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A common genetic variant within SCN10A modulates cardiac SCN5A expression.
Published in:
Journal of Clinical Investigation, 2014, v. 124, n. 4, p. 1844, doi. 10.1172/JCI73140
By:
- van den Boogaard, Malou;
- Smemo, Scott;
- Burnicka-Turek, Ozanna;
- Arnolds, David E.;
- van de Werken, Harmen J. G.;
- Klous, Petra;
- McKean, David;
- Muehlschlegel, Jochen D.;
- Moosmann, Julia;
- Okan Toka;
- Xinan H. Yang;
- Koopmann, Tamara T.;
- Adriaens, Michiel E.;
- Bezzina, Connie R.;
- de Laat, Wouter;
- Seidman, Christine;
- Seidman, J. G.;
- Christoffels, Vincent M.;
- Nobrega, Marcelo A.;
- Barnett, Phil
Publication type:
Article
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells.
Published in:
eLife, 2019, p. 1, doi. 10.7554/eLife.40364
By:
- Singh, Shuchi Agrawal;
- Lerdrup, Mads;
- Gomes, Ana-Luisa R.;
- van de Werken, Harmen J. G.;
- Johansen, Jens Vilstrup;
- Andersson, Robin;
- Sandelin, Albin;
- Helin, Kristian;
- Hansen, Klaus
Publication type:
Article
Evaluation of pre-processing methods for tear fluid proteomics using proximity extension assays.
Published in:
Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-31227-1
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
Publication type:
Article
Trained Immunity in Primary Sjögren's Syndrome: Linking Type I Interferons to a Pro-Atherogenic Phenotype.
Published in:
Frontiers in Immunology, 2022, v. 13, p. 1, doi. 10.3389/fimmu.2022.840751
By:
- Huijser, Erika;
- van Helden-Meeuwsen, Cornelia G.;
- Grashof, Dwin G. B.;
- Tarn, Jessica R.;
- Brkic, Zana;
- Huisman, Josje M. A.;
- Wahadat, M. Javad;
- van de Werken, Harmen J. G.;
- Lopes, Ana P.;
- van Roon, Joel A. G.;
- van Daele, Paul L. A.;
- Kamphuis, Sylvia;
- Wan-Fai Ng;
- Bekkering, Siroon;
- Joosten, Leo A. B.;
- Dik, Willem A.;
- Versnel, Marjan A.
Publication type:
Article
Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 14, p. 6905, doi. 10.1093/nar/gkt491
By:
- Holwerda, Sjoerd J. B.;
- van de Werken, Harmen J. G.;
- Ribeiro de Almeida, Claudia;
- Bergen, Ingrid M.;
- de Bruijn, Marjolein J. W.;
- Verstegen, Marjon J. A. M.;
- Simonis, Marieke;
- Splinter, Erik;
- Wijchers, Patrick J.;
- Hendriks, Rudi W.;
- de Laat, Wouter
Publication type:
Article
Stratification of hospitalized COVID-19 patients into clinical severity progression groups by immuno-phenotyping and machine learning.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28621-0
By:
- Mueller, Yvonne M.;
- Schrama, Thijs J.;
- Ruijten, Rik;
- Schreurs, Marco W. J.;
- Grashof, Dwin G. B.;
- van de Werken, Harmen J. G.;
- Lasinio, Giovanna Jona;
- Álvarez-Sierra, Daniel;
- Kiernan, Caoimhe H.;
- Castro Eiro, Melisa D.;
- van Meurs, Marjan;
- Brouwers-Haspels, Inge;
- Zhao, Manzhi;
- Li, Ling;
- de Wit, Harm;
- Ouzounis, Christos A.;
- Wilmsen, Merel E. P.;
- Alofs, Tessa M.;
- Laport, Danique A.;
- van Wees, Tamara
Publication type:
Article
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24812-3
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
Publication type:
Article
Robust 4C-seq data analysis to screen for regulatory DNA interactions.
Published in:
Nature Methods, 2012, v. 9, n. 10, p. 969, doi. 10.1038/nmeth.2173
By:
- 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
Publication type:
Article
ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies.
Published in:
Bioinformatics, 2022, v. 38, n. 5, p. 1437, doi. 10.1093/bioinformatics/btab809
By:
- Geer, Wesley S van de;
- Riet, Job van;
- Werken, Harmen J G van de
Publication type:
Article
Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection.
Published in:
GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad081
By:
- Hazelaar, Daan M;
- van Riet, Job;
- Hoogstrate, Youri;
- van de Werken, Harmen J G
Publication type:
Article
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data.
Published in:
GigaScience, 2021, v. 10, n. 12, p. 1, doi. 10.1093/gigascience/giab080
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
Publication type:
Article
Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44913-z
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
Publication type:
Article
Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44913-z
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
Publication type:
Article
The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-13084-7
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
Publication type:
Article
Ibrutinib directly reduces CD8+T cell exhaustion independent of BTK.
Published in:
Frontiers in Immunology, 2023, p. 1, doi. 10.3389/fimmu.2023.1201415
By:
- Ling Li;
- Manzhi Zhao;
- Kiernan, Caoimhe H.;
- Eiro, Melisa D. Castro;
- van Meurs, Marjan;
- Brouwers-Haspels, Inge;
- Wilmsen, Merel E. P.;
- Grashof, Dwin G. B.;
- van de Werken, Harmen J. G.;
- Hendriks, Rudi W.;
- Mueller, Yvonne M.;
- Katsikis, Peter D.
Publication type:
Article
The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.
Published in:
Epigenetics & Chromatin, 2016, v. 9, p. 1, doi. 10.1186/s13072-016-0089-x
By:
- Knoch, Tobias A.;
- Wachsmuth, Malte;
- Kepper, Nick;
- Lesnussa, Michael;
- Abuseiris, Anis;
- Imam, A. M. Ali;
- Kolovos, Petros;
- Zuin, Jessica;
- Kockx, Christel E. M.;
- Brouwer, Rutger W. W.;
- van de Werken, Harmen J. G.
Publication type:
Article
Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.
Published in:
Epigenetics & Chromatin, 2014, v. 7, n. 1, p. 1, doi. 10.1186/1756-8935-7-10
By:
- Kolovos, Petros;
- van de Werken, Harmen J. G.;
- Kepper, Nick;
- Zuin, Jessica;
- Brouwer, Rutger W. W.;
- Kock, Christel E. M.;
- Wendt, Kerstin S.;
- cken, Wilfred F. J. I. J.;
- Grosveld, Frank;
- Knoch, Tobias A.
Publication type:
Article
Hyperresponsive cytosolic DNA-sensing pathway in monocytes from primary Sjögren's syndrome.
Published in:
Rheumatology, 2022, v. 61, n. 8, p. 3491, doi. 10.1093/rheumatology/keac016
By:
- Huijser, Erika;
- Bodewes, Iris L A;
- Lourens, Mirthe S;
- Helden-Meeuwsen, Cornelia G van;
- Bosch, Thierry P P van den;
- Grashof, Dwin G B;
- Werken, Harmen J G van de;
- Lopes, Ana P;
- Roon, Joel A G van;
- Daele, Paul L A van;
- Brkic, Zana;
- Dik, Willem A;
- Versnel, Marjan A
Publication type:
Article
The lncRNA MIR31HG regulates p16<sup>INK4A</sup> expression to modulate senescence.
Published in:
Nature Communications, 2015, v. 6, n. 4, p. 6967, doi. 10.1038/ncomms7967
By:
- Montes, Marta;
- Nielsen, Morten M.;
- Maglieri, Giulia;
- Jacobsen, Anders;
- Højfeldt, Jonas;
- Agrawal-Singh, Shuchi;
- Hansen, Klaus;
- Helin, Kristian;
- van de Werken, Harmen J. G.;
- Pedersen, Jakob S.;
- Lund, Anders H.
Publication type:
Article
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus.
Published in:
Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r50
By:
- Kaaij, Lucas T. J.;
- van de Wetering, Marc;
- Fang, Fang;
- Decato, Benjamin;
- Molaro, Antoine;
- van de Werken, Harmen J. G.;
- van Es, Johan H.;
- Schuijers, Jurian;
- de Wit, Elzo;
- de Laat, Wouter;
- Hannon, Gregory J.;
- Clevers, Hans C.;
- Smith, Andrew D.;
- Ketting, René F.
Publication type:
Article
Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development.
Published in:
2019
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.
Publication type:
journal article
Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas.
Published in:
Neuro-Oncology Advances, 2022, v. 4, n. 1, p. 1, doi. 10.1093/noajnl/vdab177
By:
- van de Geer, Wesley S.;
- Hoogstrate, Youri;
- Draaisma, Kaspar;
- Robe, Pierre A.;
- Bins, Sander;
- Mathijssen, Ron H. J.;
- French, Pim;
- van de Werken, Harmen J. G.;
- de Vos, Filip Y. F.
Publication type:
Article
Evaluation of AXIN1 and AXIN2 as targets of tankyrase inhibition in hepatocellular carcinoma cell lines.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-87091-4
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
Publication type:
Article
Patient-Derived Xenografts and Organoids Recapitulate Castration-Resistant Prostate Cancer with Sustained Androgen Receptor Signaling.
Published in:
Cells (2073-4409), 2022, v. 11, n. 22, p. 3632, doi. 10.3390/cells11223632
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.
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
EGFRvIII transcriptome in glioblastoma: A meta-omics analysis.
Published in:
Neuro-Oncology, 2022, v. 24, n. 3, p. 429, doi. 10.1093/neuonc/noab231
By:
- Hoogstrate, Youri;
- Ghisai, Santoesha A;
- Wit, Maurice de;
- Heer, Iris de;
- Draaisma, Kaspar;
- Riet, Job van;
- Werken, Harmen J G van de;
- Bours, Vincent;
- Buter, Jan;
- Bempt, Isabelle Vanden;
- Eoli, Marica;
- Franceschi, Enrico;
- Frenel, Jean-Sebastien;
- Gorlia, Thierry;
- Hanse, Monique C;
- Hoeben, Ann;
- Kerkhof, Melissa;
- Kros, Johan M;
- Leenstra, Sieger;
- Lombardi, Giuseppe
Publication type:
Article
The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation.
Published in:
PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0208659
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.
Publication type:
Article
Overcoming immune checkpoint blockade resistance in solid tumors with intermittent ITK inhibition.
Published in:
Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-42871-y
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.
Publication type:
Article
A reported 20-gene expression signature to predict lymph node-positive disease at radical cystectomy for muscle-invasive bladder cancer is clinically not applicable.
Published in:
PLoS ONE, 2017, v. 12, n. 3, p. 1, doi. 10.1371/journal.pone.0174039
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.
Publication type:
Article
FASTAFS: file system virtualisation of random access compressed FASTA files.
Published in:
BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04455-3
By:
- Hoogstrate, Youri;
- Jenster, Guido W.;
- Werken, Harmen J. G. van de
Publication type:
Article

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