Dr Harmen J G Werken, PhD

Dr Harmen J G Werken

Dr Harmen J G Werken, PhD

Dr Harmen J G Werken

PhD

Introduction

Education

Jan 2003 - Apr 2008
Wageningen University
PhD

Experience

Feb 2018
Erasmus MC
Assistant Professor Computational Biology
Department of Urology
Feb 2013 - Aug 2014
Erasmus MC
Postdoctoral researcher/Senior Bioinformatician
Cell Biology
Feb 2013 - Aug 2014
Erasmus MC
Postdoctoral researcher/Senior Bioinformatician
Cell Biology
Sep 2014 - Jun 2014
Erasmus MC
Managing Director
Cancer Computational Biology Center
Feb 2008 - Jan 2013
Hubrecht Institute/University of Utrecht and Erasmus MC
Postdoctoral researcher
Biomedical Genomics group
Jan 2003 - Jan 2007
Wageningen University
PhD candidate
Laboratory of Microbiology

Publications

91Publications

787Reads

12Profile Views

1170PubMed Central Citations

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

Cell Rep 2019 Sep;28(10):2704-2714.e5

Amsterdam UMC, University of Amsterdam, Department of Medical Biology, Amsterdam Cardiovascular Sciences, 1105AZ Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.08.007DOI Listing
September 2019
7.207 Impact Factor

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

Br J Cancer 2019 Feb 11;120(4):444-452. Epub 2019 Feb 11.

Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/s41416-019-0381-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461884PMC
February 2019
21 Reads
4.836 Impact Factor

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

Mol Cancer Res 2019 02 26;17(2):521-531. Epub 2018 Sep 26.

Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.

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http://dx.doi.org/10.1158/1541-7786.MCR-18-0054DOI Listing
February 2019
5 Reads
4.380 Impact Factor

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

Eur Urol 2018 12 18;74(6):847-849. Epub 2018 Jun 18.

Department of Urology, Division of Experimental Urology, Medical University of Innsbruck, Innsbruck, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2018.06.002DOI Listing
December 2018
13 Reads
13.940 Impact Factor

SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data.

J Mol Diagn 2018 03 2;20(2):166-176. Epub 2018 Jan 2.

Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2017.11.011DOI Listing
March 2018
25 Reads
4.851 Impact Factor

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

van Kessel KE, van de Werken HJ, Lurkin I, Ziel-van der Made AC, Zwarthoff EC, Boormans JL, PloS one, 2017, vol. 12, no. 3, pp. e0174039, 2017

PLoS ONE

http://europepmc.org/abstract/med/28319171

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2017

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

Mohd-Sarip A, Teeuwssen M, Bot AG, De Herdt MJ, Willems SM, Baatenburg de Jong RJ, Looijenga LHJ, Zatreanu D, Bezstarosti K, van Riet J, Oole E, van Ijcken WFJ, van de Werken HJG, Demmers JA, Fodde R, Verrijzer CP, Cell reports, 2017, vol. 20, no. 1, pp. 61-75, 2017

http://europepmc.org/abstract/med/28683324

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July 2017

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

Ophthalmology 2017 04 1;124(4):573-575. Epub 2016 Dec 1.

Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ophtha.2016.10.039DOI Listing
April 2017
32 Reads
1 Citation
6.135 Impact Factor

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

Yavuzyigitoglu S, Drabarek W, Smit KN, van Poppelen N, Koopmans AE, Vaarwater J, Brands T, Eussen B, Dubbink HJ, van Riet J, van de Werken HJ, Beverloo B, Verdijk RM, Naus N, Paridaens D, Kilic E, de Klein A, Rotterdam Ocular Melanoma Study Group, Ophthalmology, 2016, 2016

Ophthalmology

http://europepmc.org/abstract/med/27916271

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2016

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

Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJ, Cancer cell, 2016, vol. 30, no. 5, pp. 806-821, 2016

Cancer Cell

http://europepmc.org/abstract/med/27846393

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December 2016

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

Development 2016 06 5;143(12):2135-46. Epub 2016 Apr 5.

Department of Anatomy, Embryology and Physiology, Academic Medical Center, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands

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http://dev.biologists.org/content/develop/early/2016/03/31/d
Web Search
http://dev.biologists.org/lookup/doi/10.1242/dev.132019
Publisher Site
http://dx.doi.org/10.1242/dev.132019DOI Listing
June 2016
9 Reads
5 Citations
6.462 Impact Factor

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

Mol Cell Biol 2015 Jun 13;35(12):2103-18. Epub 2015 Apr 13.

Cellular Signaling and Nuclear Dynamics Program, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, INSERM U964, Université de Strasbourg, Illkirch, France

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http://dx.doi.org/10.1128/MCB.01370-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438247PMC
June 2015
6 Reads
3 Citations
4.780 Impact Factor

The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence.

Nat Commun 2015 Apr 24;6:6967. Epub 2015 Apr 24.

Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark.

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http://dx.doi.org/10.1038/ncomms7967DOI Listing
April 2015
16 Reads
36 Citations
10.742 Impact Factor

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

Stem Cell Reports 2015 Jan 24;4(1):114-128. Epub 2014 Dec 24.

Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2014.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297870PMC
January 2015
16 Reads
24 Citations

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

Circ Res 2014 Aug 24;115(4):432-41. Epub 2014 Jun 24.

From the Department of Anatomy, Embryology, and Physiology, Academic Medical Center, Amsterdam, The Netherlands (J.H.v.W., I.B., M.v.d.B., S.S., P.B., V.M.C.); Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands (H.J.G.v.d.W., W.d.L.); Department of Cell Biology, Erasmus MC Rotterdam, Rotterdam, The Netherlands (H.J.G.v.d.W.); and Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (M.G.-V., C.B.-C., M.M.).

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http://dx.doi.org/10.1161/CIRCRESAHA.115.303591DOI Listing
August 2014
39 Reads
11 Citations
11.020 Impact Factor

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

Epigenetics Chromatin 2014 16;7:10. Epub 2014 Jun 16.

Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1186/1756-8935-7-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100494PMC
July 2014
21 Reads
22 Citations
5.333 Impact Factor

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

Development 2014 Jun 21;141(12):2391-401. Epub 2014 May 21.

School of Cancer Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK

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http://dx.doi.org/10.1242/dev.106054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050696PMC
June 2014
9 Reads
13 Citations
6.462 Impact Factor

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

Proc Natl Acad Sci U S A 2014 Jan 13;111(3):996-1001. Epub 2013 Dec 13.

Department of Cell Biology, Biophysical Genomics, Department of Cell Biology, Center for Biomics, Cancer Genomics Center, Erasmus Medical Center, 3015 GE, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1317788111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903193PMC
January 2014
70 Reads
199 Citations
9.810 Impact Factor

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

Mol Cell 2013 Feb 27;49(3):524-35. Epub 2012 Dec 27.

Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands; Doctoral Programme in Biomedicine and Experimental Biology, Centre for Neuroscience and Cell Biology, 3004-517 Coimbra, Portugal.

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http://dx.doi.org/10.1016/j.molcel.2012.11.021DOI Listing
February 2013
4 Reads
188 Citations
14.020 Impact Factor

4C technology: protocols and data analysis.

Methods Enzymol 2012 ;513:89-112

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/B978-0-12-391938-0.00004-5DOI Listing
December 2012
15 Reads
52 Citations
2.090 Impact Factor

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

Methods 2012 Nov 17;58(3):221-30. Epub 2012 May 17.

Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht 3584 CT, The Netherlands.

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http://dx.doi.org/10.1016/j.ymeth.2012.04.009DOI Listing
November 2012
8 Reads
74 Citations
3.645 Impact Factor

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

Nat Methods 2012 Oct 9;9(10):969-72. Epub 2012 Sep 9.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nmeth.2173DOI Listing
October 2012
24 Reads
96 Citations
32.072 Impact Factor

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

Genes Dev 2011 Jul 20;25(13):1371-83. Epub 2011 Jun 20.

Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands.

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http://dx.doi.org/10.1101/gad.633311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134081PMC
July 2011
6 Reads
107 Citations
10.800 Impact Factor

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

Nat Cell Biol 2011 Jun 26;13(8):944-51. Epub 2011 Jun 26.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ncb2278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151580PMC
June 2011
3 Reads
57 Citations
19.680 Impact Factor

Pentose metabolism in archaea

Archaea: New Models for Prokaryotic Biology

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2008

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

J Virol 2008 May 12;82(10):4874-83. Epub 2008 Mar 12.

Thermal Biology Institute, Montana State University, Bozeman, Montana, USA [corrected]

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http://dx.doi.org/10.1128/JVI.02583-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346736PMC
May 2008
3 Reads
34 Citations
4.440 Impact Factor

A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes.

J Biol Chem 2007 Nov 17;282(46):33659-70. Epub 2007 Sep 17.

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

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http://dx.doi.org/10.1074/jbc.M703424200DOI Listing
November 2007
1 Read
25 Citations
4.573 Impact Factor

Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment.

J Biol Chem 2006 Sep 17;281(37):27378-88. Epub 2006 Jul 17.

Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, the Netherlands.

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http://dx.doi.org/10.1074/jbc.M605549200DOI Listing
September 2006
5 Reads
21 Citations
4.573 Impact Factor

Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.

FEMS Microbiol Lett 2006 Jul;260(1):69-76

Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.

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http://dx.doi.org/10.1111/j.1574-6968.2006.00292.xDOI Listing
July 2006
2 Reads
14 Citations
2.121 Impact Factor

Two novel conjugative plasmids from a single strain of Sulfolobus.

Microbiology 2006 Jul;152(Pt 7):1951-68

Laboratory of Microbiology, Wageningen University, The Netherlands.

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http://dx.doi.org/10.1099/mic.0.28861-0DOI Listing
July 2006
5 Reads
11 Citations
2.560 Impact Factor

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

Proteomics 2006 Mar;6(5):1518-29

Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Sheffield, UK.

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http://dx.doi.org/10.1002/pmic.200402070DOI Listing
March 2006
5 Reads
13 Citations
3.810 Impact Factor

Top co-authors

Petra Klous
Petra Klous

Hubrecht Institute-KNAW

6
Erik Splinter
Erik Splinter

Hubrecht Institute-KNAW

5
Sjaak Philipsen
Sjaak Philipsen

Erasmus University Medical Center

5