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Research Output

Article

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Austenaa, L. M. I., Barozzi, I., Simonatto, M., Masella, S., Della Chiara, G., Ghisletti, S., Curina, A., de Wit, E., Bouwman, B. A. M., de Pretis, S., Piccolo, V., Termanini, A., Prosperini, E., Pelizzola, M., de Laat, W. & Natoli, G., 05 Nov 2015, In : Molecular Cell. 60, 3, p. 460-74 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast

van Werven, F. J., Neuert, G., Hendrick, N., Lardenois, A., Buratowski, S., van Oudenaarden, A., Primig, M. & Amon, A., 2012, In : Cell. 150, 6, p. 1170-1181

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transcriptomic and Epigenomic Profiling of Histone Deacetylase Inhibitor Treatment Reveals Distinct Gene Regulation Profiles Leading to Impaired Neutrophil Development

Govers, A. M. A. P., Wiggers, C. R. M., van Boxtel, R., Mokry, M., Nieuwenhuis, E. E. S., Creyghton, M. P., Bartels, M. & Coffer, P. J., Aug 2019, In : HemaSphere. 3, 4, p. e270

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2

Simmini, S., Bialecka, M., Huch, M., Kester, L., van de Wetering, M., Sato, T., Beck, F., van Oudenaarden, A., Clevers, H. & Deschamps, J., 2014, In : Nature Communications. 5, p. 5728

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transient but not genetic loss of miR-451 is protective in the development of pulmonary arterial hypertension

Grant, J. S., Morecroft, I., Dempsie, Y., van Rooij, E., MacLean, M. R. & Baker, A. H., Dec 2013, In : Pulmonary Circulation. 3, 4, p. 840-50 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Translational applications of adult stem cell-derived organoids

Drost, J. & Clevers, H., 15 Mar 2017, In : Development (Cambridge). 144, 6, p. 968-975 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Translational regulation shapes the molecular landscape of complex disease phenotypes

Schafer, S., Adami, E., Heinig, M., Rodrigues, K. E. C., Kreuchwig, F., Silhavy, J., van Heesch, S., Simaite, D., Rajewsky, N., Cuppen, E., Pravenec, M., Vingron, M., Cook, S. A. & Hubner, N., 2015, In : Nature Communications. 6, p. 7200

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Translation of branched-chain aminotransferase-1 transcripts is impaired in cells haploinsufficient for ribosomal protein genes

Pereboom, T. C., Bondt, A., Pallaki, P., Klasson, T. D., Goos, Y. J., Essers, P. B., Groot Koerkamp, M. J. A., Gazda, H. T., Holstege, F. C. P., Costa, L. D. & MacInnes, A. W., May 2014, In : Experimental Hematology. 42, 5, p. 394-403.e4

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transmembrane protein 2 (Tmem2) is required to regionally restrict atrioventricular canal boundary and endocardial cushion development

Smith, K., Lagendijk, A. K., Courtney, A. D., Chen, H., Paterson, S., Hogan, B. M., Wicking, C. & Bakkers, J., 2011, In : Development. 138, 19, p. 4193-4198

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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Transplantatie van gekweekte darmpjes moet baby redden

Clevers, H., 2010, In : Trouw.

Research output: Contribution to journal/periodicalArticlePopularizing

Tropism, replication competence, and innate immune responses of influenza virus: an analysis of human airway organoids and ex-vivo bronchus cultures

Hui, K. P. Y., Ching, R. H. H., Chan, S. K. H., Nicholls, J. M., Sachs, N., Clevers, H., Peiris, J. S. M. & Chan, M. C. W., Nov 2018, In : The Lancet Respiratory Medicine. 6, 11, p. 846-854 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Troy/TNFRSF19 marks epithelial progenitor cells during mouse kidney development that continue to contribute to turnover in adult kidney

Schutgens, F., Rookmaaker, M. B., Blokzijl, F., van Boxtel, R., Vries, R. R. G., Cuppen, E., Verhaar, M. C. & Clevers, H., 26 Dec 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 52, p. E11190-E11198

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy

Basak, O., Krieger, T. G., Muraro, M. J., Wiebrands, K., Stange, D. E., Frias-Aldeguer, J., Rivron, N. C., van de Wetering, M., van Es, J. H., van Oudenaarden, A., Simons, B. D. & Clevers, H., 23 Jan 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 4, p. E610-E619

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Trpv5/6 is vital for epithelial calcium uptake and bone formation

Vanoevelen, J., Janssens, A. C., Huitema, L. F., Hammond, C. J., Metz, J. R., Flik, G., Voets, T. & Schulte-Merker, S., 2011, In : FASEB Journal. 25, 9, p. 3197-3207

Research output: Contribution to journal/periodicalArticleScientificpeer-review

TTC7A mutations disrupt intestinal epithelial apicobasal polarity

Bigorgne, A. E., Farin, H. F., Lemoine, R., Mahlaoui, N., Lambert, N., Gil, M., Schulz, A., Philippet, P., Schlesser, P., Abrahamsen, T. G., Oymar, K., Davies, E. G., Ellingsen, C. L., Leteurtre, E., Moreau-Massart, B., Berrebi, D., Bole-Feysot, C., Nischke, P., Brousse, N., Fischer, A. & 2 others, Clevers, H. & de Saint Basile, G., Jan 2014, In : Journal of Clinical Investigation. 124, 1, p. 328-37 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tubuloids derived from human adult kidney and urine for personalized disease modeling

Schutgens, F., Rookmaaker, M. B., Margaritis, T., Rios, A., Ammerlaan, C., Jansen, J., Gijzen, L., Vormann, M., Vonk, A., Viveen, M., Yengej, F. Y., Derakhshan, S., de Winter-de Groot, K. M., Artegiani, B., van Boxtel, R., Cuppen, E., Hendrickx, A. P. A., van den Heuvel-Eibrink, M. M., Heitzer, E., Lanz, H. & 7 others, Beekman, J., Murk, J-L., Masereeuw, R., Holstege, F., Drost, J., Verhaar, M. C. & Clevers, H., Mar 2019, In : Nature Biotechnology. 37, 3, p. 303-313 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tumor environment: a potent driving force in colorectal cancer?

Barker, N. & Clevers, J. C., 2001, In : Trends in Molecular Medicine. 7, p. 535-537

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tumor Suppressors in Zebrafish: From TP53 to PTEN and Beyond

den Hertog, J., 2016, In : Advances in Experimental Medicine and Biology. 916, p. 87-101 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors

Koo, B. K., Spit, M., Jordens, I., Low, T. Y., Stange, D. E., van de Wetering, M., van Es, J. H., Mohammed, S., Heck, A. J. R., Maurice, M. M. & Clevers, H., 2012, In : Nature. 488, 7413, p. 665-669

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Turning basic science discoveries into successful commercial opportunities

van Rooij, E., 01 Oct 2019, In : Cardiovascular Research. 115, 12, p. e127-e129

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Twists and turns

Noël, E. S. & Bakkers, J., 28 Nov 2017, In : eLife. 6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Two members of the Tcf family implicated in Wnt/beta-catenin signaling during embryogenesis in the mouse

Korinek, V., Barker, N., Willert, K., Molenaar, M., Roose, J., Wagenaar, G., Markman, M., Lamers, W., Destree, O. & Clevers, J. C., 1998, In : Molecular and Cellular Biology. 18, p. 1248-1256

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Two novel type II receptors mediate BMP signalling and are required to establish left-right asymmetry in zebrafish.

Monteiro, R., van Dinther, M., Bakkers, J., Wilkinson, R., Patient, R., ten Dijke, P. & Mummery, C. L., 2008, In : Developmental Biology. 315, 1, p. 55-71

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Two paths to let the replisome go

D'Angiolella, V. & Guardavaccaro, D., Jul 2017, In : Cell Death and Differentiation. 24, 7, p. 1140-1141 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Two populations of endochondral osteoblasts with differential sensitivity to Hedgehog signalling.

Hammond, C. L. & Schulte-Merker, S., 2009, In : Development. 136, 23, p. 3991-4000

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Ubiad1 is an antioxidant enzyme that regulates eNOS activity by CoQ10 synthesis

Mugoni, V., Postel, R., Catanzaro, V., De Luca, E., Turco, E., Digilio, G., Silengo, L., Murphy, M. P., Medana, C., Stainier, D. Y., Bakkers, J. & Santoro, M. M., 2013, In : Cell. 152, 3, p. 504-518

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

UDP-glucose dehydrogenase polymorphisms from patients with congenital heart valve defects disrupt enzyme stability and quaternary assembly

Hyde, A. S., Farmer, E. L., Easley, K. E., van Lammeren, K., Christoffels, V. M., Barycki, J. J., Bakkers, J. & Simpson, M. A., 2012, In : Journal of Biological Chemistry. 287, 39, p. 32708-32716

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unbalancing the phosphatidylinositol-4,5-bisphosphate-cofilin interaction impairs cell steering.

Leyman, S., Sidani, M., Ritsma, L., Waterschoot, D., Eddy, R., Dewitte, D., Debeir, O., Decaestecker, C., Vandekerckhove, J., van Rheenen, J., Ampe, C., Condeelis, J. & Van Troys, M., 2009, In : Molecular Biology of the Cell. 20, 21, p. 4509-4523

Research output: Contribution to journal/periodicalArticleScientificpeer-review

UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit

Schneider, J., Skelton, R. L., Von Stetina, S. E., Middelkoop, T. C., van Oudenaarden, A., Korswagen, H. C. & Miller, D. M., 2012, In : Development. 139, 12, p. 2234-2245

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unconventional protein secretion: Diversity and consensus

Nickel, W. & Rabouille, C., Nov 2018, In : Seminars in Cell & Developmental Biology. 83, p. 1-2 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unconventional secretion: a stress on GRASP

Giuliani, F., Grieve, A. & Rabouille, C., 2011, In : Current Opinion in Cell Biology. 23, 4, p. 498-504

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Uncoupling of S phase and mitosis in cardiomyocytes and hepatocytes lacking the winged-helix transcription factor Trident

Korver, W., Schilham, M. W., Moerer, P., Hoff, M. J. V. D., Dam, K., Lamers, W. H., Medema, R. H. & Clevers, J. C., 1998, In : Current Biology. 8, p. 1327-1330

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Uncovering the true identity of naive pluripotent stem cells

Welling, M. & Geijsen, N., 2013, In : Trends in Cell Biology. 23, 9, p. 442-448

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1

van Hooff, J. J. E., Snel, B. & Kops, G. J. P. L., 01 May 2017, In : Genome Biology and Evolution. 9, 5, p. 1295-1303 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis

Huch, M., Bonfanti, P., Boj, S. F., Sato, T., Loomans, C. J., van de Wetering, M., Sojoodi, M., Li, V. S., Schuijers, J., Gracanin, A., Ringnalda, F., Begthel, H., Hamer, K., Mulder, J., van Es, J. H., de Koning, E., Vries, R. G. J., Heimberg, H. & Clevers, H., 2013, In : EMBO Journal. 32, 20, p. 2708-2721

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unraveling the ubiquitin-regulated signaling networks by mass spectrometry-based proteomics

Low, T. Y., Magliozzi, R., Guardavaccaro, D. & Heck, A. J. R., 2013, In : Proteomics. 13, 3-4, p. 526-537

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Unravelling cellular relationships during development and regeneration using genetic lineage tracing

Baron, C. S. & van Oudenaarden, A., Dec 2019, In : Nature reviews. Molecular cell biology. 20, 12, p. 753-765 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Use and application of 3D-organoid technology

Artegiani, B. & Clevers, H., 01 Aug 2018, In : Human Molecular Genetics. 27, R2, p. R99-R107

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

Drost, J., van Boxtel, R., Blokzijl, F., Mizutani, T., Sasaki, N., Sasselli, V., de Ligt, J., Behjati, S., Grolleman, J. E., van Wezel, T., Nik-Zainal, S., Kuiper, R. P., Cuppen, E. & Clevers, H., 13 Oct 2017, In : Science. 358, 6360, p. 234-238 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Using gene expression noise to understand gene regulation

Munsky, B., Neuert, G. & van Oudenaarden, A., 2012, In : Science Magazine. 336, 6078, p. 183-187

Research output: Contribution to journal/periodicalArticleScientificpeer-review

USP17- and SCFβTrCP--regulated degradation of DEC1 controls the DNA damage response

Kim, J., D'Annibale, S., Magliozzi, R., Low, T. Y., Jansen, P., Shaltiel, I. A., Mohammed, S., Heck, A. J. R., Medema, R. H. & Guardavaccaro, D., 15 Nov 2014, In : Molecular and Cellular Biology. 34, 22, p. 4177-85 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Utilization of organs from donors after circulatory death for vascularized pancreas and islet of Langerhans transplantation: recommendations from an expert group

Berney, T., Boffa, C., Augustine, T., Badet, L., de Koning, E., Pratschke, J., Socci, C. & Friend, P., 04 Sep 2015, In : Transplant international : official journal of the European Society for Organ Transplantation.

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Open Access

Validation of noise models for single-cell transcriptomics

Grün, D., Kester, L. & van Oudenaarden, A., Jun 2014, In : Nature Methods. 11, 6, p. 637-40 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Van één stamcel naar een mini-orgaan in twintig dagen

Clevers, J. C. & Voormolen, S., 13 Oct 2013, In : NRC Handelsblad.

Research output: Contribution to journal/periodicalArticlePopularizing

Variants in members of the cadherin-catenin complex, CDH1 and CTNND1, cause blepharocheilodontic syndrome

Kievit, A., Tessadori, F., Douben, H., Jordens, I., Maurice, M., Hoogeboom, J., Hennekam, R., Nampoothiri, S., Kayserili, H., Castori, M., Whiteford, M., Motter, C., Melver, C., Cunningham, M., Hing, A., Kokitsu-Nakata, N. M., Vendramini-Pittoli, S., Richieri-Costa, A., Baas, A. F., Breugem, C. C. & 17 others, Duran, K., Massink, M., Derksen, P. W. B., van IJcken, W. F. J., van Unen, L., Santos-Simarro, F., Lapunzina, P., Gil-da Silva Lopes, V. L., Lustosa-Mendes, E., Krall, M., Slavotinek, A., Martinez-Glez, V., Bakkers, J., van Gassen, K. L. I., de Klein, A., van den Boogaard, M-J. H. & van Haaften, G., Feb 2018, In : European Journal of Human Genetics. 26, 2, p. 210-219 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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

Noordermeer, D., de Wit, E., Klous, P., van de Werken, H., Simonis, M., Lopez-Jones, M., Eussen, B., Klein, A. M., Singer, R. H. & de Laat, W., 2011, In : Nature Cell Biology. 13, 8, p. 944-951

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Vasohibins encode tubulin detyrosinating activity

Nieuwenhuis, J., Adamopoulos, A., Bleijerveld, O. B., Mazouzi, A., Stickel, E., Celie, P., Altelaar, M., Knipscheer, P., Perrakis, A., Blomen, V. A. & Brummelkamp, T. R., 15 Dec 2017, In : Science. 358, 6369, p. 1453-1456 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Vegf-A mRNA transfection as a novel approach to improve mouse and human islet graft revascularisation

Staels, W., Verdonck, Y., Heremans, Y., Leuckx, G., De Groef, S., Heirman, C., de Koning, E., Gysemans, C., Thielemans, K., Baeyens, L., Heimberg, H. & De Leu, N., Aug 2018, In : Diabetologia. 61, 8, p. 1804-1810 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Vegfc/Flt4 signalling is suppressed by Dll4 in developing zebrafish intersegmental arteries.

Hogan, B. M., Herpers, R., de Witte, M., Helotera, H., Alitalo, K., Duckers, H. J. & Schulte-Merker, S., 2009, In : Development. 136, 23, p. 4001-4009

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Verbod stamcelonderzoek voorbarig

Geijsen, N., 26 Sep 2013, In : NRC Handelsblad.

Research output: Contribution to journal/periodicalArticlePopularizing