Harmen van de Werken
Harmen van de Werken
Computational Biology & Bioinformatics in Immunology and cancer (CBBI), Departments of Immunology
Patvirtintas el. paštas - Pagrindinis puslapis
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
J Zuin, JR Dixon, MIJA van der Reijden, Z Ye, P Kolovos, RWW Brouwer, ...
Proceedings of the National Academy of Sciences 111 (3), 996-1001, 2014
eRNAs are required for p53-dependent enhancer activity and gene transcription
CA Melo, J Drost, PJ Wijchers, H van de Werken, E de Wit, JAFO Vrielink, ...
Molecular cell 49 (3), 524-535, 2013
Robust 4C-seq data analysis to screen for regulatory DNA interactions
HJG van de Werken, G Landan, SJB Holwerda, M Hoichman, P Klous, ...
Nature methods 9 (10), 969-972, 2012
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA
E Splinter, E de Wit, EP Nora, P Klous, HJG van de Werken, Y Zhu, ...
Genes and Development 25 (13), 1371-1383, 2011
The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies
L Angus, M Smid, SM Wilting, J van Riet, A Van Hoeck, L Nguyen, ...
Nature genetics 51 (10), 1450-1458, 2019
Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation
E Splinter, E de Wit, HJG van de Werken, P Klous, W de Laat
Methods 58 (3), 221-230, 2012
4C Technology: Protocols and Data Analysis
HJG van de Werken, PJP de Vree, E Splinter, SJB Holwerda, P Klous, ...
Methods in Enzymology 513 (Nucleosomes, Histones & Chromatin), 89, 2012
A common genetic variant within SCN10A modulates cardiac SCN5A expression
M Van Den Boogaard, S Smemo, O Burnicka-Turek, DE Arnolds, ...
Journal of clinical investigation 124 (4), 1844-1852, 2014
Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus
HJG van de Werken, MRA Verhaart, AL VanFossen, K Willquist, DL Lewis, ...
Applied and environmental microbiology 74 (21), 6720-6729, 2008
Paneth cells respond to inflammation and contribute to tissue regeneration by acquiring stem-like features through SCF/c-Kit signaling
M Schmitt, M Schewe, A Sacchetti, D Feijtel, WS van de Geer, ...
Cell reports 24 (9), 2312-2328. e7, 2018
Variegated gene expression caused by cell-specific long-range DNA interactions
D Noordermeer, E De Wit, P Klous, H Van De Werken, M Simonis, ...
Nature cell biology 13 (8), 944-951, 2011
The lncRNA MIR31HG regulates p16INK4A expression to modulate senescence
M Montes, MM Nielsen, G Maglieri, A Jacobsen, J Højfeldt, ...
Nature Communications 6 (1), 6967, 2015
The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact
LF van Dessel, J van Riet, M Smits, Y Zhu, P Hamberg, ...
Nature communications 10 (1), 1-13, 2019
Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells
D Kurek, A Neagu, M Tastemel, N Tüysüz, J Lehmann, ...
Stem cell reports 4 (1), 114-128, 2015
Decoding the DNA methylome of mantle cell lymphoma in the light of the entire B cell lineage
AC Queiros, R Beekman, R Vilarrasa-Blasi, M Duran-Ferrer, G Clot, ...
Cancer cell 30 (5), 806-821, 2016
Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways : Evidence for enzyme recruiment
SJJ Brouns, J Walther, APL Snijders, HJG van de Werken, ...
Journal of Biological Chemistry 281 (37), 27378-27388, 2006
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus
LTJ Kaaij, M van de Wetering, F Fang, B Decato, A Molaro, ...
Genome biology 14, 1-15, 2013
Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons
M Smid, RRJ Coebergh van den Braak, HJG van de Werken, J van Riet, ...
BMC bioinformatics 19, 1-13, 2018
Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with Sulfolobus turreted icosahedral virus
AC Ortmann, SK Brumfield, J Walther, K McInnerney, SJJ Brouns, ...
Journal of virology 82 (10), 4874-4883, 2008
Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements
P Kolovos, HJG van de Werken, N Kepper, J Zuin, RWW Brouwer, ...
Epigenetics and Chromatin 7, 1-17, 2014
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Straipsniai 1–20