• Netherlands

  • Netherlands

Research Output

2019

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., Tiana, G., Smallwood, S. A., de Laat, W. & Giorgetti, L., Jun 2019, In : Nature Structural & Molecular Biology. 26, 6, p. 471-480 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Defining Adult Stem Cell Function at Its Simplest: The Ability to Replace Lost Cells through Mitosis

Post, Y. & Clevers, H., 01 Aug 2019, In : Cell Stem Cell. 25, 2, p. 174-183 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells

Han, S., Fink, J., Jörg, D. J., Lee, E., Yum, M. K., Chatzeli, L., Merker, S. R., Josserand, M., Trendafilova, T., Andersson-Rolf, A., Dabrowska, C., Kim, H., Naumann, R., Lee, J-H., Sasaki, N., Mort, R. L., Basak, O., Clevers, H., Stange, D. E., Philpott, A. & 3 others, Kim, J. K., Simons, B. D. & Koo, B-K., 05 Sep 2019, In : Cell Stem Cell. 25, 3, p. 342-356.e7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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

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

Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice

Aden, K., Bartsch, K., Dahl, J., Reijns, M. A. M., Esser, D., Sheibani-Tezerji, R., Sinha, A., Wottawa, F., Ito, G., Mishra, N., Knittler, K., Burkholder, A., Welz, L., van Es, J., Tran, F., Lipinski, S., Kakavand, N., Boeger, C., Lucius, R., von Schoenfels, W. & 11 others, Schafmayer, C., Lenk, L., Chalaris, A., Clevers, H., Röcken, C., Kaleta, C., Rose-John, S., Schreiber, S., Kunkel, T., Rabe, B. & Rosenstiel, P., Jan 2019, In : Gastroenterology. 156, 1, p. 145-159.e19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture

Giobbe, G. G., Crowley, C., Luni, C., Campinoti, S., Khedr, M., Kretzschmar, K., De Santis, M. M., Zambaiti, E., Michielin, F., Meran, L., Hu, Q., van Son, G., Urbani, L., Manfredi, A., Giomo, M., Eaton, S., Cacchiarelli, D., Li, V. S. W., Clevers, H., Bonfanti, P. & 2 others, Elvassore, N. & De Coppi, P., 11 Dec 2019, In : Nature Communications. 10, 1, p. 5658

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations

de Winter-de Groot, K. M., Berkers, G., Marck-van der Wilt, R. E. P., van der Meer, R., Vonk, A., Dekkers, J. F., Geerdink, M., Michel, S., Kruisselbrink, E., Vries, R., Clevers, H., Vleggaar, F. P., Elias, S. G., Heijerman, H. G. M., van der Ent, C. K. & Beekman, J. M., 14 Nov 2019, In : Journal of Cystic Fibrosis.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Frizzled-7 is required for Wnt signaling in gastric tumors with and without Apc mutations

Flanagan, D., Barker, N., Di Costanzo, N. S., Mason, E. A., Gurney, A., Meniel, V. S., Koushyar, S., Austin, C. R., Pearson, H. B., Boussioutas, A., Clevers, H., Phesse, T. J. & Vincan, E., Mar 2019, In : Cancer Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genetic variation in GNB5 causes bradycardia by augmenting the cholinergic response via increased acetylcholine-activated potassium current (IK,ACh)

Veerman, C. C., Mengarelli, I., Koopman, C. D., Wilders, R., van Amersfoorth, S. C., Bakker, D., Wolswinkel, R., Hababa, M., de Boer, T. P., Guan, K., Milnes, J., Lodder, E. M., Bakkers, J., Verkerk, A. O. & Bezzina, C. R., 09 Jul 2019, In : Disease Models & Mechanisms. 12, 7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Genome-lamina interactions are established de novo in the early mouse embryo

Borsos, M., Perricone, S. M., Schauer, T., Pontabry, J., de Luca, K. L., de Vries, S. S., Ruiz-Morales, E. R., Torres-Padilla, M-E. & Kind, J., May 2019, In : Nature. 569, 7758, p. 729-733 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Genome-Wide Association Study on the Early-Phase Insulin Response to a Liquid Mixed Meal: Results From the NEO Study

Li-Gao, R., Carlotti, F., de Mutsert, R., van Hylckama Vlieg, A., de Koning, E. J. P., Jukema, J. W., Rosendaal, F. R., Willems van Dijk, K. & Mook-Kanamori, D. O., Dec 2019, In : Diabetes. 68, 12, p. 2327-2336 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Glomerular Function and Structural Integrity Depend on Hyaluronan Synthesis by Glomerular Endothelium

van den Berg, B. M., Wang, G., Boels, M. G. S., Avramut, M. C., Jansen, E., Sol, W. M. P. J., Lebrin, F., Jan van Zonneveld, A., de Koning, E. J. P., Vink, H., Gröne, H-J., Carmeliet, P., van der Vlag, J. & Rabelink, T. J., Oct 2019, In : Journal of the American Society of Nephrology : JASN. 30, 10, p. 1886-1897 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Highly efficient ex vivo lentiviral transduction of primary human pancreatic exocrine cells

Balak, J. R. A., de Graaf, N., Zaldumbide, A., Rabelink, T. J., Hoeben, R. C., de Koning, E. J. P. & Carlotti, F., 01 Nov 2019, In : Scientific Reports. 9, 1, p. 15870

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

High-resolution 3D imaging of fixed and cleared organoids

Dekkers, J. F., Alieva, M., Wellens, L. M., Ariese, H. C. R., Jamieson, P. R., Vonk, A. M., Amatngalim, G. D., Hu, H., Oost, K. C., Snippert, H. J. G., Beekman, J. M., Wehrens, E. J., Visvader, J. E., Clevers, H. & Rios, A. C., Jun 2019, In : Nature Protocols. 14, 6, p. 1756-1771 16 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required for Mouse Spermatogenesis

Brandsma, I., Sato, K., van Rossum-Fikkert, S. E., van Vliet, N., Sleddens, E., Reuter, M., Odijk, H., van den Tempel, N., Dekkers, D. H. W., Bezstarosti, K., Demmers, J. A. A., Maas, A., Lebbink, J., Wyman, C., Essers, J., van Gent, D. C., Baarends, W. M., Knipscheer, P., Kanaar, R. & Zelensky, A. N., 25 Jun 2019, In : Cell Reports. 27, 13, p. 3790-3798.e7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features

Dumont, M., Gamba, R., Gestraud, P., Klaasen, S., Worrall, J. T., De Vries, S. G., Boudreau, V., Salinas-Luypaert, C., Maddox, P. S., Lens, S. M., Kops, G. J., McClelland, S. E., Miga, K. H. & Fachinetti, D., 21 Nov 2019, In : EMBO Journal. p. e102924

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Human iPSC-Derived Retinas Recapitulate the Fetal CRB1 CRB2 Complex Formation and Demonstrate that Photoreceptors and Müller Glia Are Targets of AAV5

Quinn, P. M., Buck, T. M., Mulder, A. A., Ohonin, C., Alves, C. H., Vos, R. M., Bialecka, M., van Herwaarden, T., van Dijk, E. H. C., Talib, M., Freund, C., Mikkers, H. M. M., Hoeben, R. C., Goumans, M-J., Boon, C. J. F., Koster, A. J., Chuva de Sousa Lopes, S. M., Jost, C. R. & Wijnholds, J., 2019, In : Stem Cell Reports. 12, p. 906-919

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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121 Downloads (Pure)

Human Organoids: Tools for Understanding Biology and Treating Diseases

Schutgens, F. & Clevers, H., 24 Sep 2019, In : Annual review of pathology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

Miguel-Escalada, I., Bonàs-Guarch, S., Cebola, I., Ponsa-Cobas, J., Mendieta-Esteban, J., Atla, G., Javierre, B. M., Rolando, D. M. Y., Farabella, I., Morgan, C. C., García-Hurtado, J., Beucher, A., Morán, I., Pasquali, L., Ramos-Rodríguez, M., Appel, E. V. R., Linneberg, A., Gjesing, A. P., Witte, D. R., Pedersen, O. & 16 others, Grarup, N., Ravassard, P., Torrents, D., Mercader, J. M., Piemonti, L., Berney, T., de Koning, E. J. P., Kerr-Conte, J., Pattou, F., Fedko, I. O., Groop, L., Prokopenko, I., Hansen, T., Marti-Renom, M. A., Fraser, P. & Ferrer, J., Jul 2019, In : Nature Genetics. 51, 7, p. 1137-1148 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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

van den Boogaard, M., van Weerd, J. H., Bawazeer, A. C., Hooijkaas, I. B., van de Werken, H. J. G., Tessadori, F., de Laat, W., Barnett, P., Bakkers, J. & Christoffels, V. M., 03 Sep 2019, In : Cell Reports. 28, 10, p. 2704-2714.e5

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping

Gehart, H., van Es, J. H., Hamer, K., Beumer, J., Kretzschmar, K., Dekkers, J. F., Rios, A. & Clevers, H., 21 Feb 2019, In : Cell. 176, 5, p. 1158-1173.e16

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Identification of human D lactate dehydrogenase deficiency

Monroe, G. R., van Eerde, A. M., Tessadori, F., Duran, K. J., Savelberg, S. M. C., van Alfen, J. C., Terhal, P. A., van der Crabben, S. N., Lichtenbelt, K. D., Fuchs, S. A., Gerrits, J., van Roosmalen, M. J., van Gassen, K. L., van Aalderen, M., Koot, B. G., Oostendorp, M., Duran, M., Visser, G., de Koning, T. J., Calì, F. & 8 others, Bosco, P., Geleijns, K., de Sain-van der Velden, M. G. M., Knoers, N. V., Bakkers, J., Verhoeven-Duif, N. M., van Haaften, G. & Jans, J. J., 01 Apr 2019, In : Nature Communications. 10, 1, p. 1477

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

IFN-γ: The T cell's license to kill stem cells in the inflamed intestine

Kretzschmar, K. & Clevers, H., 06 Dec 2019, In : Science immunology. 4, 42

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer

Wang, H., Xiang, D., Liu, B., He, A., Randle, H. J., Zhang, K. X., Dongre, A., Sachs, N., Clark, A. P., Tao, L., Chen, Q., Botchkarev, V. V., Xie, Y., Dai, N., Clevers, H., Li, Z. & Livingston, D. M., 27 Jun 2019, In : Cell. 178, 1, p. 135-151.e19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

van Hooff, J. J. E., Tromer, E., van Dam, T. J. P., Kops, G. J. P. L. & Snel, B., May 2019, In : BioEssays. 41, 5, p. e1900006

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Insulin/IGF-1 Drives PERIOD Synthesis to Entrain Circadian Rhythms with Feeding Time

Crosby, P., Hamnett, R., Putker, M., Hoyle, N. P., Reed, M., Karam, C. J., Maywood, E. S., Stangherlin, A., Chesham, J. E., Hayter, E. A., Rosenbrier-Ribeiro, L., Newham, P., Clevers, H., Bechtold, D. A. & O'Neill, J. S., 02 May 2019, In : Cell. 177, 4, p. 896-909.e20

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Interactions between N-terminal Modules in MPS1 Enable Spindle Checkpoint Silencing

Pachis, S. T., Hiruma, Y., Tromer, E. C., Perrakis, A. & Kops, G. J. P. L., 19 Feb 2019, In : Cell Reports. 26, 8, p. 2101-2112.e6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Intestinal Inflammation and Dysregulated Immunity in Patients With Inherited Caspase-8 Deficiency

Lehle, A. S., Farin, H. F., Marquardt, B., Michels, B. E., Magg, T., Li, Y., Liu, Y., Ghalandary, M., Lammens, K., Hollizeck, S., Rohlfs, M., Hauck, F., Conca, R., Walz, C., Weiss, B., Lev, A., Simon, A. J., Groß, O., Gaidt, M. M., Hornung, V. & 12 others, Clevers, H., Yazbeck, N., Hanna-Wakim, R., Shouval, D. S., Warner, N., Somech, R., Muise, A. M., Snapper, S. B., Bufler, P., Koletzko, S., Klein, C. & Kotlarz, D., Jan 2019, In : Gastroenterology. 156, 1, p. 275-278 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Intracranial aneurysms : (epi)genetic and pathogenic factors in the circle of Willis

Laarman, M., 18 Apr 2019, Utrecht: Utrecht University.

Research output: PhD ThesisPhD thesis

Intronic SMCHD1 variants in FSHD: testing the potential for CRISPR-Cas9 genome editing

Goossens, R., van den Boogaard, M. L., Lemmers, R. J. L. F., Balog, J., van der Vliet, P. J., Willemsen, I. M., Schouten, J., Maggio, I., van der Stoep, N., Hoeben, R. C., Tapscott, S. J., Geijsen, N., Gonçalves, M. A. F. V., Sacconi, S., Tawil, R. & van der Maarel, S. M., Dec 2019, In : Journal of Medical Genetics. 56, 12, p. 828-837 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

In vivo generation of haematopoietic stem/progenitor cells from bone marrow-derived haemogenic endothelium

Yvernogeau, L., Gautier, R., Petit, L., Khoury, H., Relaix, F., Ribes, V., Sang, H., Charbord, P., Souyri, M., Robin, C. & Jaffredo, T., Nov 2019, In : Nature Cell Biology. 21, 11, p. 1334-1345 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

In Vivo Silencing of MicroRNA-132 Reduces Blood Glucose and Improves Insulin Secretion

Bijkerk, R., Esguerra, J. L. S., Ellenbroek, J. H., Au, Y. W., Hanegraaf, M. A. J., de Koning, E. J., Eliasson, L. & van Zonneveld, A. J., Apr 2019, In : Nucleic Acid Therapeutics. 29, 2, p. 67-72 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Keeping the Heart Fitm2 during Chemotherapy

Eding, J. E. C. & van Rooij, E., 02 Jan 2019, In : Molecular Therapy. 27, 1, p. 10-12 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Lamina Associated Domains and Gene Regulation in Development and Cancer

Lochs, S. J. A., Kefalopoulou, S. & Kind, J., 21 Mar 2019, In : Cells. 8, 3

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Large-scale Production of LGR5-positive Bipotential Human Liver Stem Cells

Schneeberger, K., Sánchez-Romero, N., Ye, S., van Steenbeek, F. G., Oosterhoff, L. A., Pla Palacin, I., Chen, C., van Wolferen, M. E., van Tienderen, G., Lieshout, R., Colemonts-Vroninks, H., Schene, I., Hoekstra, R., Verstegen, M. M. A., van der Laan, L. J. W., Penning, L. C., Fuchs, S. A., Clevers, H., De Kock, J., Baptista, P. M. & 1 others, Spee, B., 12 Nov 2019, In : Hepatology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Live imaging of mRNA using RNA-stabilized fluorogenic proteins

Wu, J., Zaccara, S., Khuperkar, D., Kim, H., Tanenbaum, M. E. & Jaffrey, S. R., Sep 2019, In : Nature Methods. 16, 9, p. 862-865 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Long-term expanding human airway organoids for disease modeling

Sachs, N., Papaspyropoulos, A., Zomer-van Ommen, D. D., Heo, I., Böttinger, L., Klay, D., Weeber, F., Huelsz-Prince, G., Iakobachvili, N., Amatngalim, G. D., de Ligt, J., van Hoeck, A., Proost, N., Viveen, M. C., Lyubimova, A., Teeven, L., Derakhshan, S., Korving, J., Begthel, H., Dekkers, J. F. & 28 others, Kumawat, K., Ramos, E., van Oosterhout, M. F., Offerhaus, G. J., Wiener, D. J., Olimpio, E. P., Dijkstra, K. K., Smit, E. F., van der Linden, M., Jaksani, S., van de Ven, M., Jonkers, J., Rios, A. C., Voest, E. E., van Moorsel, C. H., van der Ent, C. K., Cuppen, E., van Oudenaarden, A., Coenjaerts, F. E., Meyaard, L., Bont, L. J., Peters, P. J., Tans, S. J., van Zon, J. S., Boj, S. F., Vries, R. G., Beekman, J. M. & Clevers, H., 15 Feb 2019, In : EMBO Journal. 38, 4

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Long-term expansion and differentiation of adult murine epidermal stem cells in 3D organoid cultures

Boonekamp, K. E., Kretzschmar, K., Wiener, D. J., Asra, P., Derakhshan, S., Puschhof, J., López-Iglesias, C., Peters, P. J., Basak, O. & Clevers, H., 16 Jul 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 29, p. 14630-14638 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development

Chrispijn, N. D., Elurbe, D. M., Mickoleit, M., Aben, M., de Bakker, D. E. M., Andralojc, K. M., Huisken, J., Bakkers, J. & Kamminga, L. M., 13 Mar 2019, In : Scientific Reports. 9, 1, p. 4327

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Macrophages Do Not Express the Phagocytic Receptor BAI1/

Hsiao, C-C., van der Poel, M., van Ham, T. J. & Hamann, J., 2019, In : Frontiers in Immunology. 10, p. 962

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
File
54 Downloads (Pure)

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance

Bertolini, J. A., Favaro, R., Zhu, Y., Pagin, M., Ngan, C. Y., Wong, C. H., Tjong, H., Vermunt, M. W., Martynoga, B., Barone, C., Mariani, J., Cardozo, M. J., Tabanera, N., Zambelli, F., Mercurio, S., Ottolenghi, S., Robson, P., Creyghton, M. P., Bovolenta, P., Pavesi, G. & 3 others, Guillemot, F., Nicolis, S. K. & Wei, C-L., 07 Mar 2019, In : Cell Stem Cell. 24, 3, p. 462-476.e6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Membrane-Bound Meet Membraneless in Health and Disease

Zhang, C. & Rabouille, C., 29 Aug 2019, In : Cells. 8, 9

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Membraneless organelles in cell biology

Rabouille, C., Dec 2019, In : Traffic. 20, 12, p. 885-886 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

MET Signaling Overcomes Epidermal Growth Factor Receptor Inhibition in Normal and Colorectal Cancer Stem Cells Causing Drug Resistance

Joosten, S. P. J., Mizutani, T., Spaargaren, M., Clevers, H. & Pals, S. T., Oct 2019, In : Gastroenterology. 157, 4, p. 1153-1155.e1

Research output: Contribution to journal/periodicalArticleScientificpeer-review