• Netherlands

  • Netherlands

Research Output

2016

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

Wijchers, P. J., Krijger, P. H. L., Geeven, G., Zhu, Y., Denker, A., Verstegen, M. J. A. M., Valdes-Quezada, C., Vermeulen, C., Janssen, M., Teunissen, H., Anink-Groenen, L. C. M., Verschure, P. J. & de Laat, W., 04 Feb 2016, In : Molecular Cell. 61, 3, p. 461-73 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

Amin, S., Neijts, R., Simmini, S., van Rooijen, C., Tan, S. C., Kester, L., van Oudenaarden, A., Creyghton, M. P. & Deschamps, J., 20 Dec 2016, In : Cell Reports. 17, 12, p. 3165-3177 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cdx is crucial for the timing mechanism driving colinear Hox activation and defines a trunk segment in the Hox cluster topology

Neijts, R., Amin, S., van Rooijen, C. & Deschamps, J., 29 Dec 2016, In : Developmental Biology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

Krijger, P. H. L., Di Stefano, B., de Wit, E., Limone, F., van Oevelen, C., de Laat, W. & Graf, T., 05 May 2016, In : Cell Stem Cell. 18, 5, p. 597-610 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis

Dekkers, J. F., Berkers, G., Kruisselbrink, E., Vonk, A., de Jonge, H. R., Janssens, H. M., Bronsveld, I., van de Graaf, E. A., Nieuwenhuis, E. E. S., Houwen, R. H. J., Vleggaar, F. P., Escher, J. C., de Rijke, Y. B., Majoor, C. J., Heijerman, H. G. M., de Winter-de Groot, K. M., Clevers, H., van der Ent, C. K. & Beekman, J. M., 22 Jun 2016, In : Science Translational Medicine. 8, 344, p. 344ra84

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Coculturing Human Islets with Proangiogenic Support Cells to Improve Islet Revascularization at the Subcutaneous Transplantation Site

Buitinga, M., Janeczek Portalska, K., Cornelissen, D-J., Plass, J., Hanegraaf, M., Carlotti, F., de Koning, E., Engelse, M., van Blitterswijk, C., Karperien, M., van Apeldoorn, A. & de Boer, J., Feb 2016, In : Tissue engineering. Part A. 22, 3-4, p. 375-85 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Comparative interactomics analysis of different ALS-associated proteins identifies converging molecular pathways

Blokhuis, A. M., Koppers, M., Groen, E. J. N., van den Heuvel, D. M. A., Dini Modigliani, S., Anink, J. J., Fumoto, K., van Diggelen, F., Snelting, A., Sodaar, P., Verheijen, B. M., Demmers, J. A. A., Veldink, J. H., Aronica, E., Bozzoni, I., den Hertog, J., van den Berg, L. H. & Pasterkamp, R. J., 10 May 2016, In : Acta Neuropathologica.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Contactomics - exploring new dimensions of 3D genome architecture

Bouwman, B., 23 Jun 2016

Research output: PhD ThesisPhD thesis

CRISPR/Cas9-Mediated Genome Editing of Mouse Small Intestinal Organoids

Schwank, G. & Clevers, H., 2016, In : Methods in Molecular Biology. 1422, p. 3-11 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization

Wang, J., Wang, Z., Yu, T., Yang, H., Virshup, D. M., Kops, G. J. P. L., Lee, S. H., Zhou, W., Li, X., Xu, W. & Rao, Z., Jul 2016, In : Protein & cell. 7, 7, p. 516-26 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation

Broutier, L., Andersson-Rolf, A., Hindley, C. J., Boj, S. F., Clevers, H., Koo, B-K. & Huch, M., Sep 2016, In : Nature Protocols. 11, 9, p. 1724-43 20 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Decrypting gastrointestinal development and homeostasis one cell at a time

Wiebrands, K., 06 Sep 2016

Research output: PhD ThesisPhD thesis

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Grün, D., Muraro, M. J., Boisset, J-C., Wiebrands, K., Lyubimova, A., Dharmadhikari, G., van den Born, M., van Es, J., Jansen, E., Clevers, H., de Koning, E. J. P. & van Oudenaarden, A., 21 Jun 2016, In : Cell Stem Cell.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Designer matrices for intestinal stem cell and organoid culture

Gjorevski, N., Sachs, N., Manfrin, A., Giger, S., Bragina, M. E., Ordóñez-Morán, P., Clevers, H. & Lutolf, M. P., 16 Nov 2016, In : Nature. 539, 7630, p. 560-564 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Differential requirement for pten lipid and protein phosphatase activity during zebrafish embryonic development

Stumpf, M. & Den Hertog, J., 01 Feb 2016, In : PLoS One. 11, 2, e0148508.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

Wang, X., Tucker, N. R., Rizki, G., Mills, R., Krijger, P. H., de Wit, E., Subramanian, V., Bartell, E., Nguyen, X-X., Ye, J., Leyton-Mange, J., Dolmatova, E. V., van der Harst, P., de Laat, W., Ellinor, P. T., Newton-Cheh, C., Milan, D. J., Kellis, M. & Boyer, L. A., 2016, In : eLife. 5

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

Jaitin, D. A., Weiner, A., Yofe, I., Lara-Astiaso, D., Keren-Shaul, H., David, E., Salame, T. M., Tanay, A., van Oudenaarden, A. & Amit, I., 15 Dec 2016, In : Cell. 167, 7, p. 1883-1896.e15

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Distinct activation of primary human BDCA1(+) dendritic cells upon interaction with stressed or infected beta cells

Schulte, B. M., Kers-Rebel, E. D., Bottino, R., Piganelli, J. D., Galama, J. M., Engelse, M. A., de Koning, E. J. & Adema, G. J., Jun 2016, In : Clinical & Experimental Immunology. 184, 3, p. 293-307 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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

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

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

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

Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Vermunt, M. W., Tan, S. C., Castelijns, B., Geeven, G., Reinink, P., de Bruijn, E., Kondova, I., Persengiev, S., Bontrop, R., Cuppen, E., de Laat, W. & Creyghton, M. P., Mar 2016, In : Nature Neuroscience. 19, 3, p. 494-503 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Erratum to: 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., 2016, In : Genome Biology. 17, p. 22

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Fine-Tuning of Pten Localization and Phosphatase Activity Is Essential for Zebrafish Angiogenesis

Stumpf, M., Blokzijl-Franke, S. & den Hertog, J., 2016, In : PLoS One. 11, 5, p. e0154771

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Function and Therapeutic Potential of Non-Coding RNAs in Cardiac Fibrosis

Creemers, E. E. & van Rooij, E., 08 Jan 2016, In : Circulation Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Generation and characterization of rat liver stem cell lines and their engraftment in a rat model of liver failure

Kuijk, E. W., Rasmussen, S., Blokzijl, F., Huch, M., Gehart, H., Toonen, P., Begthel, H., Clevers, H., Geurts, A. M. & Cuppen, E., 2016, In : Scientific Reports. 6, p. 22154

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research

Tetteh, P. W., Kretzschmar, K., Begthel, H., van den Born, M., Korving, J., Morsink, F. H. M., Farin, H., van Es, J. H., Offerhaus, G. J. A. & Clevers, H., 18 Oct 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 42, p. 11859-11864 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genetics and Genomics of Single-Gene Cardiovascular Diseases: Common Hereditary Cardiomyopathies as Prototypes of Single-Gene Disorders

Marian, A. J., van Rooij, E. & Roberts, R., 27 Dec 2016, In : Journal of the American College of Cardiology. 68, 25, p. 2831-2849 19 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genome-wide analysis reveals NRP1 as a direct HIF1α-E2F7 target in the regulation of motorneuron guidance in vivo

de Bruin, A., Cornelissen, P. W. A., Kirchmaier, B. C., Mokry, M., Iich, E., Nirmala, E., Liang, K-H., Végh, A. M. D., Scholman, K. T., Groot Koerkamp, M. J., Holstege, F. C., Cuppen, E., Schulte-Merker, S. & Bakker, W. J., 05 May 2016, In : Nucleic Acids Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Genome-wide CRISPR screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors

Steinhart, Z., Pavlovic, Z., Chandrashekhar, M., Hart, T., Wang, X., Zhang, X., Robitaille, M., Brown, K. R., Jaksani, S., Overmeer, R., Boj, S. F., Adams, J., Pan, J., Clevers, H., Sidhu, S., Moffat, J. & Angers, S., 21 Nov 2016, In : Nature Medicine.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans

Houtepen, L. C., Vinkers, C. H., Carrillo-Roa, T., Hiemstra, M., van Lier, P. A., Meeus, W., Branje, S., Heim, C. M., Nemeroff, C. B., Mill, J., Schalkwyk, L. C., Creyghton, M. P., Kahn, R. S., Joëls, M., Binder, E. B. & Boks, M. P. M., 19 Mar 2016, In : Nature Communications. 7, p. 10967

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1

Thambyrajah, R., Mazan, M., Patel, R., Moignard, V., Stefanska, M., Marinopoulou, E., Li, Y., Lancrin, C., Clapes, T., Möröy, T., Robin, C., Miller, C., Cowley, S., Göttgens, B., Kouskoff, V. & Lacaud, G., Jan 2016, In : Nature Cell Biology. 18, 1, p. 21-32 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability

Lodder, E. M., De Nittis, P., Koopman, C. D., Wiszniewski, W., Moura de Souza, C. F., Lahrouchi, N., Guex, N., Napolioni, V., Tessadori, F., Beekman, L., Nannenberg, E. A., Boualla, L., Blom, N. A., de Graaff, W., Kamermans, M., Cocciadiferro, D., Malerba, N., Mandriani, B., Akdemir, Z. H. C., Fish, R. J. & 13 others, Eldomery, M. K., Ratbi, I., Wilde, A. A. M., de Boer, T., Simonds, W. F., Neerman-Arbez, M., Sutton, V. R., Kok, F., Lupski, J. R., Reymond, A., Bezzina, C. R., Bakkers, J. & Merla, G., 2016, In : American Journal of Human Genetics. 99, p. 704-710

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability

Lodder, E. M., De Nittis, P., Koopman, C. D., Wiszniewski, W., Moura de Souza, C. F., Lahrouchi, N., Guex, N., Napolioni, V., Tessadori, F., Beekman, L., Nannenberg, E. A., Boualla, L., Blom, N. A., de Graaff, W., Kamermans, M., Cocciadiferro, D., Malerba, N., Mandriani, B., Coban Akdemir, Z. H., Fish, R. J. & 13 others, Eldomery, M. K., Ratbi, I., Wilde, A. A. M., de Boer, T., Simonds, W. F., Neerman-Arbez, M., Sutton, V. R., Kok, F., Lupski, J. R., Reymond, A., Bezzina, C. R., Bakkers, J. & Merla, G., 01 Sep 2016, In : American Journal of Human Genetics. 99, 3, p. 786

Research output: Contribution to journal/periodicalArticleScientificpeer-review

GRASP: A Multitasking Tether

Rabouille, C. & Linstedt, A. D., 2016, In : Frontiers in cell and developmental biology. 4, p. 1

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity

Josifova, D. J., Monroe, G. R., Tessadori, F., de Graaff, E., van der Zwaag, B., Mehta, S. G., Harakalova, M., Duran, K. J., Savelberg, S. M. C., Nijman, I. J., Jungbluth, H., Hoogenraad, C. C., Bakkers, J., Knoers, N. V., Firth, H. V., Beales, P. L., van Haaften, G. & van Haelst, M. M., 22 Mar 2016, In : Human Molecular Genetics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Human islets and dendritic cells generate post-translationally modified islet auto-antigens

McLaughlin, R. J., de Haan, A., Zaldumbide, A., de Koning, E. J., de Ru, A. H., van Veelen, P. A., van Lummel, M. & Roep, B. O., 09 Feb 2016, In : Clinical & Experimental Immunology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Hybrid Polycaprolactone/Alginate Scaffolds Functionalized with VEGF to Promote de Novo Vessel Formation for the Transplantation of Islets of Langerhans

Marchioli, G., Luca, A. D., de Koning, E., Engelse, M., Van Blitterswijk, C. A., Karperien, M., Van Apeldoorn, A. A. & Moroni, L., Jul 2016, In : Advanced healthcare materials. 5, 13, p. 1606-16 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Implications of Extracellular Vesicle Transfer on Cellular Heterogeneity in Cancer: What Are the Potential Clinical Ramifications?

Zomer, A. & van Rheenen, J., 15 Apr 2016, In : Cancer Research. 76, 8, p. 2071-5 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Inactivation of TGFβ receptors in stem cells drives cutaneous squamous cell carcinoma

Cammareri, P., Rose, A. M., Vincent, D. F., Wang, J., Nagano, A., Libertini, S., Ridgway, R. A., Athineos, D., Coates, P. J., McHugh, A., Pourreyron, C., Dayal, J. H. S., Larsson, J., Weidlich, S., Spender, L. C., Sapkota, G. P., Purdie, K. J., Proby, C. M., Harwood, C. A., Leigh, I. M. & 9 others, Clevers, H., Barker, N., Karlsson, S., Pritchard, C., Marais, R., Chelala, C., South, A. P., Sansom, O. J. & Inman, G. J., 2016, In : Nature Communications. 7, p. 12493

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Incidence and prevalence of thyroid dysfunction in type 1 diabetes

Nederstigt, C., Corssmit, E. P. M., de Koning, E. J. P. & Dekkers, O. M., Apr 2016, In : Journal of Diabetes and its Complications. 30, 3, p. 420-5 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Induced Quiescence of Lgr5+ Stem Cells in Intestinal Organoids Enables Differentiation of Hormone-Producing Enteroendocrine Cells

Basak, O., Beumer, J., Wiebrands, K., Seno, H., van Oudenaarden, A. & Clevers, H., 17 Nov 2016, In : Cell Stem Cell.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Interplay of PTEN subcellular localization and catalytic activities in vivo

Stumpf, M., 23 Jun 2016

Research output: PhD ThesisPhD thesis

Intravital characterization of tumor cell migration in pancreatic cancer

Beerling, E., Oosterom, I., Voest, E. E., Lolkema, M. P. & van Rheenen, J., 2016, In : IntraVital. 5, 3, p. e1261773

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

In vivo vizualisation of mono-ADP-ribosylation by dPARP16 upon amino-acid starvation

Aguilera-Gomez, A., van Oorschot, M. M., Veenendaal, T. & Rabouille, C., 22 Nov 2016, In : eLife. 5, p. 23 1 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

IκBNS enhances T follicular helper cell differentiation and function as downstream of Ascl2

Hosokawa, J., Suzuki, K., Meguro, K., Tanaka, S., Maezawa, Y., Suto, A., Fujimura, L., Sakamoto, A., Clevers, H., Ohara, O. & Nakajima, H., 28 Dec 2016, In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

LIM Kinase Inhibitor Pyr1 Reduces the Growth and Metastatic Load of Breast Cancers

Prunier, C., Josserand, V., Vollaire, J., Beerling, E., Petropoulos, C., Destaing, O., Montemagno, C., Hurbin, A., Prudent, R., de Koning, L., Kapur, R., Cohen, P. A., Albiges-Rizo, C., Coll, J-L., van Rheenen, J., Billaud, M. & Lafanechère, L., 15 Jun 2016, In : Cancer Research. 76, 12, p. 3541-52 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Localized Translation of gurken/TGF-α mRNA during Axis Specification Is Controlled by Access to Orb/CPEB on Processing Bodies

Davidson, A., Parton, R. M., Rabouille, C., Weil, T. T. & Davis, I., 15 Mar 2016, In : Cell Reports. 14, 10, p. 2451-62 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Long-Term In Vitro Expansion of Salivary Gland Stem Cells Driven by Wnt Signals

Maimets, M., Rocchi, C., Bron, R., Pringle, S., Kuipers, J., Giepmans, B. N. G., Vries, R. G. J., Clevers, H., de Haan, G., van Os, R. & Coppes, R. P., 12 Jan 2016, In : Stem Cell Reports. 6, 1, p. 150-162 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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