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List of works by Harmen van de Werken

4C technology: protocols and data analysis.

scientific article

9 Functional Genomics of the Thermo-Acidophilic Archaeon Sulfolobus solfataricus

A common genetic variant within SCN10A modulates cardiac SCN5A expression

scientific article published on 18 March 2014

A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification ⬇️

scientific article

A large permissive regulatory domain exclusively controls Tbx3 expression in the cardiac conduction system.

scientific article published on 24 June 2014

A reported 20-gene expression signature to predict lymph node-positive disease at radical cystectomy for muscle-invasive bladder cancer is clinically not applicable.

scientific article

Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.

scientific article published on 7 June 2013

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

scientific article published on 13 December 2013

Continued androgen signalling inhibition improves cabazitaxel efficacy in prostate cancer

scientific article published on 05 November 2021

Correlation of Gene Mutation Status with Copy Number Profile in Uveal Melanoma

article

Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients

scientific article published on 12 March 2020

DOC1-Dependent Recruitment of NURD Reveals Antagonism with SWI/SNF during Epithelial-Mesenchymal Transition in Oral Cancer Cells.

scientific article published in July 2017

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.

scientific article published on November 2016

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation.

scientific article

Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells

scientific article published on 24 December 2014

Evaluation of AXIN1 and AXIN2 as targets of tankyrase inhibition in hepatocellular carcinoma cell lines

scientific article published on 02 April 2021

Fractionated Radiation of Primary Prostate Basal Cells Results in Downplay of Interferon Stem Cell and Cell Cycle Checkpoint Signatures

scientific article published on 18 June 2018

Functional Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects

article

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

scientific article

Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus.

scientific article published on 5 September 2008

Identification and Characterization of a Transcribed Distal Enhancer Involved in Cardiac Kcnh2 Regulation

scientific article published on 01 September 2019

Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus

scientific article published on 01 July 2006

Identification of a regulatory domain controlling the Nppa-Nppb gene cluster during heart development and stress

scientific article published on 5 April 2016

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

scientific article published in Journal of Biological Chemistry

Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C.

scientific article

Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas

scientific article published on 30 November 2021

Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development

scientific article published on 11 February 2019

Multi-Modality Analysis Improves Survival Prediction in Enucleated Uveal Melanoma Patients

scientific article published on 01 August 2019

Oncogenic STRAP Supports Hepatocellular Carcinoma Growth by Enhancing Wnt/β-Catenin Signaling

scientific article published on 26 September 2018

PDGFRβ+ cells play a dual role as hematopoietic precursors and niche cells during mouse ontogeny

scientific article published on 19 July 2022

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

scientific article published on 23 January 2019

Paneth Cells Respond to Inflammation and Contribute to Tissue Regeneration by Acquiring Stem-like Features through SCF/c-Kit Signaling

scientific article published on 01 August 2018

Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

scientific article published in March 2006

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

scientific article

Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo ⬇️

scientific article published on 23 February 2024

Small chromosomal regions position themselves autonomously according to their chromatin class.

scientific article published on 24 March 2017

Sp1/Sp3 transcription factors regulate hallmarks of megakaryocyte maturation and platelet formation and function.

scientific article

Synchronous and metachronous urothelial carcinoma of the upper urinary tract and the bladder: Are they clonally related? A systematic review

scientific article published on 11 February 2020

TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis.

scientific article published on 13 April 2015

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

scientific article published on 16 June 2014

The EGFRvIII transcriptome in glioblastoma: A meta-omics analysis

scientific article published on 01 March 2022

The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder

scientific article published on 02 October 2020

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.

scientific article

The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets

scientific article published in 2021

The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies

scientific article published on 30 September 2019

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

scientific article published on 20 November 2019

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

scientific article

The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation

scientific article published on 28 March 2019

Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with Sulfolobus turreted icosahedral virus.

scientific article published on 12 March 2008

Variegated gene expression caused by cell-specific long-range DNA interactions

scientific article published on 26 June 2011

eRNAs are required for p53-dependent enhancer activity and gene transcription

scientific article

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