, Michael V.;
- Kloosterman, Wigard P.;
- Jamieson, Jennifer A.;
- Glenn, Laura A.;
- de Jager, Miranda W.;
- van Zanten, Jacoba;
- Allersma, Derk P.;
- Gareb, Bahez
Publication type:
Article
Micronuclei-based model system reveals functional consequences of chromothripsis in human cells.
Published in:
eLife, 2019, p. 1, doi. 10.7554/eLife.50292
By:
- Kneissig, Maja;
- Keuper, Kristina;
- de Pagter, Mirjam S.;
- van Roosmalen, Markus J.;
- Martin, Jana;
- Otto, Hannah;
- Passerini, Verena;
- Sparr, Aline Campos;
- Renkens, Ivo;
- Kropveld, Fenna;
- Vasudevan, Anand;
- Sheltzer, Jason M.;
- Kloosterman, Wigard P.;
- Storchova, Zuzana
Publication type:
Article
Mouse microRNA profiles determined with a new and sensitive cloning method.
Published in:
Nucleic Acids Research, 2006, v. 34, n. 17, p. e115, doi. 10.1093/nar/gkl653
By:
- Takada, Shuji;
- Berezikov, Eugene;
- Yamashita, Yoshihiro;
- Lagos-Quintana, Mariana;
- Kloosterman, Wigard P.;
- Enomoto, Munehiro;
- Hatanaka, Hisashi;
- Fujiwara, Shin-ichiro;
- Watanabe, Hideki;
- Soda, Manabu;
- Choi, Young Lim;
- Plasterk, Ronald H. A.;
- Cuppen, Edwin;
- Mano, Hiroyuki
Publication type:
Article
Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00899-7
By:
- Valle-Inclan, Jose Espejo;
- Stangl, Christina;
- de Jong, Anouk C.;
- van Dessel, Lisanne F.;
- van Roosmalen, Markus J.;
- Helmijr, Jean C. A.;
- Renkens, Ivo;
- Janssen, Roel;
- de Blank, Sam;
- de Witte, Chris J.;
- Martens, John W. M.;
- Jansen, Maurice P. H. M.;
- Lolkema, Martijn P.;
- Kloosterman, Wigard P.
Publication type:
Article
Clinical and molecular characterization of an infant with a tandem duplication and deletion of 19p13.
Published in:
American Journal of Medical Genetics. Part A, 2015, v. 167A, n. 8, p. 1884, doi. 10.1002/ajmg.a.37076
By:
- Tan, Ratna N. G. B.;
- Witlox, Ruben S. G. M.;
- Hilhorst‐Hofstee, Yvonne;
- Peeters‐Scholte, Cacha M. P. C. D.;
- den Hollander, Nicolette S.;
- Ruivenkamp, Claudia A. L.;
- Hoffer, Mariëtte J.V.;
- Hansson, Kerstin B.;
- van Roosmalen, Mark J.;
- Kloosterman, Wigard P.;
- Santen, Gijs W. E.
Publication type:
Article
Genome-wide patterns and properties of de novo mutations in humans.
Published in:
Nature Genetics, 2015, v. 47, n. 7, p. 822, doi. 10.1038/ng.3292
By:
- Francioli, Laurent C;
- Menelaou, Androniki;
- Renkens, Ivo;
- Kloosterman, Wigard P;
- Guryev, Victor;
- Arndt, Peter F;
- de Bakker, Paul I W;
- Polak, Paz P;
- Chun, Sung;
- Sunyaev, Shamil R;
- Koren, Amnon;
- van Duijn, Cornelia M;
- Swertz, Morris;
- Wijmenga, Cisca;
- van Ommen, Gertjan;
- Slagboom, P Eline;
- Boomsma, Dorret I;
- Ye, Kai
Publication type:
Article
In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes.
Published in:
Nature Methods, 2006, v. 3, n. 1, p. 27, doi. 10.1038/nmeth843
By:
- Kloosterman, Wigard P.;
- Wienholds, Erno;
- de Bruijn, Ewart;
- Kauppinen, Sakari;
- Plasterk, Ronald H. A.
Publication type:
Article
ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation.
Published in:
PLoS ONE, 2014, v. 9, n. 12, p. 1, doi. 10.1371/journal.pone.0113800
By:
- Sante, Tom;
- Vergult, Sarah;
- Volders, Pieter-Jan;
- Kloosterman, Wigard P.;
- Trooskens, Geert;
- De Preter, Katleen;
- Dheedene, Annelies;
- Speleman, Frank;
- De Meyer, Tim;
- Menten, Björn
Publication type:
Article
Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing.
Published in:
2023
By:
- Marcozzi, Alessio;
- Jager, Myrthe;
- Elferink, Martin;
- Straver, Roy;
- van Ginkel, Joost H.;
- Peltenburg, Boris;
- Chen, Li-Ting;
- Renkens, Ivo;
- van Kuik, Joyce;
- Terhaard, Chris;
- de Bree, Remco;
- Devriese, Lot A.;
- Willems, Stefan M.;
- Kloosterman, Wigard P.;
- de Ridder, Jeroen
Publication type:
Correction Notice
Accurate detection of circulating tumor DNA using nanopore consensus sequencing.
Published in:
NPJ Genomic Medicine, 2021, v. 6, n. 1, p. 1, doi. 10.1038/s41525-021-00272-y
By:
- Marcozzi, Alessio;
- Jager, Myrthe;
- Elferink, Martin;
- Straver, Roy;
- van Ginkel, Joost H.;
- Peltenburg, Boris;
- Chen, Li-Ting;
- Renkens, Ivo;
- van Kuik, Joyce;
- Terhaard, Chris;
- de Bree, Remco;
- Devriese, Lot A.;
- Willems, Stefan M.;
- Kloosterman, Wigard P.;
- de Ridder, Jeroen
Publication type:
Article
Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer.
Published in:
Cancers, 2022, v. 14, n. 6, p. 1511, doi. 10.3390/cancers14061511
By:
- de Witte, Chris J.;
- Kutzera, Joachim;
- van Hoeck, Arne;
- Nguyen, Luan;
- Boere, Ingrid A.;
- Jalving, Mathilde;
- Ottevanger, Petronella B.;
- van Schaik-van de Mheen, Christa;
- Stevense, Marion;
- Kloosterman, Wigard P.;
- Zweemer, Ronald P.;
- Cuppen, Edwin;
- Witteveen, Petronella O.
Publication type:
Article
Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations.
Published in:
European Journal of Human Genetics, 2014, v. 22, n. 5, p. 652, doi. 10.1038/ejhg.2013.220
By:
- Vergult, Sarah;
- Van Binsbergen, Ellen;
- Sante, Tom;
- Nowak, Silke;
- Vanakker, Olivier;
- Claes, Kathleen;
- Poppe, Bruce;
- Van der Aa, Nathalie;
- van Roosmalen, Markus J;
- Duran, Karen;
- Tavakoli-Yaraki, Masoumeh;
- Swinkels, Marielle;
- van den Boogaard, Marie-José;
- van Haelst, Mieke;
- Roelens, Filip;
- Speleman, Frank;
- Cuppen, Edwin;
- Mortier, Geert;
- Kloosterman, Wigard P;
- Menten, Björn
Publication type:
Article
Discovery of variants unmasked by hemizygous deletions.
Published in:
European Journal of Human Genetics, 2012, v. 20, n. 7, p. 748, doi. 10.1038/ejhg.2011.263
By:
- Hochstenbach, Ron;
- Poot, Martin;
- Nijman, Isaac J;
- Renkens, Ivo;
- Duran, Karen J;
- van'T Slot, Ruben;
- van Binsbergen, Ellen;
- van der Zwaag, Bert;
- Vogel, Maartje J;
- Terhal, Paulien A;
- Ploos van Amstel, Hans Kristian;
- Kloosterman, Wigard P;
- Cuppen, Edwin
Publication type:
Article
Cloning and expression of new microRNAs from zebrafish.
Published in:
Nucleic Acids Research, 2006, v. 34, n. 9, p. 2558, doi. 10.1093/nar/gkl278
By:
- Kloosterman, Wigard P.;
- Steiner, Florian A.;
- Berezikov, Eugene;
- de Bruijn, Ewart;
- van de Belt, Jose;
- Verheul, Mark;
- Cuppen, Edwin;
- Plasterk, Ronald H.A.
Publication type:
Article
Substrate requirements for let-7 function in the developing zebrafish embryo.
Published in:
Nucleic Acids Research, 2004, v. 32, n. 21, p. 6284, doi. 10.1093/nar/gkh968
By:
- Kloosterman, Wigard P.;
- Wienholds, Erno;
- Ketting, René F.;
- Plasterk, Ronald H.A.
Publication type:
Article
Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease.
Published in:
2016
By:
- van der Crabben, Saskia N.;
- Hennus, Marije P.;
- McGregor, Grant A.;
- Ritter, Deborah I.;
- Nagamani, Sandesh C. S.;
- Wells, Owen S.;
- Harakalova, Magdalena;
- Chinn, Ivan K.;
- Alt, Aaron;
- Vondrova, Lucie;
- Hochstenbach, Ron;
- van Montfrans, Joris M.;
- Terheggen-Lagro, Suzanne W.;
- van Lieshout, Stef;
- van Roosmalen, Markus J.;
- Renkens, Ivo;
- Duran, Karen;
- Nijman, Isaac J.;
- Kloosterman, Wigard P.;
- Hennekam, Eric
Publication type:
journal article
A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.
Published in:
Nature Communications, 2016, v. 7, n. 10, p. 12989, doi. 10.1038/ncomms12989
By:
- Hehir-Kwa, Jayne Y.;
- Marschall, Tobias;
- Kloosterman, Wigard P.;
- Francioli, Laurent C.;
- Baaijens, Jasmijn A.;
- Dijkstra, Louis J.;
- Abdellaoui, Abdel;
- Koval, Vyacheslav;
- Thung, Djie Tjwan;
- Wardenaar, René;
- Renkens, Ivo;
- Coe, Bradley P.;
- Deelen, Patrick;
- de Ligt, Joep;
- Lameijer, Eric-Wubbo;
- van Dijk, Freerk;
- Hormozdiari, Fereydoun;
- Uitterlinden, André G.;
- van Duijn, Cornelia M.;
- Eichler, Evan E.
Publication type:
Article
The presence of extra chromosomes leads to genomic instability.
Published in:
Nature Communications, 2016, v. 7, n. 2, p. 10754, doi. 10.1038/ncomms10754
By:
- Passerini, Verena;
- Ozeri-Galai, Efrat;
- de Pagter, Mirjam S.;
- Donnelly, Neysan;
- Schmalbrock, Sarah;
- Kloosterman, Wigard P.;
- Kerem, Batsheva;
- Storchová, Zuzana
Publication type:
Article
Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer.
Published in:
Genome Biology, 2011, v. 12, n. 10, p. 1, doi. 10.1186/gb-2011-12-10-r103
By:
- Kloosterman, Wigard P.;
- Hoogstraat, Marlous;
- Paling, Oscar;
- Tavakoli-Yarak, Masoumeh;
- Renkens, Ivo;
- Vermaat, Joost S.;
- van Roosmalen, Markus J.;
- Lieshout, Stef van;
- Nijman, Isaac J.;
- Roessingh, Wijnand;
- Slot, Ruben van 't;
- de Belt, José van;
- Guryev, Victor;
- Koudijs, Marco;
- Voest2, Emile;
- Cuppen, Edwin
Publication type:
Article
Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline†.
Published in:
Human Molecular Genetics, 2011, v. 20, n. 10, p. 1916, doi. 10.1093/hmg/ddr073
By:
- Kloosterman, Wigard P.;
- Guryev, Victor;
- van Roosmalen, Mark;
- Duran, Karen J.;
- de Bruijn, Ewart;
- Bakker, Saskia C.M.;
- Letteboer, Tom;
- van Nesselrooij, Bernadette;
- Hochstenbach, Ron;
- Poot, Martin;
- Cuppen, Edwin
Publication type:
Article
Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease.
Published in:
Molecular Cytogenetics (17558166), 2014, v. 7, n. 1, p. 186, doi. 10.1186/s13039-014-0100-9
By:
- Kloosterman, Wigard P.;
- Hochstenbach, Ron
Publication type:
Article
LPIN2 Is Associated With Type 2 Diabetes, Glucose Metabolism, and Body Composition.
Published in:
Diabetes, 2007, v. 56, n. 12, p. 3020, doi. 10.2337/db07-0338
By:
- Aulchenko, Yurii S.;
- Pullen, Jan;
- Kloosterman, Wigard P.;
- Yazdanpanah, Mojgan;
- Hofman, Albert;
- Vaessen, Norbert;
- Snijders, Pieter J. L. M.;
- Zubakov, Dmitry;
- Mackay, Ian;
- Olavesen, Mark;
- Sidhu, Balbinder;
- Smith, Vicki E.;
- Carey, Alisoun;
- Berezikov, Eugene;
- Uitterlinden, André G.;
- Plasterk, Ronald H. A.;
- Oostra, Ben A.;
- van Duijn, Cornelia M.
Publication type:
Article
Targeted Inhibition of miRNA Maturation with Morpholinos Reveals a Role for miR-375 in Pancreatic Islet Development.
Published in:
PLoS Biology, 2007, v. 5, n. 8, p. 1738, doi. 10.1371/journal.pbio.0050203
By:
- Kloosterman, Wigard P.;
- Lagendijk, Anne K.;
- Ketting, René F.;
- Moulton, Jon D.;
- Plasterk, Ronald H. A.
Publication type:
Article
sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data.
Published in:
PeerJ, 2020, p. 1, doi. 10.7717/peerj.8214
By:
- Kuzniar, Arnold;
- Maassen, Jason;
- Verhoeven, Stefan;
- Santuari, Luca;
- Shneider, Carl;
- Kloosterman, Wigard P.;
- Ridder, Jeroen de
Publication type:
Article
Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Published in:
Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01343-4
By:
- Stancu, Mircea Cretu;
- van Roosmalen, Markus J.;
- Renkens, Ivo;
- Nieboer, Marleen M.;
- Middelkamp, Sjors;
- de Ligt, Joep;
- Pregno, Giulia;
- Giachino, Daniela;
- Mandrile, Giorgia;
- Valle-Inclan, Jose Espejo;
- Korzelius, Jerome;
- de Bruijn, Ewart;
- Cuppen, Edwin;
- Talkowski, Michael E.;
- Marschall, Tobias;
- de Ridder, Jeroen;
- Kloosterman, Wigard P.
Publication type:
Article
From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.
Published in:
Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1462-9
By:
- Rang, Franka J.;
- Kloosterman, Wigard P.;
- de Ridder, Jeroen
Publication type:
Article
Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons.
Published in:
BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2246-7
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.;
- on behalf of the MATCH study group;
- Martens, John W. M.;
- Sieuwerts, Anieta M.
Publication type:
Article
Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.
Published in:
Nature Protocols, 2020, v. 15, n. 2, p. 364, doi. 10.1038/s41596-019-0242-7
By:
- Vermeulen, Carlo;
- Allahyar, Amin;
- Bouwman, Britta A. M.;
- Krijger, Peter H. L.;
- Verstegen, Marjon J. A. M.;
- Geeven, Geert;
- Valdes-Quezada, Christian;
- Renkens, Ivo;
- Straver, Roy;
- Kloosterman, Wigard P.;
- de Ridder, Jeroen;
- de Laat, Wouter
Publication type:
Article
Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-257
By:
- van Heesch, Sebastiaan;
- Kloosterman, Wigard P.;
- Lansu, Nico;
- Ruzius, Frans-Paul;
- Levandowsky, Elizabeth;
- Lee, Clarence C.;
- Zhou, Shiguo;
- Goldstein, Steve;
- Schwartz, David C.;
- Harkins, Timothy T.;
- Guryev, Victor;
- Cuppen, Edwin
Publication type:
Article
Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16641-7
By:
- Stangl, Christina;
- de Blank, Sam;
- Renkens, Ivo;
- Westera, Liset;
- Verbeek, Tamara;
- Valle-Inclan, Jose Espejo;
- González, Rocio Chamorro;
- Henssen, Anton G.;
- van Roosmalen, Markus J.;
- Stam, Ronald W.;
- Voest, Emile E.;
- Kloosterman, Wigard P.;
- van Haaften, Gijs;
- Monroe, Glen R.
Publication type:
Article
Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants.
Published in:
Genome Medicine, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13073-019-0692-0
By:
- Middelkamp, Sjors;
- Vlaar, Judith M.;
- Giltay, Jacques;
- Korzelius, Jerome;
- Besselink, Nicolle;
- Boymans, Sander;
- Janssen, Roel;
- de la Fonteijne, Lisanne;
- van Binsbergen, Ellen;
- van Roosmalen, Markus J.;
- Hochstenbach, Ron;
- Giachino, Daniela;
- Talkowski, Michael E.;
- Kloosterman, Wigard P.;
- Cuppen, Edwin
Publication type:
Article
Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells.
Published in:
Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0399-z
By:
- Middelkamp, Sjors;
- van Heesch, Sebastiaan;
- Braat, A. Koen;
- de Ligt, Joep;
- van Iterson, Maarten;
- Simonis, Marieke;
- van Roosmalen, Markus J.;
- Kelder, Martijn J. E.;
- Kruisselbrink, Evelien;
- Hochstenbach, Ron;
- Verbeek, Nienke E.;
- Ippel, Elly F.;
- Adolfs, Youri;
- Pasterkamp, R. Jeroen;
- Kloosterman, Wigard P.;
- Kuijk, Ewart W.;
- Cuppen, Edwin
Publication type:
Article
High mRNA expression of splice variant SYK short correlates with hepatic disease progression in chemonaive lymph node negative colon cancer patients.
Published in:
PLoS ONE, 2017, v. 12, n. 9, p. 1, doi. 10.1371/journal.pone.0185607
By:
- Coebergh van den Braak, Robert R. J.;
- Sieuwerts, Anieta M.;
- Kandimalla, Raju;
- Lalmahomed, Zarina S.;
- Bril, Sandra I.;
- van Galen, Anne;
- Smid, Marcel;
- Biermann, Katharina;
- van Krieken, J. Han J. M.;
- Kloosterman, Wigard P.;
- Foekens, John A.;
- Goel, Ajay;
- Martens, John W. M.;
- IJzermans, Jan N. M.;
- null, null
Publication type:
Article

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