Publications

Cuppen group

Search for publications of Edwin Cuppen in PubMed

Book chapters

Articles
<2002 - 2002 - 2003 - 2004 - 2005 - 2006 - 2007 - 2008 - 2009 - 2010

2011
116. Westendorp B, Mokry M, Groot Koerkamp MJA, Holstege FCP, Cuppen E, de Bruin A (2011). E2F7 represses a network of oscillatin cell cycle genes to conrol S-phase progression. Nucl. Acid Res., in press

115. 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, in press

114. 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, in press

113. 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 (2011). Primary colorectal cancers and their subsequent hepatic metastases are genetically different: implicantions for selection of patients for targeted treatment. Clin Cancer Res, in press

112. Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E (2011). Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. Nucleic Acids Res, in press

111. Koudijs MJ, Klijn C, van der Weyden L, Kool J, Ten Hoeve J, Sie D, Prasetyanti PR, Schut E, Kas S, Whipp T, Cuppen E, Wessels L, Adams DJ, Jonkers J. (2011). High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors. Genome Res. 21:2181-9

110. 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 Biol. 12:R103

109. 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.

108. Harakalova M, Mokry M, Hrdlickova B, Renkens I, Duran K, van Roekel H, Lansu N, van Roosmaalen M, de Bruijn E, Nijman IJ, Kloosterman WP, Cuppen E. (2011). Multiplexed array-based and in solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing. Nat. Protocols, 6:1870-86

107. van Boxtel R, Kuiper RV, Toonen PW, van Heesch S, Hermsen R, de Bruin A, Cuppen E. (2011) Homozyggous and heterozygous P53 knockout rats develop metastasizing sarcomis with high frequency. Am. J. Pathol.,179:1616-22

106. Mul JD, NadraK, Jagalur NB, Nijman IJ, Toonen PW, Medard J, Gres S, de Bruijn A, Han G, Brouwers JF, Carman GM, Saulnier-Blache J, Meijer D, Chrast R, Cuppen E. (2011). A hypomorphic mutation in Lpin1 induces progressively improving neuropathy and lipodystropy in the rat. J Biol Chem. 286:26781-93

105. 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

104. 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:e19600

103. Wansleeben C, van Gurp L, Feitsma H, Kroon C, Rieter E, Verberne M, Guryev V, Cuppen E, Meijlink F. (2011). An ENU-Mutagenesis Screen in the Mouse: Identification of Novel Developmental Gene Functions.PLoS One 6:e19357

102. Mul JD, van Boxtel R, Bergen DJ, Brans MA, Brakkee JH, Toonen PW, Garner KM, Adan RA, Cuppen E. (2011). Melanocortin Receptor 4 Deficiency Affects Body Weight Regulation, Grooming Behavior, and Substrate Preference in the Rat. Obesity, in press

101. 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:e15669

100. 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. 20:1916-24

99. 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 Res. 4:271-80

98. 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 patent with Down's syndrome and a congenital heart defect. Eur J Hum Genet 19:389-93

97. 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 27:41-7

96. Edwards CJ, Ginja C, Kantanen J, Perez-Pardal L, Tresset A, Stock F; European Cattle Genetic Diversity Consortium, Gama LT, Penedo MC, Bradley DG, Lenstra JA, and Nijman, IJ (2011). Dual origins of dairy cattle frarming-evidence from a comprehensive survey of European Y-chromosomal variation. PLoS One 6:e15922

95. 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

2010

94. 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. 2010 Nov 30;5(11):e15092

93. Wansleeben C, Feitsma H, Tertoolen L, Kroon C, Guryev V, Cuppen E, and Meijlink F (2010). A novel mutant allele of Ncx1: a single amino acid substitution leads to cardiac dysfunction. Int J Dev Biol 54:1465-71

92. Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E. (2010). Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nature Methods 7:913-5

91. 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

90. van Boxtel R, Cuppen E. (2010). Rat traps: filling the toolbox for manipulating the rat genome. Genome Biol. 11:217

89 .  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. 8:97-108

88. van Boxtel R, Vroling B, Toonen P, Nijman IJ, van Roekel H, Verheul M, Baakman C, Guryev V, Vriend G, Cuppen E. (2010). Systematic generation of in vivo G protein-coupled receptor mutants in the rat. Pharmacogenomics J. 11:326-36

87. 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

86. 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. 7:2424-34

85. 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 Res. 20:791-803

84. Linsen SE, de Wit E, de Bruijn E, Cuppen E. (2010). Small RNA expression and strain specificity in the rat. BMC Genomics 11:249.

83. 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. 137:1067-73.

82. Johannes F, Wardenaar R, Colomé-Tatché 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.

81. 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:e116

80. 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

79. 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. 67:224-30

78. 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:E477-88

2009

77. de Wit E, Linsen SE, Cuppen E, Berezikov E. (2009). Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res., 19:2064-2074.

76. Pereira F, Queirós S, Gusmão 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.

75 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. Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods 6:474-476.

74. 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.

73. 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

72. 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.

71. 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.

70. 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.

69. Homberg, J, la Fleur, SE, and Cuppen, E. (2010). Serotonin transporter deficiency increases abdobminal fat in female, but not male rats. Obesity, 18:137-45

68. 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.

67. 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.

2008

66. 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.

65. Linsen, S.E.V., Tops, B.B.J., and Cuppen, E. (2008). miRNA's: small changes, widespread effects. Cell Research, 18:1157-9

64. Feitsma, H., Akay, A., and Cuppen, E. (2008). Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos. Nucl. Acids Res. 36:4047-4056.

63. 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.

62. 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

61. 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.

60. 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.

59. 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.

58. 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

57. 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

56. 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.

55. 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.

54. Homberg, J., van den Bos, R., den Heijer, E., Suer, R., and Cuppen, E. (2008). Serotonin transporter dosage modulates long-term decision-making in rat and human. Neuropharmacology, 55: 80-84.

53. 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.

52. 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

51. 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.

50. 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.

49. Feitsma, H. and Cuppen, E. (2008). Zebrafish as a cancer model. Molecular Cancer Res., 6:685-694

48. 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

47. 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

46. 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.

2007

45. 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., 26:5083-5092

44. Berezikov, E., Chung, W.J., Willis, J., Cuppen, E., and Lai, E.C. (2007). Mammalian mirtron genes. Mol. Cell 28:328-336

43. 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

42. 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, 195:175-182.

41. 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.

40. 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

39. 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

2006

38. 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

37. 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

36. 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

35. 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. Nucl. Acid Res., 34: e117.

34. 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, 16:1289-1298.

33. 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.

32. Berezikov, E., Cuppen, E., and Plasterk, R. (2006). Approaches to microRNA discovery. Nature Genet. 38:, S2-S7.

31. 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. Nucl. Acid Res., 34:2558-2569.

30. Smits, B.M.G. and Cuppen, E. (2006). Rat Genetics: the Next Episode. Trends in Genetics, 22:232-40.

29. Smits, B.M.G. and Cuppen, E. (2006). Rats go genomic. Genome Biology, 7:306

28. 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.

27. 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 ENU-driven Target-Selected Mutagenesis. Pharmacogenetics and Genomics, 16(3):159-169.

2005

26. 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.

25. 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
[Supplemental files and movies]

24. Berezikov, E., Guryev, V., and Cuppen, E. (2005). CONREAL Web Server: Identification and Visualization of Conserved Transcription Factor Binding Sites. Nucl. Acid Res., 33:W447-W450.

23. Cuppen, E. (2005). Haplotype-based genetics in mice and rats. Trends Genet., 21:318-322.

22. 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

21. 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

20. 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., 16:106-116

2004

19. 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.

18. 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

17. 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.

16. Smits, B.M.G., Mudde, J., Plasterk, R.H.A., and Cuppen E. (2004). Target-selected mutagenesis of the rat. Genomics, 83:332-334.

15. 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.

2003

14. 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.

13. 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.

12. 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.

11. 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.

10. 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. Curr Biol., 13:516-21 .

2002

9. Berezikov, E., Plasterk, R.H.A., and Cuppen, E. (2002). GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics, 18:1396-7.

before 2002

8. 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.

7. 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.

6. 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.

5. 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.

4. 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.

3. 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.

2. 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.

1. 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.


Book Chapters

11.Kettleborough RN, Bruijn E, Eeden F, Cuppen E, Stemple DL (2011). High-throughput target-selected gene inactivation in zebrafish. Methods Cell Biol. 2011;104:121-7.

10. 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. 104:219-35.

9. 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.

8.van Boxtel R, Cuppen E (2011). Generation of genetically modified rodents using random ENU mutagenesis. Methods Mol Biol. 2011;693:295-308

7. van Boxtel R, Gould MN, Cuppen E, Smits BM (2010). ENU Mutagenesis to Generate Genetically Modified Rat Models. Methods Mol Biol. 597:151-67.

6. Cuppen E. (2010). DNA isolation from rat tail or ear. Cold Spring Harb Protoc. doi:10.1101/pdb.prot5434.

5. de Bruijn E, Cuppen E, and Feitsma H. (2009). Highly efficient ENU Mutagenesis in Zebrafish. Methods Mol Biol. 546:3-12.

4. 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

3. Cuppen E (2007). Genotyping by Allel-Specific Amplification (KASPar). Cold Spring Harb Protoc. doi:10.1101/pdb.prot4841

2. Cuppen E (2007). Genotyping by Dideoxy resequencing. Cold Spring Harb Protoc. doi:10.1101/pdb.prot4842

1. Berezikov, E., Guryev, V., Cuppen, E. (2007). Exploring Conservation of Transcription Factor Binding Sites with CONREAL. Methods Mol Biol. 395:437-448.

Patents



About the group leader
About the research