• Netherlands

  • Netherlands

Research Output

2018

Itch/β-arrestin2-dependent non-proteolytic ubiquitylation of SuFu controls Hedgehog signalling and medulloblastoma tumorigenesis

Infante, P., Faedda, R., Bernardi, F., Bufalieri, F., Lospinoso Severini, L., Alfonsi, R., Mazzà, D., Siler, M., Coni, S., Po, A., Petroni, M., Ferretti, E., Mori, M., De Smaele, E., Canettieri, G., Capalbo, C., Maroder, M., Screpanti, I., Kool, M., Pfister, S. M. & 3 others, Guardavaccaro, D., Gulino, A. & Di Marcotullio, L., 07 Mar 2018, In : Nature Communications. 9, 1, p. 976

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Leader of the SAC: molecular mechanisms of Mps1/TTK regulation in mitosis

Pachis, S. T. & Kops, G. J. P. L., Aug 2018, In : Open Biology. 8, 8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Live imaging of cell division in 3D stem-cell organoid cultures

Bolhaqueiro, A. C. F., van Jaarsveld, R. H., Ponsioen, B., Overmeer, R. M., Snippert, H. J. & Kops, G. J. P. L., 2018, In : Methods in Cell Biology. 145, p. 91-106 16 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Long-Term Expansion of Functional Mouse and Human Hepatocytes as 3D Organoids

Hu, H., Gehart, H., Artegiani, B., LÖpez-Iglesias, C., Dekkers, F., Basak, O., van Es, J., Chuva de Sousa Lopes, S. M., Begthel, H., Korving, J., van den Born, M., Zou, C., Quirk, C., Chiriboga, L., Rice, C. M., Ma, S., Rios, A., Peters, P. J., de Jong, Y. P. & Clevers, H., 29 Nov 2018, In : Cell. 175, 6, p. 1591-1606.e19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Mapping the physical network of cellular interactions

Boisset, J-C., Vivié, J., Grün, D., Muraro, M. J., Lyubimova, A. & van Oudenaarden, A., Jul 2018, In : Nature Methods. 15, 7, p. 547-553 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures

Jager, M., Blokzijl, F., Sasselli, V., Boymans, S., Janssen, R., Besselink, N., Clevers, H., van Boxtel, R. & Cuppen, E., Jan 2018, In : Nature Protocols. 13, 1, p. 59-78 20 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Measuring Nucleosome Assembly Activity with the Nucleosome Assembly and Quantification (NAQ) Assay

Mattiroli, F., Gu, Y. & Luger, K., 05 Feb 2018, In : Bio-Protocol. 8, 3

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1

Sauer, P. V., Gu, Y., Liu, W. H., Mattiroli, F., Panne, D., Luger, K. & Churchill, M. E., 02 Nov 2018, In : Nucleic Acids Research. 46, 19, p. 9907-9917 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Modeling Human Digestive Diseases With CRISPR-Cas9-Modified Organoids

Fujii, M., Clevers, H. & Sato, T., 23 Nov 2018, In : Gastroenterology.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Modelling Cryptosporidium infection in human small intestinal and lung organoids

Heo, I., Dutta, D., Schaefer, D. A., Iakobachvili, N., Artegiani, B., Sachs, N., Boonekamp, K. E., Bowden, G., Hendrickx, A. P. A., Willems, R. J. L., Peters, P. J., Riggs, M. W., O'Connor, R. & Clevers, H., Jul 2018, In : Nature Microbiology. 3, 7, p. 814-823 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Modulation of the secretory pathway by amino-acid starvation

van Leeuwen, W., van der Krift, F. & Rabouille, C., 02 Jul 2018, In : Journal of Cell Biology. 217, 7, p. 2261-2271 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Molecules: Protein-Tyrosine Phosphatase Inhibitors

den Hertog, J. (Guest ed.), 2018, In : Molecules. Special Issue

Research output: Contribution to journal/periodicalSpecial issue (editorship)Scientific

MUSCLEMOTION: A Versatile Open Software Tool to Quantify Cardiomyocyte and Cardiac Muscle Contraction In Vitro and In Vivo

Sala, L., van Meer, B. J., Tertoolen, L. T., Bakkers, J., Bellin, M., Davis, R. P., Denning, C. N., Dieben, M. A., Eschenhagen, T., Giacomelli, E., Grandela, C., Hansen, A., Holman, E., Jongbloed, M. R., Kamel, S. M., Koopman, C. D., Lachaud, Q., Mannhardt, I., Mol, M. P., Mosqueira, D. & 7 others, Orlova, V. V., Passier, R., Ribeiro, M. C., Saleem, U., Smith, G., Burton, F. L. L. & Mummery, C. L., 02 Feb 2018, In : Circulation Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

Attardi, A., Fulton, T., Florescu, M., Shah, G., Muresan, L., Lenz, M. O., Lancaster, C., Huisken, J., van Oudenaarden, A. & Steventon, B., 09 Nov 2018, In : Development (Cambridge). 145, 21

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Notch ligand Dll1 mediates cross-talk between mammary stem cells and the macrophageal niche

Chakrabarti, R., Celià-Terrassa, T., Kumar, S., Hang, X., Wei, Y., Choudhury, A., Hwang, J., Peng, J., Nixon, B., Grady, J. J., DeCoste, C., Gao, J., van Es, J. H., Li, M. O., Aifantis, I., Clevers, H. & Kang, Y., 29 Jun 2018, In : Science. 360, 6396

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Optogenetic sensors in the zebrafish heart: a novel in vivo electrophysiological tool to study cardiac arrhythmogenesis

van Opbergen, C. J. M., Koopman, C. D., Kok, B. J. M., Knöpfel, T., Renninger, S. L., Orger, M. B., Vos, M. A., van Veen, T. A. B., Bakkers, J. & de Boer, T. P., 2018, In : Theranostics. 8, 17, p. 4750-4764 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer

Tiriac, H., Belleau, P., Engle, D. D., Plenker, D., Deschênes, A., Somerville, T. D. D., Froeling, F. E. M., Burkhart, R. A., Denroche, R. E., Jang, G-H., Miyabayashi, K., Young, C. M., Patel, H., Ma, M., LaComb, J. F., Palmaira, R. L. D., Javed, A. A., Huynh, J. C., Johnson, M., Arora, K. & 50 others, Robine, N., Shah, M., Sanghvi, R., Goetz, A. B., Lowder, C. Y., Martello, L., Driehuis, E., LeComte, N., Askan, G., Iacobuzio-Donahue, C. A., Clevers, H., Wood, L. D., Hruban, R. H., Thompson, E., Aguirre, A. J., Wolpin, B. M., Sasson, A., Kim, J., Wu, M., Bucobo, J. C., Allen, P., Sejpal, D. V., Nealon, W., Sullivan, J. D., Winter, J. M., Gimotty, P. A., Grem, J. L., DiMaio, D. J., Buscaglia, J. M., Grandgenett, P. M., Brody, J. R., Hollingsworth, M. A., O'Kane, G. M., Notta, F., Kim, E., Crawford, J. M., Devoe, C., Ocean, A., Wolfgang, C. L., Yu, K. H., Li, E., Vakoc, C. R., Hubert, B., Fischer, S. E., Wilson, J. M., Moffitt, R., Knox, J., Krasnitz, A., Gallinger, S. & Tuveson, D. A., Sep 2018, In : Cancer Discovery. 8, 9, p. 1112-1129 18 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Organoids in cancer research

Drost, J. & Clevers, H., Jul 2018, In : Nature reviews. Cancer. 18, 7, p. 407-418 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Origins and divergence of the eukaryotic kinetochore

van Hooff, J. J. E., 2018, Utrecht University.

Research output: PhD ThesisPhD thesis

Paneth Cells Respond to Inflammation and Contribute to Tissue Regeneration by Acquiring Stem-like Features through SCF/c-Kit Signaling

Schmitt, M., Schewe, M., Sacchetti, A., Feijtel, D., van de Geer, W. S., Teeuwssen, M., Sleddens, H. F., Joosten, R., van Royen, M. E., van de Werken, H. J. G., van Es, J., Clevers, H. & Fodde, R., 28 Aug 2018, In : Cell Reports. 24, 9, p. 2312-2328.e7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Vértesy, Á., Arindrarto, W., Roost, M. S., Reinius, B., Torrens-Juaneda, V., Bialecka, M., Moustakas, I., Ariyurek, Y., Kuijk, E., Mei, H., Sandberg, R., van Oudenaarden, A. & Chuva de Sousa Lopes, S. M., 14 May 2018, In : Nature Communications. 9, 1, p. 1873

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

Geeven, G., Teunissen, H., de Laat, W. & de Wit, E., 06 Sep 2018, In : Nucleic Acids Research. 46, 15, p. e91

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

PRMT6 Regulates RAS/RAF Binding and MEK/ERK-Mediated Cancer Stemness Activities in Hepatocellular Carcinoma through CRAF Methylation

Chan, L. H., Zhou, L., Ng, K. Y., Wong, T. L., Lee, T. K., Sharma, R., Loong, J. H., Ching, Y. P., Yuan, Y-F., Xie, D., Lo, C. M., Man, K., Artegiani, B., Clevers, H., Yan, H. H., Leung, S. Y., Richard, S., Guan, X-Y., Huen, M. S. Y. & Ma, S., 16 Oct 2018, In : Cell Reports. 25, 3, p. 690-701.e8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Profiling proliferative cells and their progeny in damaged murine hearts

Kretzschmar, K., Post, Y., Bannier-Hélaouët, M., Mattiotti, A., Drost, J., Basak, O., Li, V. S. W., van den Born, M., Gunst, Q. D., Versteeg, D., Kooijman, L., van der Elst, S., van Es, J. H., van Rooij, E., van den Hoff, M. J. B. & Clevers, H., 26 Dec 2018, In : Proceedings of the National Academy of Sciences of the United States of America.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
Open Access

Revealing the role of tumor heterogeneity and plasticity in breast cancer

Seinstra, D., 2018, Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access
Open Access

ROCKin' Intestinal Cell Fate: A Potential Avenue to Improve Glucose Sensitivity

Beumer, J. & Clevers, H., Oct 2018, In : Gastroenterology. 155, 4, p. 974-976 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

RVCL-S and CADASIL display distinct impaired vascular function

de Boer, I., Stam, A. H., Buntinx, L., Zielman, R., van der Steen, I., van den Maagdenberg, A. M. J. M., de Koning, E. J. P., Ferrari, M. D., de Hoon, J. N. & Terwindt, G. M., 04 Sep 2018, In : Neurology. 91, 10, p. e956-e963

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Shaping up with morphogen gradients

Garric, L. & Bakkers, J., Sep 2018, In : Nature Cell Biology. 20, 9, p. 998-999 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Wimmers, F., Subedi, N., van Buuringen, N., Heister, D., Vivié, J., Beeren-Reinieren, I., Woestenenk, R., Dolstra, H., Piruska, A., Jacobs, J. F. M., van Oudenaarden, A., Figdor, C. G., Huck, W. T. S., de Vries, I. J. M. & Tel, J., 20 Aug 2018, In : Nature Communications. 9, 1, p. 3317

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation

Gladka, M. M., Molenaar, B., de Ruiter, H., van der Elst, S., Tsui, H., Versteeg, D., Lacraz, G. P. A., Huibers, M. M. H., van Oudenaarden, A. & van Rooij, E., 10 Jul 2018, In : Circulation. 138, 2, p. 166-180 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Single-Cell Sequencing of the Mammalian Heart

Molenaar, B. & van Rooij, E., 12 Oct 2018, In : Circulation Research. 123, 9, p. 1033-1035 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Single-Cell Transcriptomics Meets Lineage Tracing

Kester, L. & van Oudenaarden, A., 02 Aug 2018, In : Cell Stem Cell. 23, 2, p. 166-179 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta

Baron, C. S., Kester, L., Klaus, A., Boisset, J-C., Thambyrajah, R., Yvernogeau, L., Kouskoff, V., Lacaud, G., van Oudenaarden, A. & Robin, C., 28 Jun 2018, In : Nature Communications. 9, 1, p. 2517

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion

McGough, I. J., de Groot, R. E. A., Jellett, A. P., Betist, M. C., Varandas, K. C., Danson, C. M., Heesom, K. J., Korswagen, H. C. & Cullen, P. J., 13 Sep 2018, In : Nature Communications. 9, 1, p. 3737

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Spatially resolved RNA-sequencing of the embryonic heart identifies a role for Wnt/β-catenin signaling in autonomic control of heart rate

Burkhard, S. B. & Bakkers, J., 05 Feb 2018, In : eLife. 7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

Ebbing, A., Vértesy, Á., Betist, M. C., Spanjaard, B., Junker, J. P., Berezikov, E., van Oudenaarden, A. & Korswagen, H. C., 17 Dec 2018, In : Developmental Cell. 47, 6, p. 801-813.e6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Stratifying infants with cystic fibrosis for disease severity using intestinal organoid swelling as a biomarker of CFTR function

de Winter-de Groot, K. M., Janssens, H. M., van Uum, R. T., Dekkers, J. F., Berkers, G., Vonk, A., Kruisselbrink, E., Oppelaar, H., Vries, R., Clevers, H., Houwen, R. H. J., Escher, J. C., Elias, S. G., de Jonge, H. R., de Rijke, Y. B., Tiddens, H. A. W. M., van der Ent, C. K. & Beekman, J. M., Sep 2018, In : European Respiratory Journal. 52, 3

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Studying cellular heterogeneity and drug sensitivity in colorectal cancer using organoid technology

Sasaki, N. & Clevers, H., Oct 2018, In : Current Opinion in Genetics & Development. 52, p. 117-122 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification

Roovers, E. F., Kaaij, L. J. T., Redl, S., Bronkhorst, A. W., Wiebrands, K., de Jesus Domingues, A. M., Huang, H-Y., Han, C-T., Riemer, S., Dosch, R., Salvenmoser, W., Grün, D., Butter, F., van Oudenaarden, A. & Ketting, R. F., 06 Aug 2018, In : Developmental Cell. 46, 3, p. 285-301.e9

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Temporal precision of regulated gene expression

Gupta, S., Varennes, J., Korswagen, H. C. & Mugler, A., Jun 2018, In : PLoS Computational Biology. 14, 6, p. e1006201

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The Majority of CD45 Ter119 CD31 Bone Marrow Cell Fraction Is of Hematopoietic Origin and Contains Erythroid and Lymphoid Progenitors

Boulais, P. E., Mizoguchi, T., Zimmerman, S., Nakahara, F., Vivié, J., Mar, J. C., van Oudenaarden, A. & Frenette, P. S., 16 Oct 2018, In : Immunity. 49, 4, p. 627-639.e6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The Myofibroblasts' War on Drugs

Puschhof, J. & Clevers, H., 24 Sep 2018, In : Developmental Cell. 46, 6, p. 669-670 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The planar cell polarity protein VANG-1/Vangl negatively regulates Wnt/β-catenin signaling through a Dvl dependent mechanism

Mentink, R. A., Rella, L., Radaszkiewicz, T. W., Gybel, T., Betist, M. C., Bryja, V. & Korswagen, H. C., Dec 2018, In : PLoS Genetics. 14, 12, p. e1007840

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The single-cell transcriptional landscape of hematopoiesis

Baron, C., 17 May 2018, Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access

TMEM59 potentiates Wnt signaling by promoting signalosome formation

Gerlach, J. P., Jordens, I., Tauriello, D. V. F., van 't Land-Kuper, I., Bugter, J. M., Noordstra, I., van der Kooij, J., Low, T. Y., Pimentel-Muiños, F. X., Xanthakis, D., Fenderico, N., Rabouille, C., Heck, A. J. R., Egan, D. A. & Maurice, M. M., 24 Apr 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 17, p. E3996-E4005

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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