• Netherlands

  • Netherlands

Research Output

2016

Modeling Development and Disease with Organoids

Clevers, H., 16 Jun 2016, In : Cell. 165, 7, p. 1586-97 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Modeling pancreatic cancer with organoids

Baker, L. A., Tiriac, H., Clevers, H. & Tuveson, D. A., Apr 2016, In : Trends in Cancer. 2, 4, p. 176-190 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Model organoids provide new research opportunities for ductal pancreatic cancer

Boj, S. F., Hwang, C-I., Baker, L. A., Engle, D. D., Tuveson, D. A. & Clevers, H., Jan 2016, In : Molecular & Cellular Oncology. 3, 1, p. e1014757

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Modulating microRNAs in cardiac surgery patients: Novel therapeutic opportunities?

Biglino, G., Caputo, M., Rajakaruna, C., Angelini, G., van Rooij, E. & Emanueli, C., 27 Nov 2016, In : Pharmacology & Therapeutics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Mule Regulates the Intestinal Stem Cell Niche via the Wnt Pathway and Targets EphB3 for Proteasomal and Lysosomal Degradation

Dominguez-Brauer, C., Hao, Z., Elia, A. J., Fortin, J. M., Nechanitzky, R., Brauer, P. M., Sheng, Y., Mana, M. D., Chio, I. I. C., Haight, J., Pollett, A., Cairns, R., Tworzyanski, L., Inoue, S., Reardon, C., Marques, A., Silvester, J., Cox, M. A., Wakeham, A., Yilmaz, O. H. & 5 others, Sabatini, D. M., van Es, J. H., Clevers, H., Sato, T. & Mak, T. W., 04 Aug 2016, In : Cell Stem Cell.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2

San, B., Chrispijn, N. D., Wittkopp, N., van Heeringen, S. J., Lagendijk, A. K., Aben, M., Bakkers, J., Ketting, R. F. & Kamminga, L. M., 2016, In : Scientific Reports. 6, p. 24658

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

On the shoulders of Hubrecht: From embryos to stem cells

Rabouille, C. & Deschamps, J., 2016, In : Developmental Biology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Organoid biobanking: identifying the ethics: Organoids revive old and raise new ethical challenges for basic research and therapeutic use

Boers, S. N., van Delden, J. J., Clevers, H. & Bredenoord, A. L., Jul 2016, In : EMBO Reports. 17, 7, p. 938-41 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Organoid culture systems for prostate epithelial and cancer tissue

Drost, J., Karthaus, W. R., Gao, D., Driehuis, E., Sawyers, C. L., Chen, Y. & Clevers, H., Feb 2016, In : Nature Protocols. 11, 2, p. 347-58 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Organoids: Modeling Development and the Stem Cell Niche in a Dish

Kretzschmar, K. & Clevers, H., 26 Sep 2016, In : Developmental Cell. 38, 6, p. 590-600 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient

Adolphe, C., Junker, J. P., Lyubimova, A., van Oudenaarden, A. & Wainwright, B., 04 Aug 2016, In : Journal of Investigative Dermatology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Pathways of Unconventional Protein Secretion

Rabouille, C., 15 Dec 2016, In : Trends in Cell Biology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint

Tromer, E., Bade, D., Snel, B. & Kops, G. J. P. L., Dec 2016, In : Biology Open. 6, 12

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Plasmalemma Vesicle-Associated Protein Has a Key Role in Blood-Retinal Barrier Loss: Am J Pathol

Wisniewska-Kruk, J., van der Wijk, A. E., van Veen, H. A., Gorgels, T. G., Vogels, I. M., Versteeg, D., Van Noorden, C. J., Schlingemann, R. O. & Klaassen, I., Apr 2016, In : The American journal of pathology. 186, 4, p. 1044-1054 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity

Beerling, E., Seinstra, D., de Wit, E., Kester, L., van der Velden, D., Maynard, C., Schäfer, R., van Diest, P., Voest, E., van Oudenaarden, A., Vrisekoop, N. & van Rheenen, J., 03 Mar 2016, In : Cell Reports. 14, 10, p. 2281-8 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos

Neijts, R., Amin, S., van Rooijen, C., Tan, S., Creyghton, M. P., de Laat, W. & Deschamps, J., 01 Sep 2016, In : Genes & Development. 30, 17, p. 1937-42 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Programs for the persistence, vigilance and control of human CD8(+) lung-resident memory T cells

Hombrink, P., Helbig, C., Backer, R. A., Piet, B., Oja, A. E., Stark, R., Brasser, G., Jongejan, A., Jonkers, R. E., Nota, B., Basak, O., Clevers, H. C., Moerland, P. D., Amsen, D. & van Lier, R. A. W., Dec 2016, In : Nature Immunology. 17, 12, p. 1467-1478 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Rare novel variants in the ZIC3 gene cause X-linked heterotaxy

Paulussen, A. D. C., Steyls, A., Vanoevelen, J., van Tienen, F. H., Krapels, I. P. C., Claes, G. R., Chocron, S., Velter, C., Tan-Sindhunata, G. M., Lundin, C., Valenzuela, I., Nagy, B., Bache, I., Maroun, L. L., Avela, K., Brunner, H. G., Smeets, H. J. M., Bakkers, J. & van den Wijngaard, A., 13 Jul 2016, In : European Journal of Human Genetics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Receptor protein tyrosine phosphatase alpha enhances rheumatoid synovial fibroblast signaling and promotes arthritis in mice

Stanford, S. M., Svensson, M. N. D., Sacchetti, C., Pilo, C. A., Wu, D. J., Kiosses, W. B., Hellvard, A., Bergum, B., Aleman Muench, G. R., Elly, C., Liu, Y-C., den Hertog, J., Elson, A., Sap, J., Mydel, P., Boyle, D. L., Corr, M., Firestein, G. S. & Bottini, N., 25 Jan 2016, In : Arthritis and Rheumatology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon

Sasaki, N., Sachs, N., Wiebrands, K., Ellenbroek, S. I. J., Fumagalli, A., Lyubimova, A., Begthel, H., van den Born, M., van Es, J. H., Karthaus, W. R., Li, V. S. W., López-Iglesias, C., Peters, P. J., van Rheenen, J., van Oudenaarden, A. & Clevers, H., 29 Aug 2016, In : Proceedings of the National Academy of Sciences of the United States of America.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Regulation and plasticity of intestinal stem cells during homeostasis and regeneration

Beumer, J. & Clevers, H., 15 Oct 2016, In : Development. 143, 20, p. 3639-3649 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Regulation of disease-associated gene expression in the 3D genome

Krijger, P. H. L. & de Laat, W., Dec 2016, In : Nature reviews. Molecular cell biology. 17, 12, p. 771-782 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Reparative inflammation takes charge of tissue regeneration

Karin, M. & Clevers, H., 21 Jan 2016, In : Nature. 529, 7586, p. 307-15 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tetteh, P. W., Basak, O., Farin, H. F., Wiebrands, K., Kretzschmar, K., Begthel, H., van den Born, M., Korving, J., de Sauvage, F., van Es, J. H., van Oudenaarden, A. & Clevers, H., 04 Feb 2016, In : Cell Stem Cell. 18, 2, p. 203-13 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

RNF43 germline and somatic mutation in serrated neoplasia pathway and its association with BRAF mutation

Yan, H. H. N., Lai, J. C. W., Ho, S. L., Leung, W. K., Law, W. L., Lee, J. F. Y., Chan, A. K. W., Tsui, W. Y., Chan, A. S. Y., Lee, B. C. H., Yue, S. S. K., Man, A. H. Y., Clevers, H., Yuen, S. T. & Leung, S. Y., 21 Jun 2016, In : Gut.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Selection of polymers for application in scaffolds applicable for human pancreatic islet transplantation

Smink, A. M., de Haan, B. J., Paredes-Juarez, G. A., Wolters, A. H. G., Kuipers, J., Giepmans, B. N. G., Schwab, L., Engelse, M. A., van Apeldoorn, A. A., de Koning, E., Faas, M. M. & de Vos, P., 2016, In : Biomedical materials (Bristol, England). 11, 3, p. 035006

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Self-Cloning CRISPR

Arbab, M. & Sherwood, R. I., 17 Aug 2016, In : Current Protocols in Stem Cell Biology. 38, p. 5b.5.1-5b.5.16

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Sequential intravital imaging reveals in vivo dynamics of pancreatic tissue transplanted under the kidney capsule in mice

van Gurp, L., Loomans, C. J. M., van Krieken, P. P., Dharmadhikari, G., Jansen, E., Ringnalda, F. C. A. S., Beerling, E., van Rheenen, J. & de Koning, E. J. P., 21 Jul 2016, In : Diabetologia.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Shedding light on hematopoietic stem cells: formation, regulation, and utilization

Robin, C., Nov 2016, In : FEBS Letters. 590, 22, p. 3963-3964 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Simultaneous pancreas-kidney transplantation in patients with type 1 diabetes reverses elevated MBL levels in association with MBL2 genotype and VEGF expression

Bijkerk, R., van der Pol, P., Khairoun, M., van Gijlswijk-Jansen, D. J., Lievers, E., de Vries, A. P. J., de Koning, E. J., de Fijter, H. W., Roelen, D. L., Vossen, R. H. A. M., van Zonneveld, A. J., van Kooten, C. & Reinders, M. E. J., Apr 2016, In : Diabetologia. 59, 4, p. 853-8 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

Mooijman, D., Dey, S. S., Boisset, J-C., Crosetto, N. & van Oudenaarden, A., 27 Jun 2016, In : Nature Biotechnology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

SMArt CRISPR

Arbab, M., 12 May 2016

Research output: PhD ThesisPhD thesis

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration

Wu, C-C., Kruse, F., Vasudevarao, M. D., Junker, J. P., Zebrowski, D. C., Fischer, K., Noël, E. S., Grün, D., Berezikov, E., Engel, F. B., van Oudenaarden, A., Weidinger, G. & Bakkers, J., 11 Jan 2016, In : Developmental Cell. 36, 1, p. 36-49 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Stathmin 1/2-triggered microtubule loss mediates Golgi fragmentation in mutant SOD1 motor neurons

Bellouze, S., Baillat, G., Buttigieg, D., de la Grange, P., Rabouille, C. & Haase, G., 2016, In : Molecular Neurodegeneration. 11, 1, p. 43

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Studying extracellular vesicle transfer by a Cre-loxP method

Zomer, A., Steenbeek, S. C., Maynard, C. & van Rheenen, J., Jan 2016, In : Nature Protocols. 11, 1, p. 87-101 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Studying Kinetochore Kinases

Saurin, A. T. & Kops, G. J. P. L., 2016, In : Methods in Molecular Biology. 1413, p. 333-47 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Studying Protein-Tyrosine Phosphatases in Zebrafish

Hale, A. J. & den Hertog, J., 2016, In : Methods in Molecular Biology. 1447, p. 351-72 22 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening

Verissimo, C. S., Overmeer, R. M., Ponsioen, B., Drost, J., Mertens, S., Verlaan-Klink, I., Gerwen, B. V., van der Ven, M., Wetering, M. V. D., Egan, D. A., Bernards, R., Clevers, H., Bos, J. L. & Snippert, H. J., 15 Nov 2016, In : eLife. 5

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype

Fessler, E., Drost, J., van Hooff, S. R., Linnekamp, J. F., Wang, X., Jansen, M., De Sousa E Melo, F., Prasetyanti, P. R., IJspeert, J. E., Franitza, M., Nürnberg, P., van Noesel, C. J., Dekker, E., Vermeulen, L., Clevers, H. & Medema, J. P., 2016, In : EMBO Molecular Medicine. 8, 7, p. 745-60 16 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The Caenorhabditis elegans Q neuroblasts: A powerful system to study cell migration at single-cell resolution in vivo

Rella, L., Fernandes Póvoa, E. E. & Korswagen, H. C., Apr 2016, In : Genesis. 54, 4, p. 198-211 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The extertion of cell-cell adhesions

le Duc, Q., 12 Jan 2016

Research output: PhD ThesisPhD thesis

The Generation of Organoids for Studying Wnt Signaling

Drost, J., Artegiani, B. & Clevers, H., 2016, In : Methods in Molecular Biology. 1481, p. 141-59 19 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model: Dis Model Mech

Homberg, J. R., Olivier, J. D., VandenBroeke, M., Youn, J., Ellenbroek, A. K., Karel, P., Shan, L., van Boxtel, R., Ooms, S., Balemans, M., Langedijk, J., Muller, M., Vriend, G., Cools, A. R., Cuppen, E. & Ellenbroek, B. A., 05 Oct 2016, In : Disease Models & Mechanisms. 9, 10, p. 1147-1158 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The second decade of 3C technologies: detailed insights into nuclear organization

Denker, A. & de Laat, W., 15 Jun 2016, In : Genes & Development. 30, 12, p. 1357-82 26 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Tissue-specific designs of stem cell hierarchies

Visvader, J. E. & Clevers, H., Apr 2016, In : Nature Cell Biology. 18, 4, p. 349-55 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tissue-specific mutation accumulation in human adult stem cells during life

Blokzijl, F., de Ligt, J., Jager, M., Sasselli, V., Roerink, S., Sasaki, N., Huch, M., Boymans, S., Kuijk, E., Prins, P., Nijman, I. J., Martincorena, I., Mokry, M., Wiegerinck, C. L., Middendorp, S., Sato, T., Schwank, G., Nieuwenhuis, E. E. S., Verstegen, M. M. A., van der Laan, L. J. W. & 8 others, de Jonge, J., IJzermans, J. N. M., Vries, R. G., van de Wetering, M., Stratton, M. R., Clevers, H., Cuppen, E. & van Boxtel, R., 13 Oct 2016, In : Nature. 538, 7624, p. 260-264 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Tomo-seq: A method to obtain genome-wide expression data with spatial resolution

Kruse, F., Junker, J. P., van Oudenaarden, A. & Bakkers, J., 2016, In : Methods in Cell Biology. 135, p. 299-307 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transcriptional Dynamics at Brain Enhancers: from Functional Specialization to Neurodegeneration

Vermunt, M. W. & Creyghton, M. P., 2016, In : Current Neurology and Neuroscience Reports. 16, 10, p. 94

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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

Vessel co-option mediates resistance to anti-angiogenic therapy in liver metastases

Frentzas, S., Simoneau, E., Bridgeman, V. L., Vermeulen, P. B., Foo, S., Kostaras, E., Nathan, M. R., Wotherspoon, A., Gao, Z-H., Shi, Y., Van den Eynden, G., Daley, F., Peckitt, C., Tan, X., Salman, A., Lazaris, A., Gazinska, P., Berg, T. J., Eltahir, Z., Ritsma, L. & 11 others, van Rheenen, J., Khashper, A., Brown, G., Nyström, H., Sund, M., Van Laere, S., Loyer, E., Dirix, L., Cunningham, D., Metrakos, P. & Reynolds, A. R., Nov 2016, In : Nature Medicine. 22, 11, p. 1294-1302 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review