• Netherlands

  • Netherlands

Research Output

Article

DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus

Kaaij, L. T., van de Wetering, M., Fang, F., Decato, B., Molaro, A., van de Werken, H. J., van Es, J. H., Schuijers, J., de Wit, E., de Laat, W., Hannon, G. J., Clevers, H. C., Smith, A. D. & Ketting, R. F., 2013, In : Genome Biology. 14, 5, p. 50

Research output: Contribution to journal/periodicalArticleScientificpeer-review

DNA Methylation Landscapes of Human Fetal Development

Slieker, R. C., Roost, M. S., van Iperen, L., Suchiman, H. E. D., Tobi, E. W., Carlotti, F., de Koning, E. J. P., Slagboom, P. E., Heijmans, B. T. & Chuva de Sousa Lopes, S. M., Oct 2015, In : PLoS Genetics. 11, 10, p. e1005583

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dominant missense mutations in ABCC9 cause Cantu syndrome

Harakalova, M., van Harssel, J. J., Terhal, P. A., van Lieshout, S., Duran, K., Renkens, I., Amor, D. J., Wilson, L. C., Kirk, E. P., Turner, C. L., Shears, D., Garcia-Minaur, S., Lees, M. M., Ross, A., Venselaar, H., Vriend, G., Takanari, H., Rook, M. B., van der Heyden, M. A., Asselbergs, F. W. & 11 others, Breur, H. M., Swinkels, M. E., Scurr, I. J., Smithson, S. F., Knoers, N. V., van der Smagt, J. J., Nijman, I. J., Kloosterman, W. P., van Haelst, M. M., van Haaften, G. & Cuppen, E., 2012, In : Nature Genetics. 44, 7, p. 793-796

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Dominant-negative ALK2 allele associates with congenital heart defects.

Smith, K., 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. M., ten Dijke, P. & Bakkers, J., 2009, In : Circulation. 119, 24, p. 3062-3069

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Down-regulation of Rap1 activity is involved in ephrinB1-induced cell contraction.

Riedl, J. A., Brandt, D. T., Batlle, E., Price, L. S., Clevers, J. C. & Bos, J. L., 2005, In : The Biochemical journal. 389, p. 465-469

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Drosophila patterning is established by differential association of mRNAs with P bodies

Weil, T. T., Parton, R. M., Herpers, B., Soetaert, J., Veenendaal, T., Xanthakis, D., Dobbie, I. M., Halstead, J. M., Hayashi, R., Rabouille, C. & Davis, I., 2012, In : Nature Cell Biology. 14, 12, p. 1305-1315

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Drosophila RpS3a, a novel Minute gene situated between the segment polarity genescubitus interruptus and dTCF

Beest, M. V., Mortin, M. & Clevers, J. C., 1998, In : Nucleic Acids Research. 26, p. 4471-4475

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Drosophila Tcf and Groucho interact to repress Wingless signalling activity

Cavallo, R. A., Cox, R. T., Moline, M. M., Roose, J., Polevoy, G. A., Clevers, J. C., Peifer, M. & Bejsovec, A., 1998, In : Nature. 395, p. 604-608

Research output: Contribution to journal/periodicalArticleScientificpeer-review

dTcf antagonises Wingless signalling during the development and patterning of the wing in Drosophila

Lawrence, N., Dearden, P., Hartley, D., Roose, J., Clevers, J. C. & Arias, A. M., 2000, In : International Journal of Developmental Biology. 44, p. 749-756

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation

Edwards, C. J., Ginja, C., Kantanen, J., Perez-Pardal, L., Tresset, A., Stock, F., Gama, L. T., Penedo, M. C., Bradley, D. G., Lenstra, J. A. & Nijman, I. J., 2011, In : PLoS One. 6, 1, p. 15922

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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Dual regulatory switch through interactions of Tcf7l2/Tcf4 with stage-specific partners propels oligodendroglial maturation

Zhao, C., Deng, Y., Liu, L., Yu, K., Zhang, L., Wang, H., He, X., Wang, J., Lu, C., Wu, L. N., Weng, Q., Mao, M., Li, J., van Es, J. H., Xin, M., Parry, L., Goldman, S. A., Clevers, H. & Lu, Q. R., 2016, In : Nature Communications. 7, p. 10883

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis

Sacristan, C., Ahmad, M. U. D., Keller, J., Fermie, J., Groenewold, V., Tromer, E., Fish, A., Melero, R., Carazo, J. M., Klumperman, J., Musacchio, A., Perrakis, A. & Kops, G. J., Jul 2018, In : Nature Cell Biology. 20, 7, p. 800-810 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Marks, H., Kerstens, H. H. D., Barakat, T. S., Splinter, E., Dirks, R. A. M., van Mierlo, G., Joshi, O., Wang, S-Y., Babak, T., Albers, C. A., Kalkan, T., Smith, A., Jouneau, A., de Laat, W., Gribnau, J. & Stunnenberg, H. G., 2015, In : Genome Biology. 16, 1, p. 149

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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Dynamics of Lgr6(+) Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis

Füllgrabe, A., Joost, S., Are, A., Jacob, T., Sivan, U., Haegebarth, A., Linnarsson, S., Simons, B. D., Clevers, H., Toftgård, R. & Kasper, M., 21 Oct 2015, In : Stem Cell Reports.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

Semrau, S., Goldmann, J. E., Soumillon, M., Mikkelsen, T. S., Jaenisch, R. & van Oudenaarden, A., 23 Oct 2017, In : Nature Communications. 8, 1, p. 1096

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dynamics of Translation of Single mRNA Molecules In Vivo

Yan, X., Hoek, T. A., Vale, R. D. & Tanenbaum, M. E., 05 May 2016, In : Cell. 165, 4, p. 976-89 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dysfunctional AMPK activity, signalling through mTOR and survival in response to energetic stress in LKB1-deficient lung cancer.

Carretero, J., Medina, P. P., Blanco, R., Smit, L., Tang, M., Roncador, G., Maestre, L., Conde, E., Lopez-Rios, F., Clevers, J. C. & Sanchez-Cespedes, M., 2006, In : Oncogene advance online publication.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

E2F7 and E2F8 promote angiogenesis through transcriptional activation of VEGFA in cooperation with HIF1

Weijts, B. G., Bakker, W. J., Cornelissen, P. W., Liang, K. H., Schaftenaar, F. H., Westendorp, B., de Wolf, C. A., Paciejewska, M., Scheele, C. L., Kent, L., Leone, G., Schulte-Merker, S. & de Bruin, A., 2012, In : EMBO Journal. 31, 19, p. 3871-3884

Research output: Contribution to journal/periodicalArticleScientificpeer-review

E2F7 represses a network of oscillating cell cycle genes to control S-phase progression

Westendorp, B., Mokry, M., Groot Koerkamp, M. J., Holstege, F. C., Cuppen, E. & de Bruin, A., 2012, In : Nucleic Acids Research. 40, 8, p. 3511-3523

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Ectopic activation of lymphoid high mobility group-box transcription factor TCF-1 and overexpression in colorectal cancer cells

Mayer, K., Hieronymus, T., Castrop, J., Clevers, J. C. & Ballhausen, W. G., 1997, In : International Journal of Cancer. 72, p. 625-630

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Ectopic Activation of the Spindle Assembly Checkpoint Signaling Cascade Reveals Its Biochemical Design

Chen, C., Whitney, I. P., Banerjee, A., Sacristan, C., Sekhri, P., Kern, D. M., Fontan, A., Kops, G. J. P. L., Tyson, J. J., Cheeseman, I. M. & Joglekar, A. P., 07 Jan 2019, In : Current Biology. 29, 1, p. 104-119.e10

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Ectopic Wnt signal determines the eyeless phenotype of zebrafish masterblind mutant

Water, S. V. D., Wetering, M. V. D., Joore, J., Esseling, J., Bink, R., Clevers, J. C. & Zivkovic, D., 2001, In : Development. 128, p. 3877-3888

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Editorial: Golgi Pathology in Neurodegenerative Diseases

Rabouille, C. & Haase, G., 2016, In : Frontiers in Neuroscience. 9, p. 489

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Editorial overview: Cell organelles

Rabouille, C. & Antonny, B., Aug 2017, In : Current Opinion in Immunology. 47, p. iv-vi

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Effective CRISPR/Cas9-based nucleotide editing in zebrafish to model human genetic cardiovascular disorders

Tessadori, F., Roessler, H. I., Savelberg, S. M. C., Chocron, S., Kamel, S. M., Duran, K. J., van Haelst, M. M., van Haaften, G. & Bakkers, J., 18 Oct 2018, In : Disease Models & Mechanisms. 11, 10

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Effective Therapeutic Intervention and Comprehensive Genetic Analysis of mTOR Signaling in PEComa: A Case Report

Weeber, F., Koudijs, M. J., Hoogstraat, M., Besselink, N. J. M., VAN Lieshout, S., Nijman, I. J., Cuppen, E., Offerhaus, G. J. & Voest, E. E., Jun 2015, In : Nature Biotechnology. 35, 6, p. 3399-403 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Effect of vertical sleeve gastrectomy in melanocortin receptor 4-deficient rats

Mul, J. D., Begg, D. P., Alsters, S. I., van Haaften, G., Duran, K. J., D'Alessio, D. A., le Roux, C. W., Woods, S. C., Sandoval, D. A., Blakemore, A. I., Cuppen, E., van Haelst, M. M. & Seeley, R. J., 2012, In : American Journal of Physiology - Endocrinology and Metabolism. 303, 1, p. 103-110

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing

Stassen, J. H., Seidl, M. F., Vergeer, P. W., Nijman, I. J., Snel, B., Cuppen, E. & van den Ackerveken, G., 2012, In : Molecular Plant Pathology. 13, 7, p. 719-731

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Efficient cryopreservation of human pluripotent stem cells by surface-based vitrification

Neubauer, J. C., Beier, A. F., Geijsen, N. & Zimmermann, H., 2015, In : Methods in Molecular Biology. 1257, p. 321-8 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles

Mokry, M., Hatzis, P., de Bruijn, E., Koster, J., Versteeg, R., Schuijers, J., van de Wetering, M. L., Guryev, V., Clevers, H. & Cuppen, E., 2010, In : PLoS One. 5, 11, p. 15092

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Efficient intracellular delivery of native proteins

D'Astolfo, D. S., Pagliero, R. J., Pras, A., Karthaus, W. R., Clevers, H., Prasad, V., Lebbink, R. J., Rehmann, H. & Geijsen, N., 23 Apr 2015, In : Cell. 161, 3, p. 674-90 17 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates

Smits, B. M., Guryev, V., Zeegers, D., Wedekind, D., Hedrich, H. J. & Cuppen, E., 2005, In : BMC Genomics. 6, p. 170

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Efficient target-selected mutagenesis in zebrafish

Wienholds, E., van Eeden, F., Kosters, M., Mudde, J. B., Plasterk, R. & Cuppen, E., 2003, In : Genome Research. 13, 12, p. 2700-2707

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Eilandjestransplantatie bij diabetes: hoop voor de toekomst?

de Koning, E., 2012, In : Reed Business. p. 10-13

Research output: Contribution to journal/periodicalArticlePopularizing

Embryonic hematopoiesis under microscopic observation

Klaus, A. & Robin, C., 15 Aug 2017, In : Developmental Biology. 428, 2, p. 318-327 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Embryonic Microglia Derive from Primitive Macrophages and Are Replaced by cmyb-Dependent Definitive Microglia in Zebrafish

Ferrero, G., Mahony, C. B., Dupuis, E., Yvernogeau, L., Di Ruggiero, E., Miserocchi, M., Caron, M., Robin, C., Traver, D., Bertrand, J. Y. & Wittamer, V., 03 Jul 2018, In : Cell Reports. 24, 1, p. 130-141 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Embryonic template-based generation and purification of pluripotent stem cell-derived cardiomyocytes for heart repair

Dierickx, P., Doevendans, P. A., Geijsen, N. & van Laake, L. W., 2012, In : Journal of Cardiovascular Translational Research. 5, 5, p. 566-580

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

Deschamps, J. & Duboule, D., 15 Jul 2017, In : Genes and Development. 31, 14, p. 1406-1416 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Endoglin-mediated vascular remodeling: mechanisms underlying hereditary hemorrhagic telangiectasia.

Lebrin, F. & Mummery, C. L., 2008, In : Trends in Cardiovascular Medicine. 18, 1, p. 25-32

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Endosteal and Perivascular Subniches in a 3D Bone Marrow Model for Multiple Myeloma

Braham, M. V. J., Ahlfeld, T., Akkineni, A. R., Minnema, M. C., Dhert, W. J. A., Öner, F. C., Robin, C., Lode, A., Gelinsky, M. & Alblas, J., May 2018, In : Tissue Engineering - Part C: Methods. 24, 5, p. 300-312 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Endothelial apoptosis in pulmonary hypertension is controlled by a microRNA/programmed cell death 4/caspase-3 axis

White, K., Dempsie, Y., Caruso, P., Wallace, E., McDonald, R. A., Stevens, H., Hatley, M. E., Van Rooij, E., Morrell, N. W., MacLean, M. R. & Baker, A. H., Jul 2014, In : Hypertension. 64, 1, p. 185-94 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Endothelial cells dynamically compete for the tip cell position during angiogenic sprouting

Jakobsson, L., Franco, C. A., Bentley, K., Collins, R. T., Ponsioen, B., Aspalter, I. M., Rosewell, I., Busse, M., Thurston, G., Medvinsky, A., Schulte-Merker, S. & Gerhardt, H., 2010, In : Nature Cell Biology. 12, 10, p. 943-953

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Endothelial cell-specific FGD5 involvement in vascular pruning defines neovessel fate in mice

Cheng, C., Haasdijk, R., Tempel, D., van de Kamp, E. H., Herpers, R., Bos, F., den Dekker, W. K., Blonden, L. A., de Jong, R., Burgisser, P. E., Chrifi, I., Biessen, E. A., Dimmeler, S., Schulte-Merker, S. & Duckers, H. J., 2012, In : Circulation. 125, 25, p. 3142-3158

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enhanced cardiomyogenesis of human embryonic stem cells by a small molecular inhibitor of p38 MAPK.

Graichen, R., Xu, X., Braam, S. R., Balakrishnan, T., Norfiza, S., Sieh, S., Soo, S. Y., Tham, S. C., Mummery, C. L., Colman, A., Zweigerdt, R. & Davidson, B. P., 2008, In : Differentiation. 76, 4, p. 357-370

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enhancer hubs and loop collisions identified from single-allele topologies

Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J. H. I., Jalink, K., Teunissen, H., Renkens, I. J., Kloosterman, W. P., Rowland, B. D., de Wit, E., de Ridder, J. & de Laat, W., Aug 2018, In : Nature Genetics. 50, 8, p. 1151-1160 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

Dreijerink, K. M. A., Groner, A. C., Vos, E. S. M., Font-Tello, A., Gu, L., Chi, D., Reyes, J., Cook, J., Lim, E., Lin, C. Y., de Laat, W., Rao, P. K., Long, H. W. & Brown, M., 07 Mar 2017, In : Cell Reports. 18, 10, p. 2359-2372 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Enhancers reside in a unique epigenetic environment during early zebrafish development

Kaaij, L. J. T., Mokry, M., Zhou, M., Musheev, M., Geeven, G., Melquiond, A. S. J., de Jesus Domingues, A. M., de Laat, W., Niehrs, C., Smith, A. D. & Ketting, R. F., 2016, In : Genome Biology. 17, 1, p. 146

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

van Es, J. H., Wiebrands, K., López-Iglesias, C., van de Wetering, M., Zeinstra, L., van den Born, M., Korving, J., Sasaki, N., Peters, P. J., van Oudenaarden, A. & Clevers, H., 16 Dec 2019, In : Proceedings of the National Academy of Sciences of the United States of America.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enteroendocrine cells switch hormone expression along the crypt-to-villus BMP signalling gradient

Beumer, J., Artegiani, B., Post, Y., Reimann, F., Gribble, F., Nguyen, T. N., Zeng, H., Van den Born, M., Van Es, J. H. & Clevers, H., Aug 2018, In : Nature Cell Biology. 20, 8, p. 909-916 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enterovirus 71 infection of human airway organoids reveals VP1-145 as a viral infectivity determinant

van der Sanden, S. M. G., Sachs, N., Koekkoek, S. M., Koen, G., Pajkrt, D., Clevers, H. & Wolthers, K. C., 09 May 2018, In : Emerging Microbes & Infections . 7, 1, p. 84

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access