Curriculum Vitae, March 2014

Prof. dr. ir. E.P.J.G. Cuppen

Curriculum Vitae
Personal data
Name:
Address:

Phone:
Date of birth:
Nationality:

Prof. dr. ir. Edwin P.J.G. Cuppen

Palestrinalaan 24
3723 KN Bilthoven
The Netherlands
+31 6 50124992 / +31 30 2121969
August 11, 1970
Netherlands

Current work
-

Principle Investigator at the Hubrecht Institute, Utrecht, The Netherlands

Professor of Genome Biology, Department of Biology, Utrecht University
Professor of Human Genetics, Head of Research, Department of Medical Genetics, University Medical Center
Utrecht, The Netherlands

Address:

Genome Biology Group

Hubrecht Institute
Uppsalalaan 8
3584 CT Utrecht
The Netherlands

Department of Medical Genetics

University Medical Center,
Universiteitsweg 100
3584 GG Utrecht
The Netherlands

Phone:
E-mail:
Web:
Social Media:

+31 30 21 21 969, +31 88 75 50701 (secretary +31 88 75 68312)

e.cuppen@hubrecht.eu, ecuppen@umcutrecht.nl
http://www.hubrecht.eu/research/cuppen, http://www.umcutrecht.nl/genetics
Twitter: @ecuppen, LinkedIn: nl.linkedin.com/pub/edwin-cuppen/46/2b8/a50

Short Profile
Edwin Cuppen (1970) obtained his masters in molecular sciences at the Agricultural University Wageningen in
1994 (cum laude) and his PhD degree in 1999 at the Radboud University in Nijmegen in the group of Prof. Be Wieringa.
During his education, he spent half a year in het Jaenish lab at the Whitehead Institute in Boston. From 1999 to 2002 he
performed postdoctoral research at the Netherlands Cancer Institute in Amsterdam and the Hubrecht Institute in Utrecht,
The Netherlands, in the group of Prof. Ronald Plasterk. In 2002 he became staff scientist at the Hubrecht Institute and in
2007 he was appointed professor of Genome Biology at the Biology department of the Utrecht University. In 2009 he was
appointed professor of Human Genetics and head of the research section of the Medical Genetics department of the
University Medical Center Utrecht, while continuing his work at the Hubrecht Institute.
His area of expertise is in genomics and genetics and his scientific interests are in functional and personal
genomics. In 2005, Edwin Cuppen was awarded a European Young Investigators Award for his work on naturally
occurring and induced genetic variation in the laboratory rat. He was one of the first to generate gene knockout models in
the rat and showed the widespread effect of copy number variation on gene expression levels. In 2013, he was awarded
a prestigious NWO Vici grant for dissecting the molecular mechanisms behind structural genomic variation.
In his current work he combines experimental methods, including next-generation sequencing technology and
animal model studies, with bioinformatic approaches to identify functional elements in genomes and to understand the
effects of genetic variation under normal and disease conditions. His research group has a long track record in highthroughput DNA analysis and was among the first to pioneer next-generation sequencing technology. His group
developed and improved various NGS-based techniques and is now routinely applying NGS-based techniques in a wide
range of systems from human patients to zebrafish and rat models and adult stem cell culturing systems (normal and
tumor derived organoids). His group has specialized in studing genomic structural variation and they are using NGSbased techniques like (small) RNA sequencing, ChIP-Seq, and 4C-seq to detect molecular consequences and dissect
underlying biological mechanisms. Furthermore, within the Medical Center settings, he is involved in implementing NGS
approaches for diagnostic purposes in clinical genetics and personalized cancer treatment (cofounder of Center for
Personalized Cancer Treatment).
Edwin Cuppen is inventor on various patents and cofounder of the biotech startup company InteRNA
Technologies that focuses on miRNA-based diagnostics and therapeutics. He is also an advisor for several biotech
startups in the area of genomics technology and bioinformatics.

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Curriculum Vitae, March 2014

Prof. dr. ir. E.P.J.G. Cuppen

Education
1995 - 1998
1988 - 1994

PhD at the University of Nijmegen, Faculty of Medical Sciences, Department of Cell Biology and
Histology
MSc Cum Laude at the Agricultural University of Wageningen, Molecular Sciences, chemical-biological
orientation

Relevant work
Present:
- April 2009 - present (50%)
Professor of Human Genetics, Head of Research, Department of Medical Genetics, Division Biomedical Genetics,
University Medical Center Utrecht, The Netherlands
- August 2005 present (50%)
Principle Investigator (tenured) at the Hubrecht Institute for Developmental Biology and Stem Cell Research,
Netherlands Royal Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
Past positions:
- June 2007 - 2012
Professor of Genome Biology, Department of Biology, Faculty of Beta Sciences, Utrecht University, The Netherlands
- January 2002 July 2005
Junior Group leader / staff scientist at the Hubrecht Laboratory, Utrecht, The Netherlands. Subject: Vertebrate
Functional Genomics and Bioinformatics.
- January 1999 December 2001
Post-doc in the Functional Genomics group of Prof. Dr. R.H.A. Plasterk at the Netherlands Cancer Institute, Section of
Molecular Biology, Amsterdam, The Netherlands from January 1999 till February 2000 and the Netherlands Institute for
Developmental Biology / Hubrecht lab, Utrecht, The Netherlands from March 2000 till December 2001. Subject:
Heterotrimeric G-protein signalling in C.elegans.
- January 1995 - December 1998
Ph.D. at the University of Nijmegen, Department of Cell Biology, Institute for Cellular Signaling and Faculty of Medical
Sciences, The Netherlands (promoter: prof. dr. B. Wieringa; co-promoter: dr. W.J.A.J. Hendriks). Title of thesis:
Characterization of the molecular environment of the protein tyrosine phosphatase PTP-BL.
- September 1994 - December 1994
Participation as scientific co-worker in a research project at the Department of Cell Biology, Faculty of Medical
Sciences, University of Nijmegen, Nijmegen, The Netherlands, funded by Genetics Institute, Cambridge, MA, USA.
Subject: Construction of a knock-out mouse model for the cPLA2 gene.
- January 1994 - July 1994
Undergraduate student project at the Whitehead Institute for Biomedical Research, M.I.T., Cambridge, MA, USA, under
supervision of Dr. P.W. Laird and Prof. R. Jaenisch. Subject: Establishment of ES cell lines expressing different levels
of DNA methyltransferase by homologous recombination and analysis of DNA methyltransferase-mediated
mutagenicity.
- May 1993 - November 1993
Student project at the Department of Cell Biology and Histology, Faculty of Medical Sciences, University of Nijmegen,
The Netherlands, under supervision of Dr. G. Janssen and Prof. B. Wieringa. Subject: Protein expression studies on
the myotonic dystrophy protein kinase (DM-PK).
- October 1992 - April 1993
Student project at the Department of Molecular Biology, Agricultural University of Wageningen, The Netherlands, under
supervision of Prof. A. van Kammen. Subject: Identification and characterization of YAC clones containing molecular
markers linked to nematode resistance in tomato.

Awards
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European Young Investigators (EURYI) Award 2005 (1.2 M , European Science Foundation).
NWO Vici grant 2013 (1.5 M )

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Curriculum Vitae, March 2014

Prof. dr. ir. E.P.J.G. Cuppen

Academic advisory activities

- 2013 present: member 'wetenschappelijke raad KiKa' (scientific council foundation Children Cancer Free)
- 2012 2014: Expert panel member Finnish Academy of Sciences
- 2010 present: Advisory Board Liverpool Centre for Genomic Research
- 2010 present: Advisory Board Knockout Rat Consortium (www.knockoutrat.org)
- 2009 2012: Member FWO expert panel, Belgium
- 2007/2008: Member Scientific Advisory Board ELSYS (Young European Scientists in Life Science)
- 2008: Member scientific site visit committee CGM, Paris, France
- 2007: Expert reviewer FP6 panel
- 2005: Member scientific site visit committee Roslin Institute, Edinburg, UK
- Reviewer for various journals, including Nucleic Acids Research, Genomics, Bioinformatics, BMC Genomics, BMC
Bioinformatics, Bioinformatics, Genome Biology, Genome Research, PNAS, Nature Genetics, Nature, Nature Methods,
Cell.
- Reviewer and committee member for various national and international funding agencies (NWO, KWF, KiKa, BBSRC,
Wellcome Trust, CR-UK, CNRS)

Commercial advisory activities

- 2013 present: Scientific Advisor Elly Lilly (rat genomics) (renummerated)
- 2012 present: Scientific Advisory Board Cergentis BV (targeted sequencing technology) (renummerated)
- 2012 present: Scientific Advisory Board Genalice (high volume data analysis) (renummerated)
- 2008 2012: Scientific Advisor Philips Research (DNA analysis technology) (renummerated)
- 2006 present: Scientific Advisory Board InteRNA Technologies BV (miRNA-based therapeutics) (renummerated)

Other national and international scientific activities

nd

- 2013: Scientific committe 2 International Conference on Genomics, Ghent, Belgium

- 2013: Chair program committee Federa Dag Next-generation sequencing 2013
- 2007 present: Organizer annual Cold Spring Harbor/Wellcome Trust meeting Rat genomics and models
- 2010 present: Steering Committee member Center for Personalized Cancer Treatment (www.CPCT.nl)
- 2010 present: Steering Committee member EU FP7 program EURATRANS (www.euratrans.eu)
- 2012 present: Mentor Steyn Parve coaching program UMC Utrecht
- 2011 2013: Director Netherlands Center for Genome Diagnostics (CGD)
- 2008 2012: Organizer annual Dutch Next-Generation Sequencing Users Meeting
- 2009 2012: Chair Jury X-track Honors Program
- 2010: Co-organizer first European (ESF) next-generation sequencing meeting
- 2007 2009: Member program committee NWO Computational Life Sciences II.

Scientific Publications
154 articles, 11 book chapters
Total number of citations: 5,725
H-index is 39 (source Scopus, 1-3-2014)
average impact factor: 9.5
first/last author on 53% of articles, international
collaboration for 31% of articles
45 papers (29%) with impact factor > 10
6 patent (applications)
Researcher ID (www.researcherid.com): F-5696-2011
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van Heesch S, van Iterson M, Jacobi J, Boymans S, Essers PB, de Bruijn E, Hao W, Macinnes AW, Cuppen E, Simonis M
(2014). Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome
Biology 15(1):R6 (IF = 10.3)
Schuijers J, Mokry M, Hatzis P, Cuppen E, Clevers H (2014). Wnt-induced transcriptional activation is exclusively mediated by
TCF/LEF. EMBO J. 33(2):146-56 (IF = 9.8)
Hoogstraat M, de Pagter MS, Cirkel GA, van Roosmalen MJ, Harkins TT, Duran K, Kreeftmeijer J, Renkens I, Witteveen PO,
Lee CC, Nijman IJ, Guy T, van 't Slot R, Jonges TN, Lolkema MP, Koudijs MJ, Zweemer RP, Voest EE, Cuppen E*,
Kloosterman WP* (2014). Genomic and transcriptomic plasticity in treatment-naive ovarian cancer. Genome Research,
24(2):200-11 (IF = 14.4)
Schwank G, Koo BK, Sasselli V, Dekkers JF, Heo I, Demircan T, Sasaki N, Boymans S, Cuppen E, van der Ent CK,
Nieuwenhuis EE, Beekman JM, Clevers H (2013). Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell
organoids of cystic fibrosis patients. Cell Stem Cell,13(6):653-8 (IF = 25.3)

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Prof. dr. ir. E.P.J.G. Cuppen

Mokry M, Middendorp S, Wiegerinck CL, Witte M, Teunissen H, Meddens CA, Cuppen E, Clevers H, Nieuwenhuis EE (2013).
Many Inflammatory Bowel Disease Risk Loci Include Regions That Regulate Gene Expression in Immune Cells and the
Intestinal Epithelium. Gastroenterology pii: S0016-5085(13)01739-3 (IF = 12.8)
Low TY, van Heesch S, van den Toorn H, Giansanti P, Cristobal A, Toonen P, Schafer S, Hbner N, van Breukelen B,
Mohammed S, Cuppen E*, Heck AJ*, Guryev V (2013). Quantitative and Qualitative Proteome Characteristics Extracted from
In-Depth Integrated Genomics and Proteomics Analysis. Cell Reports, 5(5):1469-78 (IF = no impact factor yet)
Nijman IJ, van Montfrans JM, Hoogstraat M, Boes ML, van de Corput L, Renner ED, van Zon P, van Lieshout S, Elferink MG,
van der Burg M, Vermont CL, van der Zwaag B, Janson E, Cuppen E, Ploos van Amstel JK, van Gijn ME (2013). Targeted
next-generation sequencing: A novel diagnostic tool for primary immunodeficiencies. J Allergy Clin Immunol, pii: S00916749(13)01367-5 (IF = 10.1)
van der Crabben SN, Harakalova M, Brilstra EH, van Berkestijn FM, Hofstede FC, van Vught AJ, Cuppen E, Kloosterman W,
Ploos van Amstel HK, van Haaften G, van Haelst MM (2014). Expanding the spectrum of phenotypes associated with
germline PIGA mutations: A child with developmental delay, accelerated linear growth, facial dysmorphisms, elevated alkaline
phosphatase, and progressive CNS abnormalities. Am J Med Genet A, 164A(1):29-35 (IF = 2.3)
Atanur SS, Garcia Diaz A, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PM, Otto GW, Chun M, Ma J,
Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M,
Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Pettretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ
(2013). Genome Sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell
154:691-703. (IF = 32)
Vergult S, Van Binsbergen E, Sante T, Nowak S, Vanakker O, Claes K, Poppe B, Van der Aa N, van Roosmalen MJ, Duran
K, Tavakoli-Yaraki M, Swinkels M, van den Boogaard MJ, van Haelst M, Roelens F, Speleman F, Cuppen E, Mortier G,
Kloosterman WP, Menten B (2013). Mate pair sequencing for the detection of chromosomal aberrations in patients with
intellectual disability and congenital malformations. Eur J Hum Genet, in press (IF = 4.3)
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW,
Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, Jagodic M, Tuncel J,
Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T,
Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G,
Bauerfeind A, Bihoreau MT, Heinig M, Lee YA, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop
M, Lansu N, Toonen P, Ruzius FP, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas
T, Jones EY, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hubner N,
Fernandez-Teruel A*, Cuppen E*, Mott R*, Flint J*. (2013). Combined sequence-based and genetic mapping analysis of
complex traits in outbred rats. Nature Genetics, 45:767-775 (IF = 35.2)
Van Heesch S, Mokry M, Boskova V, Junker W, Mehon R, Toonen P, Shull JD, Aitman TJ, Cuppen E*, Guryev V* (2013).
Systematic biases in DNA copy number originate from isolation procedures. Genome Biology, 14:R33 (IF = 10.3)
Kettleborough RNW*, Busch-Nentwich EM*, Harvey SA*, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C,
Nijman IJ, Fnyes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E*, Stemple DL* (2013).
A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature, 496:494497 (IF = 38.6)
Van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, Zhou S, Goldstein S, Schwartz DC, Harkins
TT, Guryev V*, Cuppen E* (2013). Improving mammalian genome scaffolding using large insert mate-pair next-generation
sequencing. BMC Genomics, 14(1):257 (IF = 4.4)
Kloosterman W, Cuppen E. (2103). Chromothripsis in congenital disorders and cancer: similarities and differences. Curr Opin
Cell Biol, 25:341-348 (IF = 11.4)
Van Nuland R, van Schaik FMA, Simonis M, van Heesch S, Cuppen E, Boelens R, Timmers MTM, van Ingen H (2013).
Nucleosomal DNA binding drives the recognition of H3K36 methylated nucleosomes by the PSIP1-PWWP domain. Epigenet
Chromat, 6:12 (IF = 4.2)
Lolkema MP, Gadellaa-van Hooijdonk CG, Bredenoord AL, Kapitein P, Roach N, Cuppen E, Knoers NV, Voest EE (2013).
Ethical, Legal, and Counseling Challenges Surrounding the Return of Genetic Results in Oncology. J Clin Oncol, 31:18421848 (IF = 18)
Mul JD, ODuibhir E, Shrestha YB, Koppen A, Vargovic P, Toonen PW, Zarebidaki E, Kvetnansky R, Kalkhoven E, Cuppen E,
Bartness TJ (2013). Pmch-deficiency in rats is associated with normal adipocyte differentiation and lower sympathetic adipose
drive. PLoS One 8(3):e60214 (IF = 3.7)
Stoffels M, Szperl A, Simon A, Netea MG, Plantinga TS, van Deuren M, Kamphuis S, Lachmann HJ, Cuppen E, Kloosterman
WP, Frenkel J, van Diemen CC, Wijmenga C, van Gijn M, van der Meer JW (2013). MEFV mutations affecting pyrin amino
acid 577 cause autosomal dominant autoinflammatory disease. Ann Rheum. Dis, in press (IF = 9.1)
Leptidis S, El Azzouzi H, Lok SI, de Weger R, Olieslagers S, Kisters N, Silva GJ, Heymans S, Cuppen E, Berezikov E, De
Windt LJ, da Costa Martins P (2013). A Deep Sequencing Approach to Uncover the miRNOME in the Human Heart. PLoS
One 8(2):e57800 (IF = 3.7)
Eijkelenboom A, Mokry M, de Wit E, Smits LM, Polderman PE, van Triest MH, van Boxtel R, Schulze A, de Laat W, Cuppen
E, Burgering BM (2013). Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II
profiling. Mol Syst Biol 9:638 (IF = 11.3)
Boj SF, van Es JH, Huch M, Li VS, Jos A, Hatzis P, Mokry M, Haegebarth A, van den Born M, Chambon P, Voshol P, Dor Y,
Cuppen E, Fillat C, Clevers H (2012). Diabetes Risk Gene and Wnt Effector Tcf7l2/TCF4 Controls Hepatic Response to
Perinatal and Adult Metabolic Demand. Cell 151:1595-607 (IF = 32)
Nadra K, Mdard JJ, Mul JD, Han GS, Grs S, Pende M, Metzger D, Chambon P, Cuppen E, Saulnier-Blache JS, Carman
GM, Desvergne B, Chrast R (2012). Cell autonomous lipin 1 function is essential for development and maintenance of white
and brown adipose tissue. Mol Cell Biol 32:4794-810 (IF = 5.4)
Harakalova M, van der Smagt J, de Kovel CG, Van't Slot R, Poot M, Nijman IJ, Medic J, Joziasse I, Deckers J, RoosHesselink JW, Wessels MW, Baars HF, Weiss MM, Pals G, Golmard L, Jeunemaitre X, Lindhout D, Cuppen E, Baas AF
(2012). Incomplete segregation of MYH11 variants with thoracic aortic aneurysms and dissections and patent ductus
arteriosus. Eur J Hum Genet 21:487-493 (IF = 4.3)
Aguado-Fraile E, Ramos E, Senz-Morales D, Conde E, Blanco-Snchez I, Stamatakis K, del Peso L, Cuppen E, Brne B,
Bermejo ML (2012). miR-127 protects proximal tubule cells against ischemia/reperfusion: identification of kinesin family
member 3B as miR-127 target. PLoS One 7:e44305 (IF = 3.7)
Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S,
Giardino D, Hansson K, Ruivenkamp CA, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten
B, Larizza L, Guryev V, Poot M, Cuppen E (2012). Constitutional chromothripsis rearrangements involve clustered double-

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stranded DNA breaks and nonhomologous repair mechanisms. Cell Reports 1:648-55 (highlighted in Nat Rev Cancer
12:510-511) (IF = no impact factor yet)
Harakalova M, van den Boogaard MJ, Sinke R, van Lieshout S, van Tuil MC, Duran K, Renkens I, Terhal PA, de Kovel C,
Nijman IJ, van Haelst M, Knoers NV, van Haaften G, Kloosterman W, Hennekam RC, Cuppen E, Ploos van Amstel HK
(2012). X-exome sequencing identifies a HDAC8 variant in a large pedigree with X-linked intellectual disability, truncal
obesity, gynaecomastia, hypogonadism and unusual face. J Med Genet 49(8):539-43 (IF = 5.7)
Poel JB, van Haastert RJ, de Gunst T, Schultz IJ, Gommans WM, Verheul M, Cerisoli F, van Noort PI, Prevost GP,
Schaapveld RQJ, Cuppen E (2012). A functional screen identifies specific microRNAs capable of inhibiting human melanoma
cell viability. Plos One 7:e43569 (IF = 3.7)
Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL,
Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA,
Asselbergs FW, Breur HM, Swinkels ME, Scurr IJ, Smithson SF, Knoers NV, van der Smagt JJ, Nijman IJ, Kloosterman WP,
van Haelst MM, van Haaften G, Cuppen E. (2012). Dominant missense mutations in ABCC9 cause Cant syndrome. Nature
Genetics 44:793-6 (IF = 35.2)
Northrup E, Zschemisch NH, Eisenbltter R, Glage S, Wedekind D, Cuppen E, Dorsch M, Hedrich HJ. (2012). The ter
Mutation in the Rat Dnd1 Gene Initiates Gonadal Teratomas and Infertility in Both Genders. PLoS One 7(5):e38001 (IF = 3.7)
Simonis M, Atanur SS, Linsen SEV, Guryev V, Ruzius F, Game L, LansuN, de Bruijn E, van Heesch S, Jones SJM, Pravenec
M, Aitman TJ, Cuppen E (2012). Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH
recombinant inbred panel. Genome Biology 13(4):r31 (IF = 10.3)
Fuchs SA, Harakalova M, van Haaften G, van Hasselt PM, Cuppen E, Houwen RJ. (2012). Application of exome sequencing
in the search of genetic causes or rare disorders of copper metabolism. Metallomics, 4(7):606-13 (IF = 4.1)
Mul JM, Begg DP, Alters SIM, van Haaften G, Duran KJ, d'Alessio DA, le Roux CW, Woods SC, Sandoval DA, Blakemore
AIF, Cuppen E, van Haelst MM, Seeley RJ. (2012). Effect of vertical sleeve gastrectomy in melanocortin receptor 4-deficient
rats. Am J Physiol Endocrinol Metab, 303(1):E103-10 (IF = 4.5)
Itsara A, Vissers LE, Steinberg KM, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA,
Wilson RK, Jenkins RB, Veltman JA, Eichler EE. (2012). Resolving the breakpoints of the 17q21.31 microdeletion syndrome
with next-generation sequencing. Am J Hum Genet 90:599-613 (IF = 11.2)
Blauw HM, van Rheenen W, Koppers M, Van Damme P, Waibel S, Lemmens R, van Vught PW, Meyer T, Schulte C, Gasser
T, Cuppen E, Pasterkamp RJ, Robberecht W, Ludolph AC, Veldink JH, van den Berg LH. (2012). NIPA1 polyalanine repeat
expansions are associated with amyotrophic lateral sclerosis. Hum Mol Genet 21:2497-502 (IF = 7.7)
Blauw HM, Barnes CP, van Vught PW, van Rheenen W, Verheul M, Cuppen E, Veldink JH, van den Berg LH (2012). SMN1
gene duplications are associated with sporadic ALS. Neurology 78:776-80 (IF = 8.2)
Westendorp B, Mokry M, Groot Koerkamp MJA, Holstege FCP, Cuppen E, de Bruin A (2012). E2F7 represses a network of
oscillatin cell cycle genes to conrol S-phase progression. Nucl Acids Res 40:3511-23 (IF = 8.3)
Hochstenbach R, Poot M, Nijman IJ, Renkens I, Duran KJ, van 't Slot R, van Binsbergen E, van der Zwaag B, Vogel MJ,
Terhal PA, Ploos van Amstel HK, Kloosterman WP, Cuppen E (2011). Discovery of variants unmasked by hemizygous
deleteions. Eur J Hum Genet 20(7):748-53 (IF = 4.3)
van Es MA, Schelhaas HJ, van Vught PW, Ticozzi N, Andersen PM, Groen EJ, Schulte C, Blauw HM, Koppers M, Diekstra
FP, Fumoto K, Leclerc AL, Keagle P, Bloem BR, Scheffer H, van Nuenen BF, van Blitterswijk M, van Rheenen W, Wills AM,
Lowe PP, Hu GF, Yu W, Kishikawa H, Wu D, Folkerth RD, Mariani C, Goldwurm S, Pezzoli G, Van Damme P, Lemmens R,
Dahlberg C, Birve A, Fernndez-Santiago R, Waibel S, Klein C, Weber M, van der Kooi AJ, de Visser M, Verbaan D, van
Hilten JJ, Heutink P, Hennekam EA, Cuppen E, Berg D, Brown RH Jr, Silani V, Gasser T, Ludolph AC, Robberecht W, Ophoff
RA, Veldink JH, Pasterkamp RJ, de Bakker PI, Landers JE, van de Warrenburg BP, van den Berg LH. (2011). Angiogenin
variants in Parkinson disease and amyotrophic lateral sclerosis. Ann Neurol 70(6):964-73 (IF = 11.2)
Stassen J, Seidl M, Vergeer P, Nijman IJF, Snel B, Cuppen E, van den Ackerveken AFJM (2012). Effector identficition in the
lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. Mol Plant Pathol 13(7):719-31 (IF =
3.9)
Vermaat JS, Nijman IJ, Koudijs MJ, Gerritse FL, Scherer S, Mokry M, Roessingh W, Lansu N, de Bruin E, van Hillegersberg
R, van Diest P, Cuppen E, Voest EE (2012). Primary colorectal cancers and their subsequent hepatic metastases are
genetically different: implicantions for selection of patients for targeted treatment. Clin Cancer Res 18(3):688-99 (IF = 7.8)
Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, Vermaat JS, van Roosmalen MJ, van Lieshout S,
Nijman IJ, Roessingh W, van 't Slot R, van de Belt J, Guryev V, Koudijs M, Voest E, Cuppen E. (2011). Chromothripsis is a
common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biology 12:R103
(IF = 10.3)
Poell JB, van Haastert RJ, Cerisoli F, Bolijn AS, Timmer LM, Diosdado-Calvo B, Meijer GA, van Puijenbroek AA, Berezikov E,
Schaapveld RQ, Cuppen E (2011). Functional microRNA screening using a comprehensive lentiviral human microRNA
expression library. BMC Genomics 12:546 (IF = 4.4)
Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius F, Clevers H, Cuppen E. (2012). Integrated genome-wide analysis of
transcription factor occupancy, RNA polymerase II binding and steady state RNA levels identifies differentially regulated
functional gene classes. Nucleic Acids Res 40:148-58 (IF = 8.3)
Harakalova M, Mokry M, Hrdlickova B, Renkens I, Duran K, van Roekel H, Lansu N, de Bruijn E, Nijman IJ, Kloosterman W,
Cuppen E (2011). Multiplexed genomic enrichment for flexible targeted next-generation sequencing. Nature Protocols
6:1870-86 (IF = 8)
Koudijs MJ, Klijn C, van der Weyden L, Kool J, ten Hoeve J, Sie D, Prasetyanti PR, Kas S, Whipp T, Cuppen E, Wessels L,
Adams DJ, Jonkers J. (2011). High-throughput semi-quantitative analysis of insertional mutations in heterogeneous tumors.
Genome Research 21:2181-9 (IF = 14.4)
van Boxtel R, Kuiper RV, Toonen PW, van Heesch S, Hermsen R, de Bruin A, Cuppen E (2011). Homozygous and
heterozygous P53 knockout rats develop metastasizing sarcomas with high frequency. Am J Pathol 179:1616-22 (IF = 4.5)
Blauw HM, Barnes CP, Vught PWJ, van Rheenen W, Verheul M, Cuppen E, Veldink JH, van den Berg LH (2012). SMN1
gene duplications are associated with sporadic ALS. Neurology 78(11):776-80 (IF = 8.2)
Mul JD, Nadra K, Jagalur NB, Nijman IJ, Toonen PW, Mdard JJ, Grs S, de Bruin A, Han GS, Brouwers JF, Carman GM,
Saulnier-Blache JS, Meijer D, Chrast R, Cuppen E. (2011). A hypomorphic mutation in lpin1 induces progressively improving
neuropathy and lipodystrophy in the rat. J Biol Chem 286(30):26781-93 (IF = 4.7)
Mokry M, Nijman IJ, van Dijken A, Benjamins R, Heidstra R, Scheres B, Cuppen E. (2011). Identification of factors required
for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach. BMC
Genomics 12:256 (IF = 4.4)

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51) Mul JD, la Fleur SE, Toonen PW, Afrasiab-Middelman A, Binnekade R, Schetters D, Verheij MM, Sears RM, Homberg JR,
Schoffelmeer AN, Adan RA, DiLeone RJ, De Vries TJ, Cuppen E. (2011). Chronic loss of melanin-concentrating hormone
affects motivational aspects of feeding in the rat. PLoS One 6(5):e19600 (IF = 3.7)
52) Wansleeben C, van Gurp L, Feitsma H, Kroon C, Rieter E, Verberne M, Guryev V, Cuppen E, Meijlink F. (2011). An ENUmutagenesis screen in the mouse: identification of novel developmental gene functions. PLoS One 6(4):e19357 (IF = 3.7)
53) Mul JD, van Boxtel R, Bergen DJ, Brans MA, Brakkee JH, Toonen PW, Garner KM, Adan RA, Cuppen E. (2012).
Melanocortin Receptor 4 Deficiency Affects Body Weight Regulation, Grooming Behavior, and Substrate Preference in the
Rat. Obesity 20(3):612-21 (IF = 3.9)
54) Held N, Smits BM, Gockeln R, Schubert S, Nave H, Northrup E, Cuppen E, Hedrich HJ, Wedekind D. (2011). A mutation in
Myo15 leads to Usher-like symptoms in LEW/Ztm-ci2 rats. PLoS One 6(3):e15669 (IF = 3.7)
55) Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, Bakker SC, Letteboer T, van Nesselrooij B,
Hochstenbach R, Poot M, Cuppen E. (2011). Chromothripsis as a mechanism driving complex de novo structural
rearrangements in the germline. Hum Mol Genet 20(10):1916-24 (IF = 7.7)
56) Harakalova M, Nijman IJ, Medic J, Mokry M, Renkens I, Blankensteijn JD, Kloosterman W, Baas AF, Cuppen E. (2011).
Genomic DNA Pooling Strategy for Next-Generation Sequencing-Based Rare Variant Discovery in Abdominal Aortic
Aneurysm Regions of Interest-Challenges and Limitations. J Cardiovasc Transl 4(3):271-80 (IF = 3.1)
57) Edwards CJ, Ginja C, Kantanen J, Prez-Pardal L, Tresset A, Stock F; European Cattle Genetic Diversity Consortium, Gama
LT, Penedo MC, Bradley DG, Lenstra JA, Nijman IJ. (2011). Dual origins of dairy cattle farming--evidence from a
comprehensive survey of European Y-chromosomal variation. PLoS One 6(1):e15922 (IF = 3.7)
58) Joziasse IC, Smith KA, Chocron S, van Dinther M, Guryev V, van de Smagt JJ, Cuppen E, Ten Dijke P, Mulder BJ, Maslen
CL, Reshey B, Doevendans PA, Bakkers J. (2011). ALK2 mutation in a patient with Down's syndrome and a congenital heart
defect. Eur J Hum Genet 19(4):389-93 (IF = 4.3)
59) Bredenoord AL, Kroes HY, Cuppen E, Parker M, van Delden JJ. (2011). Disclosure of individual genetic data to research
participants: the debate reconsidered. Trends Genet 27(2):41-7 (IF = 9.8)
60) Sleigh JN, Buckingham SD, Esmaeili B, Viswanathan M, Cuppen E, Westlund BM, Sattelle DB. (2011). A novel
Caenorhabditis elegans allele smn-1(cb131), mimicking a mild form of spinal muscular atrophy, provides a convenient drug
screening platform highlighting new and pre-approved compounds. Hum Mol Genet 20:245-260 (IF = 7.7)
61) Mokry M, Hatzis P, de Bruijn E, Koster J, Versteeg R, Schuijers J, van de Wetering M, Guryev V, Clevers H, Cuppen E.
(2010). Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles. PLoS One
30;5(11):e1509 (IF = 3.7)
62) Nijman I, Mokry M, van Boxtel R, Toonen P, de Bruijn E, and Cuppen E. (2010). Mutation discovery by targeted genomic
enrichment of multiplexed barcoded samples. Nature Methods 7:913-5 (IF = 23.6)
63) Wansleeben C, Feitsma H, Tertoolen L, Kroon C, Guryev V, Cuppen E, Meijlink F. (2010). A novel mutant allele of Ncx1: a
single amino acid substitution leads to cardiac dysfunction. Int J Dev Biol 54(10):1465-71 (IF = 2.6)
64) van Boxtel R, Cuppen E. (2010). Rat traps: Filling the toolbox of rat genetics. Genome Biology 11:217 (IF = 10.3)
65) Chan JS, Snoeren EM, Cuppen E, Waldinger MD, Olivier B, Oosting RS. (2010). The Serotonin Transporter Plays an
Important Role in Male Sexual Behavior: A Study in Serotonin Transporter Knockout Rats. J Sex Med 8(1):97-108 (IF = 3.5)
66) Lyddon R, Cuppen E, Haroutunian V, Siever LJ, Dracheva S. (2010). No link of serotonin 2C receptor editing to serotonin
transporter genotype. Neuroreport 21:1080-4 (IF = 1.4)
67) van Boxtel R, Vroling B, Toonen P, Nijman IJ, van Roekel H, Verheul M, Baakman C, Guryev V, Vriend G, Cuppen E. (2011).
Systematic generation of in vivo G protein-coupled receptor mutants in the rat. Pharmacogenomics J 11(5):326-36 (IF = 5.1)
68) Homberg J, Nijman IJ, Kuijpers S, Cuppen E. (2010). Identification of genetic modifiers of behavioral phenotypes in serotonin
transporter knockout rats. BMC Genet 11:37 (IF = 2.8)
69) Snoeren E, Chan J, Bovens A, Cuppen E, Waldinger M, Olivier B, Oosting R. (2010). Serotonin transporter null mutation and
sexual behavior in female rats: 5-HT1A receptor desensitization. J Sex Med 7(7):2424-34 (IF = 3.5)
70) Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren
WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E,
Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. (2010). The genome sequence of the spontaneously hypertensive rat:
Analysis and functional significance. Genome Research 20(6):791-803 (IF = 14.4)
71) Linsen SE, de Wit E, de Bruijn E, Cuppen E. (2010). Small RNA expression and strain specificity in the rat. BMC Genomics
11:249 (IF = 4.4)
72) Wansleeben C, Feitsma H, Montcouquiol M, Kroon C, Cuppen E, Meijlink F. (2010). Planar cell polarity defects and defective
Vangl2 trafficking in mutants for the COPII gene Sec24b. Development 137(7):1067-73 (IF = 6.2)
73) Johannes F, Wardenaar R, Colom-Tatch M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen
RC. (2010). Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 26(8):1000-6 (IF = 5.3)
74) Mokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, Cuppen E. (2010). Accurate SNP and mutation
detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids
Res 38(10):e116 (IF = 8.3)
75) Kim K, Warden CH, Griffey SM, Vilches-Moure JG, Hansen S, Cuppen E, Nijman IJ, Chiu S, Stern JS. (2010). Genes
unlinked to the leptin receptor influence urinary albumin excretion in obese Zucker rats. Physiol Genomics 41:297-305 (IF =
2.8)
76) Groen EJ, van Es MA, van Vught PW, Spliet WG, van Engelen-Lee J, de Visser M, Wokke JH, Schelhaas HJ, Ophoff RA,
Fumoto K, Pasterkamp RJ, Dooijes D, Cuppen E, Veldink JH, van den Berg LH. (2010). FUS mutations in familial
amyotrophic lateral sclerosis in the Netherlands. Arch Neurol 67(2):224-30 (IF = 7.6)
77) Mul J, Yi CX, van den Berg SA, Ruiter M, Toonen P, van der Elst M, Voshol PJ, Ellenbroek B, Kalsbeek A, la Fleur SE,
Cuppen E. (2010). Pmch expression during early development is critical for normal energy homeostasis. Am J Physiol
Endocrinol Metab 298(3):E477-88 (IF = 4.5)
78) de Wit E, Linsen SE, Cuppen E*, Berezikov E.* (2009). Repertoire and evolution of miRNA genes in four divergent nematode
species. Genome Research 19:2064-2074 (IF = 14.4)
79) Pereira F, Queirs S, Gusmo L, Nijman IJ, Cuppen E, Lenstra JA; the Econogene Consortium, Davis SJ, Nejmeddine F,
Amorim A. (2009). Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North
Africa. Mol Biol Evol 26:2765-2673 (IF = 10.4)
80) Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S,
Tewari M, Cuppen E. (2009). Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods
6:474-476 (IF = 23.6)
81) Homberg JR, Mul JD, de Wit E, Cuppen E. (2009) Complete knockout of the nociceptin/orphanin FQ receptor in the rat does
not induce compensatory changes in mu, delta and kappa opioid receptors. Neuroscience 163:308-15 (IF = 3.1)

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82) Brittijn SA, Duivesteijn SJ, Belmamoune M, Bertens LF, Bitter W, de Bruijn JD, Champagne DL, Cuppen E, Flik G,
Vandenbroucke-Grauls CM, Janssen RA, de Jong IM, de Kloet ER, Kros A, Meijer AH, Metz JR, van der Sar AM, Schaaf MJ,
Schulte-Merker S, Spaink HP, Tak PP, Verbeek FJ, Vervoordeldonk MJ, Vonk FJ, Witte F, Yuan H, Richardson MK. (2009)
Zebrafish development and regeneration: new tools for biomedical research. Int J Dev Biol 53:835-850 (IF = 2.6)
83) Smith, K.A., Joziasse, I.C., Chocron, S., van Dinther, M., Guryev, V., Verhoeven, M.C., Rehmann, H., van der Smagt, J.J.,
Doevendans, P.A., Cuppen, E., Mulder, B.J., ten Dijke, P., Bakkers, J. (2009) Dominant-negative ALK2 allele associates with
congenital heart defects. Circulation 119:3062-9 (IF = 15.2)
84) Guryev V. and Cuppen E. (2009). Next-generation sequencing approaches in genetic rodent model systems to study
functional effects of human genetic variation. FEBS Lett 583:1668-1673 (IF = 3.6)
85) Adamovic, T., McAllister, D., Guryeve, V., Wang, X., Wendt Andrae, J., Cuppen, E., Jacob, H.J, and Sugg, S.L. (2009).
Microalterations of inherently unstable genomic regions in rat mammary carcinomas as revealed by long oligonucleotide array
comparative genomic hybridization. Cancer Res 69:5159-5167 (IF = 8.7)
86) Homberg, J, la Fleur, SE, and Cuppen, E. (2009). Serotonin transporter deficiency increases abdobminal fat in female, but not
male rats. Obesity 18:137-145 (IF = 3.9)
87) Matondo RB, Punt C, Homberg J, Toussaint MJ, Kisjes R, Korporaal SJ, Akkerman JW, Cuppen E, and de Bruin A. (2009).
Deletion of the Serotonin Transporter in Rats Disturbs Serotonin Homeostasis Without Impairing Liver Regeneration. Am J
Physiol Gastrointest Liver Physiol 296: G963-G968 (IF = 3.6)
88) van den Bos R, Homberg J, Gijsbers E, den Heijer E, and Cuppen E. (2009). The effect of COMT Val(158) Met genotype on
decision-making and preliminary findings on its interaction with the 5-HTTLPR in healthy females. Neuropharmacology
56:493-498 (IF = 4.1)
89) van Boxtel, R., Toonen, P.W., Verheul, M., van Roekel, H.S., Nijman, I.J., Guryev, V., and Cuppen, E. (2008). Improved
generation of rat gene knockouts by target-selected mutagenesis in mismatch repair-deficient animals. BMC Genomics 9:460
(IF = 4.4)
90) Linsen, S.E.V., Tops, B.B.J., and Cuppen, E. (2008). miRNA's: small changes, widespread effects. Cell Research 18:1157-9
(IF = 10.5)
91) Feitsma, H., Akay, A., and Cuppen, E. (2008). Alkylation damage causes MMR-dependent chromosomal instability in
vertebrate embryos. Nucleic Acids Res 36:4047-4056 (IF = 8.3)
92) Olivier, J.D., Cools, A.R., Olivier, B., Homberg, J.R., Cuppen, E., and Ellenbroek, B.A. (2008). Stress-induced hyperthermia
and basal body temperature are mediated by different 5-HT(1A) receptor populations: A study in SERT knockout rats. Eur J
Pharmacol 590:190-197 (IF = 2.6)
93) Kruisselbrink, E., Guryev, V., Brouwer, K., Pontier, D.B., Cuppen, E., and Tijsterman, M. (2008). Mutagenic capacity of
endogenous G4 DNA underlies genome instability in FANCJ-defective C. elegans. Current Biology 18:900-905 (IF = 9.5)
94) Homberg, J., de Boer, S., Raaso, H.S., Olivier, J.D.A., Verheul, M., Ronken, E., Cools, A.R., Ellenbroek, B.A., Schoffelmeer,
A.N.M., Vanderschuren, L.J.M.J., de Vries, T.J., and Cuppen, E. (2008). Adaptations in pre- and postsynaptic 5-HT1A
receptor function and cocaine supersensitivity in serotonin transporter knockout rats. Psychopharmacology 200:367-380 (IF
= 4.1)
95) Guryev, V., Saar, K., Adamovic, T., Verheul, M., van Heesch, S., Cook, S., Pravenec, M., Aitman, T., Jacob, H., Shull, JD.,
Hubner, N., and Cuppen, E. (2008). Distribution and functional impact of DNA copy number variation in the rat. Nature
Genetics 40:538-545 (IF = 35.2)
96) The STAR Consortium: Saar, K., Beck, A., Bihoreau, M., Birney, E., Brocklebank, D., Chen, Y., Cuppen, E., Demonchy, S.,
Dopazo, J., Flicek, P., Foglio, M., Fujiyama, A., Gut, I.G., Gauguier, D., Guido, R., Guryev, V., Heinig, M., Hummel, O., Jahn,
N., Klages, S., Kren, V., Kube, M., Kuhl, H., Kuramoto, T., Kuroki, Y., Lechner, D., Lee, Y., Lopez-Bigas, N., Lathrop, G.M.,
Mashimo, T., Medina, I., Mott, R., Patone, G., Perrier-Cornet, J., Platzer, M., Pravenec, M., Reinhardt, R., Sakaki, Y.,
Schilhabel, M., Schulz, H., Serikawa, T., Shikhagaie, M., Tatsumoto, S., Taudien, S., Toyoda, A., Voigt, B., Zelenika, D.,
Zimdahl, H., and Hubner, N. (2008). SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics 40:560-566
(IF = 35.2)
97) Aitman, T.J., Critser, J.K., Cuppen, E., Dominiczak, A., Fernandez-Suarez, X.M., Flint, J., Gauguier, D., Geurts, A.M., Gould,
M., Harris, P.C., Holmdahl, R., Hubner, N., Izsvak, Z., Jacob, H.J., Kuramoto, T., Kwitek, A.E. Marrone, A., Tomoji, M.,
Moreno, C., Mullins, J., Mullins, L., Olsson, T., Pravenec, M., Riley, L., Saar, K., Serikawa, T., Shull, J.D., Szpirer, C.,
Twigger, S.N., Voigt, B., Worley, K. (2008). Progress and prospects in rat genetics: a community view. Nature Genetics
40:516-522 (IF = 35.2)
98) Nijman IJ, Kuipers S, Verheul M, Guryev V, and Cuppen E. (2008) A genome-wide SNP panel for mapping and association
studies in the rat. BMC Genomics 9:95 (IF = 4.4)
99) Feitsma, H., Kuiper, R.V., Korving, J., Nijman, I.J., and Cuppen, E. (2008). Zebrafish with mutations in mismatch repair genes
develop neurofibromas and other tumors. Cancer Research 68: 5059-5066 (IF = 8.7)
100) van Boxtel, R., Toonen, P., van Roekel, H., Verheul, M., Smits, B.M., Korving, J., de Bruin, A., and Cuppen, E. (2008). Lack of
DNA mismatch repair protein MSH6 in the rat results in hereditary non-polyposis colorectal cancer-like tumorigenesis.
Carcinogenesis 29:1290-1297 (IF = 5.6)
101) Homberg, J., van den Bos, R., den Heijer, E., Suer, R., and Cuppen, E. (2008). Serotonin transporter dosage modulates longterm decision-making in rat and human. Neuropharmacology 55: 80-84 (IF = 4.1)
102) Nijman, I.J., van Boxtel, D.C.J., van Cann, L.M., Marnoch, Y., Cuppen, E., and Lenstra, J.A. (2008). Phylogeny of Y
chromosomes from bovine species. Cladistics 24: 723-726 (IF = 5)
103) Feitsma, H., de Bruijn, E., van de Belt, J., Nijman, I.J., Cuppen, E. (2008). Mismatch repair deficiency does not enhance ENU
mutagenesis in the zebrafish germ line. Mutagenesis 23:325-329 (IF = 3.5)
104) Weiss, H., Arndt, T., Jorns, A., Lenzen, S., Cuppen, E., Hedrich, HJ, Fiedge, M., Wedekind, D. (2008). The mutation of the
LEW.1AR1-iddm rat maps to the telomeric end of rat chromosome 1. Mamm Genome 19:292-297 (IF = 2.4)
105) Olivier JD, van der Hart MG, van Swelm RP, Dederen PJ, Homberg JR, Cremers T, Deen PM, Cuppen E, Cools AR,
Ellenbroek BA. (2008). A study in male and female 5-HT transporter knockout rats: An animal model for anxiety and
depression disorders. Neuroscience 152:573-84 (IF = 3.1)
106) Feitsma, H. and Cuppen, E. (2008). Zebrafish as a cancer model. Molecular Cancer Res 6:685-694 (IF = 4.4)
107) Mokry, M. and Cuppen, E. (2008). The Atp1a1 gene from inbred Dahl salt sensitive rats does not contain the A1079T
missense transversion. Hypertension 51:922-927 (IF = 6.9)
108) Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W,
Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG. (2008). Genome-wide pattern of TCF7L2/TCF4
chromatin occupancy in colorectal cancer cells. Mol Cell Biol 28:2732-2744 (IF = 5.4)
109) Leal, M., Feitsma, H., Cuppen, E., Franca, L., and Schulz, R. (2008). Meiosis can be completed in male zebrafish (Danio
rerio) lacking the DNA mismatch repair gene mlh1. Cell Tissue Res 332:133-9 (IF = 3.7)

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110) Frische EW, Pellis-van Berkel W, van Haaften G, Cuppen E, Plasterk RH, Tijsterman M, Bos JL, Zwartkruis FJ. (2007) RAP-1
and the RAL-1/exocyst pathway coordinate hypodermal cell organization in Caenorhabditis elegans. EMBO J 26:5083-92 (IF
= 9.8)
111) Berezikov, E., Chung, W.J., Willis, J., Cuppen, E., and Lai, E.C. (2007). Mammalian mirtron genes. Molecular Cell 28:328336 (IF = 15.3)
112) Homberg, J.R., Pattij, T., Janssen, M.C.W., Ronken, E., De Boer, S.F., Schoffelmeer, A.N.M., and Cuppen, E., (2007).
Serotonin transporter deficiency in rats improves inhibitory control but not behavioral flexibility. Eur J Neurosci 26:2066-2073
(IF = 3.8)
113) Homberg, J.R., Schiepers, O.J., Schoffelmeer, A.N.M., Cuppen, E., Vanderschuren, L.J.. (2007). Acute and constitutive
increases in central serotonin levels reduce social play behaviour in peri-adolescent rats. Psychopharmacology 195:175-82
(IF = 4.1)
114) Homberg, J.R., Olivier, J.D.A., Smits, B.M.G., Mul, J.D., Mudde, J, Verheul, M., Nieuwenhuizen, O.F.M., Cools, A.R., Ronken,
E., Cremers, T., Schoffelmeer, A.N.M., Ellenbroek, B.A., and Cuppen, E. (2007). Characerization of the serotonin transporter
knockout rat: A selective change in the functioning of the serotonergic system. Neuroscience 146:1662-1676 (IF = 3.1)
115) Cuppen, E., Gort, E., Hazendonk, E., Mudde, J., v.d. Belt, J., Nijman, I.J., Guryev, V., and Plasterk, R.H.A. (2007). Efficient
target-selected mutagenesis in Caenorhabditis elegans: towards a knockout for every gene. Genome Research 17:649-658
(IF = 14.4)
116) Feitsma, H., Leal, M.C., Moens, P.B., Cuppen, E.*, and Schulz, R.W.* (2007). Mlh1 deficiency in zebrafish results in male
sterility and aneuploid as well as triploid progeny in females. Genetics 175:1561-1569 (IF = 4.4)
117) Taniguchi, Y., Takeda, S., Furutani-Seiki, M., Kamei, Y., Todo, T., Sasado, T., Deguchi, T., Kondoh, H., Mudde, J., Yamazoe,
J., Hidaka, M., Mitani, H., Toyoda, A., Sakaki, Y., Plasterk, R., and Cuppen, E. (2006). Generation of medaka gene knockout
models by target-selected mutagenesis. Genome Biology 7:R116 (IF = 10.3)
118) Berezikov. E., Thuemmler, F., van Laake, L., Kondova, I., Bontrop, R., Cuppen, E., and Plasterk, R.H.A. (2006). Diversity of
microRNAs in human and chimpanzee brain. Nature Genetics 38:1375-1377 (IF = 35.2)
119) Homberg, J., Mudde, J., Braam, B., Ellenbroek, B., Cuppen, E*., and Joles, J.A.* (2006). Blood pressure in mutant rats
lacking the 5-hydroxytryptamine (5-HT) transporter. Hypertension 48: e115-116e (IF = 6.9)
120) Takada, S., Berezikov, E., Yamashita, Y., Lagos-Quitana, M., Kloosterman, W., Enomoto, M., Hatanaka, H., Fujiwara, S.,
Watanabe, H., Soda, M., Choi, Y.L., Plasterk, R., Cuppen, E., and Mano H. (2006). Mouse microRNA profilies determined
with a new and sensitive cloning method. Nucleic Acids Res 34: e117 (IF = 8.3)
121) Berezikov, E., van Tetering, G., Verheul, M., van de Belt, J., van Laake, L., Vos, J., Verloop, R., van de Wetering, M., Guryev,
V., Takada, S., van Zonneveld, A.J., Mano, H., Plasterk, R.H.A., and Cuppen, E. (2006). Many novel mammalian microRNA
candidates identified by extensive cloning and RAKE analysis. Genome Research 34: e117 (IF = 14.4)
122) Guryev, V., Smits, B.M.G., van de Belt, J., Verheul, M., Hubner, N., and Cuppen, E. (2006). Haplotype Block Structure Is
Conserved across Mammals. PLOS Genetics 2(7): e121 (IF = 8.5)
123) Berezikov, E., Cuppen, E., and Plasterk, R. (2006). Approaches to microRNA discovery. Nature Genetics 38:S2-S7 (IF =
35.2)
124) Kloosterman, W., Steiner, F., Berezikov, E., de Bruijn, E., van de Belt, J., Verheul, M., Cuppen, E., and Plasterk, R. (2006).
Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res 34:2558-2569 (IF = 8.3)
125) Smits, B.M.G. and Cuppen, E. (2006). Rat Genetics: the Next Episode. Trends Genet 22:232-40 (IF = 9.8)
126) Smits, B.M.G. and Cuppen, E. (2006). Rats go genomic. Genome Biology 7:306 (IF = 10.3)
127) Guryev, V., Koudijs, M.J., Berezikov, E., Johnson, S.L., Plasterk, R.H.A., van Eeden, F.J.M., and Cuppen, E. (2006). Genetic
Variation in the Zebrafish. Genome Research 16: 491-497 (IF = 14.4)
128) Smits, B.M.G., Mudde, J.B., van de Belt, J., Verheul, M., Olivier, J., Homberg, J., Guryev, V., Cools, A.R., Ellenbroek, B.A.,
Plasterk, R.H.A., and Cuppen, E. (2006). Generation of Gene Knockouts and Mutant Models in the Laboratory Rat by ENUdriven Target-Selected Mutagenesis. Pharmacogenetics and Genomics 16(3):159-169 (IF = 3.6)
129) Smits, B.M.G., Guryev, V., Zeegers, D., Wedekind, D., Hedrich, H.J., and Cuppen, E. (2005). Efficient Single Nucleotide
Polymorphism Discovery in Laboratory Rat Strains using Wild Rat-derived SNP Candidates. BMC Genomics 6:170 (IF = 4.4)
130) Smits, B.M.G., Peters, T.A., Mul, J.D., Croes, H.J., Fransen, J.A.M., Beynon, A.J., Guryev, V., Plasterk, R.H.A, and Cuppen,
E. (2005). Identification of a rat model for Usher syndrome type 1B by ENU mutagenesis-driven forward genetics. Genetics
70:1887-1896 (IF = 4.4)
131) Berezikov, E., Guryev, V., and Cuppen, E. (2005). CONREAL Web Server: Identification and Visualization of Conserved
Transcription Factor Binding Sites. Nucleic Acids Res 33:W447-W450 (IF = 8.3)
132) Cuppen, E. (2005). Haplotype-based genetics in mice and rats. Trends in Genetics 21:318-322 (IF = 9.8)
133) Guryev, V., Berezikov, E., and Cuppen, E. (2005). CASCAD: a database of annotated candidate single nucleotide
polymorphisms associated with expressed sequences. BMC Genomics 6(1):10 (IF = 4.4)
134) Berezikov, E., Guryev, V., Belt, J. v.d., Wienholds, E., Plasterk, R.H.A, and Cuppen, E. (2005). Phylogenetic Shadowing and
Computational Identification of Human microRNA Genes. Cell 120:21-24 (IF = 32)
135) van Berkel, W.P., Verheijen, M.H., Cuppen, E., Asahina, M., de Rooij, J., Jansen, G., Plasterk, R.H., Bos, J.L., Zwartkruis,
F.J. (2005) Requirement of the Caenorhabditis elegans RapGEF pxf-1 and rap-1 for Epithelial Integrity. Mol Biol Cell 16:106116 (IF = 4.6)
136) Guryev, V., Berezikov, E., Malik, R., Plasterk, R.H.A., and Cuppen, E. (2004) Single Nucleotide Polymorphisms associated
with rat expressed sequences. Genome Research 14:1438-1443 (IF = 14.4)
137) Smits, B.M.G., van Zutphen, B.F.M., Plasterk, R.H.A, and Cuppen, E. (2004) Genetic variation in coding regions between and
within commonly used inbred rat strains. Genome Research 14:1285-1290 (IF = 14.4)
138) Smits, B.M.G., D'Souza, U.M., Berezikov, E., Cuppen, E.*, Sluyter, F.* (2004) Identifying polymorphisms in the Rattus
norvegicus D3 dopamine receptor gene and regulatory region. Genes Brain Behav 3: 138-148 (IF = 3.6)
139) Smits, B.M.G., Mudde, J., Plasterk, R.H.A., and Cuppen E. (2004). Target-selected mutagenesis of the rat. Genomics
83:332-334 (IF = 3)
140) Berezikov, E., Guryev, V., Plasterk R.H.A., and Cuppen, E. (2004). CONREAL: Conserved Regulatory Elements Anchored
Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting. Genome Research
14:170-178 (IF = 14.4)
141) Wienholds, E., van Eeden, F., Kosters, M., Mudde, J., Plasterk, R.H.A., and Cuppen, E. (2003). Efficient target-selected
mutagenesis in zebrafish. Genome Research 13:2700-2707 (IF = 14.4)
142) Wienholds, E., Koudijs, M., van Eeden, F., Cuppen, E., and Plasterk, R.H.A. (2003). The microRNA-producing enzyme Dicer1
is essential for zebrafish development. Nature Genetics 35:217-128 (IF = 35.2)
143) Hurlstone, A. F. L., Haramis, A.-P. G., Wienholds, E., Begthel, H., Eeden, F. v., Cuppen, E., Zivkovic, D., Plasterk, R. H. A.,
and Clevers, H. (2003). The Wnt/beta-catenin pathway regulates cardiac valve formation. Nature 425:633-637 (IF = 38.6)

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Prof. dr. ir. E.P.J.G. Cuppen

144) Cuppen, E., Van der Linden, A.M., Jansen, G., and Plasterk, R.H.A. (2003). Proteins interacting with Caenorhabdites elegans
G-alpha subunits. Comp Funct Genomics 4:479-491 (IF = 0.9)
145) Van der Linden, A.M., Moorman, C., Cuppen, E., Korswagen, H.C., Plasterk, R.H.A. (2003). Hyperactivation of the G(12)mediated signaling pathway in Caenorhabditis elegans induces a developmental growth arrest via Protein Kinase C. Current
Biology 13:516-21 (IF = 9.5)
146) Berezikov, E., Plasterk, R.H.A., and Cuppen, E. (2002). GENOTRACE: cDNA-based local GENOme assembly from TRACE
archives. Bioinformatics 18:1396-7 (IF = 5.3)
147) Chan M.F., van Amerongen R., Nijjar T., Cuppen E., Jones P.A., Laird P.W. (2001). Reduced rates of gene loss, gene
silencing, and gene mutation in Dnmt1-deficient embryonic stem cells. Mol Cell Biol 21:7587-600 (IF = 5.4)
148) van der Linden, A.M., Simmer, F., Cuppen E., and Plasterk, R.H.A. (2001). The G protein beta subunit GPB-2 in
Caenorhabditis elegans regulates the Go(alpha)-Gq(alpha) signaling network through interactions with the RGS proteins
EGL-10 and EAT-16. Genetics 158:221-35 (IF = 4.4)
149) Cuppen, E., van Ham, M., Wansink, D.G., Leeuw, A. de, Wieringa, B. and Hendriks, W. (2000). The zyxin-related protein
TRIP6 interacts with PDZ motifs in the adaptor protein RIL and the protein tyrosine phosphatase PTP-BL. Eur J Cell Biol
79:283-93 (IF = 3.2)
150) Cuppen, E., Wijers, M., Schepens, J., Fransen, J., Wieringa, B. and Hendriks, W. (1999). A FERM domain governs apical
confinement of PTP-BL in epithelial cells. J Cell Sci 112:3299-308 (IF = 5.9)
151) Cuppen, E., Van Ham, M., Pepers, B., Wieringa, B. and Hendriks, W. (1999). Identification and molecular characterization of
BP75, a novel bromodomain-containing protein. FEBS Lett 459:291-8. (IF = 3.6)
152) Cuppen, E., Gerrits, H., Pepers, B., Wieringa, B. and Hendriks, W. (1998). PDZ motifs in PTP-BL and RIL bind to internal
protein segments in the LIM domain protein RIL. Mol Biol Cell 9:671-83 (IF = 4.6)
153) Cuppen, E., Nagata, S., Wieringa, B. and Hendriks, W. (1997). No evidence for involvement of mouse protein-tyrosine
phosphatase-BAS-like / Fas-associated phosphatase-1 in Fas-mediated apoptosis. J Biol Chem 272:30215-20 (IF = 4.7)
154) Schepens, J., Cuppen, E. and Hendriks, W. (1997). The neuronal nitric oxide synthase PDZ motif binds to -GDXV*
carboxyterminal sequences. FEBS Lett 409:53-6 (IF = 3.6)
*shared first/last authorship

Books, or contributions to books

-

Linsen SE, Cuppen E. (2012). Methods for small RNA preparation for digital gene expression profiling by next-generation
sequencing. Methods Mol Biol. 822:205-17.
Clark MD, Guryev V, Bruijn E, Nijman IJ, Tada M, Wilson C, Deloukas P, Postlethwait JH, Cuppen E, Stemple DL. (2011). Single
nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish. Methods Cell Biol. 2011;104:219-35.
Kettleborough RN, Bruijn E, Eeden F, Cuppen E, Stemple DL. (2011). High-throughput target-selected gene inactivation in
zebrafish. Methods Cell Biol. 104:121-7.
van Boxtel R, Cuppen E (2011). Generation of genetically modified rodents using random ENU mutagenesis. Methods Mol Biol.
2011;693:295-308
Cuppen E. (2010). DNA isolation from rat tail or ear. Cold Spring Harb Protocols 2010(5):pdb.prot5434.
van Boxtel R, Gould MN, Cuppen E*, Smits BM* (2009). ENU Mutagenesis to Generate Genetically Modified Rat Models. Methods
Mol Biol. 2010;597:151-67
de Bruijn E, Cuppen E*, and Feitsma H*. (2009). Highly efficient ENU Mutagenesis in Zebrafish. Methods Mol Biol. 546:3-12.
Smits BM, Haag JD, Gould MN, Cuppen E (2008) Rat Knockout and Mutant Models, In: Sourcebook of Models for Biomedical
Research, Editor: Conn MP, Humana Press, Totowa NJ, p171-178
Cuppen E (2007). Genotyping by Allel-Specific Amplification (KASPar). Cold Spring Harb Protoc. doi:10.1101/pdb.prot4841
Cuppen E (2007). Genotyping by Dideoxy resequencing. Cold Spring Harb Protoc. doi:10.1101/pdb.prot4842
Berezikov E, Guryev V, Cuppen E. (2007). Exploring Conservation of Transcription Factor Binding Sites with CONREAL. Methods
Mol Biol. 2007;395:437-48.

Patent (applications):
-

Weijzen, S., Schaapveld, R., Bourajjaj, M., van Haastert, R., Griffioen, A., van Beijnum, J., Cuppen, E., Berezikov, E., van
Puijenbroek, A., Gommans, W., Negar, B., (2011). Mir-190b for treating neo-angiogenesis. US application no 61/521,917 and
61/522,346
Weijzen, S., Schaapveld, R., Bourajjaj, M., van Haastert, R., Griffioen, A., van Beijnum, J., Cuppen, E., Berezikov, E., van
Puijenbroek, A., Gommans, W., van Noort, P., Negar, B., (2011). Mir-142 for treating neo-angiogenesis. US application no
61/521,931
Weijzen, S., Schaapveld, R., Bouraijaj, M., van Haastert, R., Griffioen, A., van Beijnum, J., Cuppen, E., Berezikov, E., van
Puijenbroek, A., Gommans, W. (2011). Mir for treating neo-angiogenesis. EPC:11150645.7-1212
van Boxtel, R. and Cuppen, E. (2007). Animals of the rattus genus wherein msh6 expression is functionally decreased and
methods for the generation of specific mutants there from. WO2009072882
Cuppen, E., Meijer, G., Berezikov, E., Diosdado, B., (2007). Small RNA molecules, precursors thereof, means and methods for
detecting them, and uses thereof in typing samples. WO2009008720
Berezikov, E., Cuppen, E., Plasterk, R., (2006). New nucleic acid molecules and collections thereof, their application and
identification. WO2007081204

Public software and databases developed in my lab

-

Tagbrowser (http://genetics.genomicscenter.nl/tagbrowser/), unpublished: Browser for mulit-level visualization of raw NGS data
LIMSTILL (http://limstill.niob.knaw.nl), unpublished: Laboratory Information Management System (LIMS) for the Identification of
Mutations and SNPs by Sequencing and TILling
CASCAD (http://cascad.niob.knaw.nl) (Guryev et al., 2004, Genome Res. 14:1438-1443; Guryev et al., 2005, BMC Genomics
6(1):10): Candidate SNP database for rat and zebrafish
CONREAL (http://conreal.niob.knaw.nl) (Berezikov et al., 2004, Genome Res. 14:170-178; Berezikov et al., 2005, Nucl. Acid Res.
33:W447-W450): Tool for the identification of conserved regulatory elements in promoter regions
GENOTRACE (http://genotrace.niob.knaw.nl) (Berezikov et al., 2002, Bioinformatics 18:1396-1397): Local genome assembly tool
utilizing raw trace data from whole genome sequencing projects

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Curriculum Vitae, March 2014

Prof. dr. ir. E.P.J.G. Cuppen

Grants
-

NWO Vici (2014-2019): Dissecting structural variation

KWF Stand up to cancer (2013-2017): Cancer organoid genomics
NWO Zwaartekracht (2013-2022): Cancer Genomics Netherlands
NGI Zenith (2012-2016): Genetic integrity of adult stem cells
Center for Genome Diagnostics (CGD), Netherlands Genomics Initiative (2011-2013): Next-generation sequencing in diagnostics
Center for Personalized Cancer Treatment (CPCT), KWF/Alpe dhuzes (2011)
NWO TOP-CW (2009 current): Rat genomics
EU FP7 EURATRANS (2010-current): Rat systems genetics
EU FP7 ZFHEALTH (2010-current): Zebrafish genetics
NBIC (NGI) BioRange-2 and BioAssist (2010 2013): Next-generation sequencing data analysis
CGC-2 (NGI) (2009-2013): Cancer genetics
Leducq transatlantic network (2009): miRNA in heart
SMARTMIX (EZ and OCW) consortium (2008 current): Zebrafish knockout models
NCSB (NGI) (2008 2013): Cancer systems genetics
NBIC (NGI) Biorange-1 (2006-2009): Bioinformatics analysis for mutation analysis
EU FP6 ZFMODELS (2004-2009): Zebrafish knockout models
NWO groot (2005): High-throughput mutation discovery
IOP Genomics (2002-2007): Rat reverse genetics

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