• Netherlands

  • Netherlands

Research Output

2016

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

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramanan, V., Trehan, K., Ong, M-L., Luna, J. M., Hoffmann, H-H., Espiritu, C., Sheahan, T. P., Chandrasekar, H., Schwartz, R. E., Christine, K. S., Rice, C. M., van Oudenaarden, A. & Bhatia, S. N., Jul 2016, In : Virology. 494, p. 236-47 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Visualization of a short-range Wnt gradient in the intestinal stem-cell niche

Farin, H. F., Jordens, I., Mosa, M. H., Basak, O., Korving, J., Tauriello, D. V. F., de Punder, K., Angers, S., Peters, P. J., Maurice, M. M. & Clevers, H., 18 Feb 2016, In : Nature. 530, 7590, p. 340-3 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Who Is in the Driver's Seat: Tracing Cancer Genes Using CRISPR-Barcoding

Drost, J. & Clevers, H., 04 Aug 2016, In : Molecular Cell. 63, 3, p. 352-4 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

αE-catenin-dependent mechanotransduction is essential for proper convergent extension in zebrafish

Han, M. K. L., Hoijman, E., Nöel, E., Garric, L., Bakkers, J. & de Rooij, J., 2016, In : Biology Open. 5, 10, p. 1461-1472 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
2015

A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary

Soh, Y. Q. S., Junker, J. P., Gill, M. E., Mueller, J. L., van Oudenaarden, A. & Page, D. C., Sep 2015, In : PLoS Genetics. 11, 9, p. e1005531

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A Long-Distance Chromatin Affair

Denker, A. & de Laat, W., 27 Aug 2015, In : Cell. 162, 5, p. 942-3 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers, P. B., Nonnekens, J., Goos, Y. J., Betist, M. C., Viester, M. D., Mossink, B., Lansu, N., Korswagen, H. C., Jelier, R., Brenkman, A. B. & MacInnes, A. W., 13 Jan 2015, In : Cell Reports.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

An EphB-Abl signaling pathway is associated with intestinal tumor initiation and growth

Kundu, P., Genander, M., Strååt, K., Classon, J., Ridgway, R. A., Tan, E. H., Björk, J., Martling, A., van Es, J., Sansom, O. J., Clevers, H., Pettersson, S. & Frisén, J., 01 Apr 2015, In : Science Translational Medicine. 7, 281, p. 281ra44

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Animal and in silico models for the study of sarcomeric cardiomyopathies

Duncker, D. J., Bakkers, J., Brundel, B. J., Robbins, J., Tardiff, J. C. & Carrier, L., 01 Apr 2015, In : Cardiovascular Research. 105, 4, p. 439-448 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

An inducible mouse model for microvillus inclusion disease reveals a role for myosin Vb in apical and basolateral trafficking

Schneeberger, K., Vogel, G. F., Teunissen, H., van Ommen, D. D., Begthel, H., El Bouazzaoui, L., van Vugt, A. H. M., Beekman, J. M., Klumperman, J., Müller, T., Janecke, A., Gerner, P., Huber, L. A., Hess, M. W., Clevers, H., van Es, J. H., Nieuwenhuis, E. E. S. & Middendorp, S., 06 Oct 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 40, p. 12408-13 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A novel Dock8 gene mutation confers diabetogenic susceptibility in the LEW.1AR1/Ztm-iddm rat, an animal model of human type 1 diabetes

Arndt, T., Wedekind, D., Jörns, A., Tsiavaliaris, G., Cuppen, E., Hedrich, H-J. & Lenzen, S., Dec 2015, In : Diabetologia. 58, 12, p. 2800-9 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

AntimiR-34a to Enhance Cardiac Repair After Ischemic Injury

Gladka, M. M. & van Rooij, E., 14 Aug 2015, In : Circulation Research. 117, 5, p. 395-7 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer

Dow, L. E., O'Rourke, K. P., Simon, J., Tschaharganeh, D. F., van Es, J. H., Clevers, H. & Lowe, S. W., 18 Jun 2015, In : Cell. 161, 7, p. 1539-52 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A. R. R., Carninci, P., Hayashizaki, Y., Daub, C. O., Okada-Hatakeyama, M. & Mar, J. C., 2015, In : PLoS One. 10, 12, p. e0144176

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Architectural hallmarks of the pluripotent genome

Bouwman, B. A. M. & de Laat, W., 07 May 2015, In : FEBS Letters.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts

Schuijers, J., Junker, J. P., Mokry, M., Hatzis, P., Koo, B-K., Sasselli, V., van der Flier, L. G., Cuppen, E., van Oudenaarden, A. & Clevers, H., 05 Feb 2015, In : Cell Stem Cell. 16, 2, p. 158-70 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
Open Access

Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression

van Zon, J. S., Kienle, S., Huelsz-Prince, G., Barkoulas, M. & van Oudenaarden, A., 2015, In : Nature Communications. 6, p. 7053

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Characterization and dynamics of pericentromere-associated domains in mice

Wijchers, P. J., Geeven, G., Eyres, M., Bergsma, A. J., Janssen, M., Verstegen, M., Zhu, Y., Schell, Y., Vermeulen, C., de Wit, E. & de Laat, W., 16 Apr 2015, In : Genome Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Chromatin conformation capture strategies in molecular diagnostics

de Vree, P. J. P., 09 Jul 2015, Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access

Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring

de Pagter, M. S., van Roosmalen, M. J., Baas, A. F., Renkens, I., Duran, K. J., van Binsbergen, E., Tavakoli-Yaraki, M., Hochstenbach, R., van der Veken, L. T., Cuppen, E. & Kloosterman, W. P., 02 Apr 2015, In : American Journal of Human Genetics. 96, 4, p. 651-6 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cloning-free CRISPR

Arbab, M., Srinivasan, S., Hashimoto, T., Geijsen, N. & Sherwood, R. I., 27 Oct 2015, In : Stem Cell Reports.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Controlled aggregation of primary human pancreatic islet cells leads to glucose-responsive pseudoislets comparable to native islets

Hilderink, J., Spijker, S., Carlotti, F., Lange, L., Engelse, M., van Blitterswijk, C., de Koning, E., Karperien, M. & van Apeldoorn, A., 17 Mar 2015, In : Journal of Cellular and Molecular Medicine.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Controlling the diversity of cell populations in a stem cell culture

Heo, I. & Clevers, H., 14 Jul 2015, In : Cell Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome

Letourneau, A., Santoni, F. A., Bonilla, X., Reza Sailani, M., Gonzalez, D., Kind, J., Chevalier, C., Thurman, R., Sandstrom, R. S., Hibaoui, Y., Garieri, M., Popadin, K., Falconnet, E., Gagnebin, M., Gehrig, C., Vannier, A., Guipponi, M., Farinelli, L., Robyr, D., Migliavacca, E. & 8 others, Borel, C., Deutsch, S., Feki, A., Stamatoyannopoulos, J. A., Herault, Y., van Steensel, B., Guigo, R. & Antonarakis, S. E., 02 Dec 2015, In : Nature.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

CTCF Binding Polarity Determines Chromatin Looping

de Wit, E., Vos, E. S. M., Holwerda, S. J. B., Valdes-Quezada, C., Verstegen, M. J. A. M., Teunissen, H., Splinter, E., Wijchers, P. J., Krijger, P. H. L. & de Laat, W., 27 Oct 2015, In : Molecular Cell.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

DAMP production by human islets under low oxygen and nutrients in the presence or absence of an immunoisolating-capsule and necrostatin-1

Paredes-Juarez, G. A., Sahasrabudhe, N. M., Tjoelker, R. S., de Haan, B. J., Engelse, M. A., de Koning, E. J. P., Faas, M. M. & de Vos, P., 2015, In : Scientific Reports. 5, p. 14623

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Datasets from an interaction proteomics screen for substrates of the SCF(βTrCP) ubiquitin ligase

Magliozzi, R., Peng, M., Mohammed, S., Guardavaccaro, D., Heck, A. J. R. & Low, T. Y., Sep 2015, In : Data in Brief. 4, p. 229-34 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

DAZL regulates Tet1 translation in murine embryonic stem cells

Welling, M., Chen, H-H., Muñoz, J., Musheev, M. U., Kester, L., Junker, J. P., Mischerikow, N., Arbab, M., Kuijk, E., Silberstein, L., Kharchenko, P. V., Geens, M., Niehrs, C., van de Velde, H., van Oudenaarden, A., Heck, A. J. & Geijsen, N., Jul 2015, In : EMBO Reports. 16, 7, p. 791-802 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Deficiency or inhibition of lysophosphatidic acid receptor 1 protects against hyperoxia-induced lung injury in neonatal rats

Chen, X., Walther, F. J., van Boxtel, R., Laghmani, E. H., Sengers, R. M. A., Folkerts, G., DeRuiter, M. C., Cuppen, E. & Wagenaar, G. T. M., 23 Oct 2015, In : Acta Physiologica (Oxford, England).

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Design and Analysis of Single-Cell Sequencing Experiments

Grün, D. & van Oudenaarden, A., 05 Nov 2015, In : Cell. 163, 4, p. 799-810 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Detailed imaging and genetic analysis reveal a secondary BRAF(L) (505H) resistance mutation and extensive intrapatient heterogeneity in metastatic BRAF mutant melanoma patients treated with vemurafenib

Hoogstraat, M., Gadellaa-van Hooijdonk, C. G., Ubink, I., Besselink, N. J. M., Pieterse, M., Veldhuis, W., van Stralen, M., Meijer, E. F. J., Willems, S. M., Hadders, M. A., Kuilman, T., Krijgsman, O., Peeper, D. S., Koudijs, M. J., Cuppen, E., Voest, E. E. & Lolkema, M. P., May 2015, In : Pigment Cell & Melanoma Research. 28, 3, p. 318-23 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Developmental Alterations in Heart Biomechanics and Skeletal Muscle Function in Desmin Mutants Suggest an Early Pathological Root for Desminopathies

Ramspacher, C., Steed, E., Boselli, F., Ferreira, R., Faggianelli, N., Roth, S., Spiegelhalter, C., Messaddeq, N., Trinh, L., Liebling, M., Chacko, N., Tessadori, F., Bakkers, J., Laporte, J., Hnia, K. & Vermot, J., 16 Jun 2015, In : Cell Reports. 11, 10, p. 1564-76 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Development and application of human adult stem or progenitor cell organoids

Rookmaaker, M. B., Schutgens, F., Verhaar, M. C. & Clevers, H., Sep 2015, In : Nature Reviews Nephrology. 11, 9, p. 546-54 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Development and trafficking function of haematopoietic stem cells and myeloid cells during fetal ontogeny

Heinig, K., Sage, F., Robin, C. & Sperandio, M., 17 May 2015, In : Cardiovascular Research.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Differential Stoichiometry among Core Ribosomal Proteins

Slavov, N., Semrau, S., Airoldi, E., Budnik, B. & van Oudenaarden, A., 03 Nov 2015, In : Cell Reports. 13, 5, p. 865-73 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Discovery of molecular markers to discriminate corneal endothelial cells in the human body

Yoshihara, M., Ohmiya, H., Hara, S., Kawasaki, S., Hayashizaki, Y., Itoh, M., Kawaji, H., Tsujikawa, M. & Nishida, K., 2015, In : PLoS One. 10, 3, p. e0117581

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Disease Modeling and Gene Therapy of Copper Storage Disease in Canine Hepatic Organoids

Nantasanti, S., Spee, B., Kruitwagen, H. S., Chen, C., Geijsen, N., Oosterhoff, L. A., van Wolferen, M. E., Pelaez, N., Fieten, H., Wubbolts, R. W., Grinwis, G. C., Chan, J., Huch, M., Vries, R. R. G., Clevers, H., de Bruin, A., Rothuizen, J., Penning, L. C. & Schotanus, B. A., 06 Oct 2015, In : Stem Cell Reports.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

DNA Methylation Landscapes of Human Fetal Development

Slieker, R. C., Roost, M. S., van Iperen, L., Suchiman, H. E. D., Tobi, E. W., Carlotti, F., de Koning, E. J. P., Slagboom, P. E., Heijmans, B. T. & Chuva de Sousa Lopes, S. M., Oct 2015, In : PLoS Genetics. 11, 10, p. e1005583

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

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., 2015, In : Genome Biology. 16, 1, p. 149

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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Dynamics of Lgr6(+) Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis

Füllgrabe, A., Joost, S., Are, A., Jacob, T., Sivan, U., Haegebarth, A., Linnarsson, S., Simons, B. D., Clevers, H., Toftgård, R. & Kasper, M., 21 Oct 2015, In : Stem Cell Reports.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Effective Therapeutic Intervention and Comprehensive Genetic Analysis of mTOR Signaling in PEComa: A Case Report

Weeber, F., Koudijs, M. J., Hoogstraat, M., Besselink, N. J. M., VAN Lieshout, S., Nijman, I. J., Cuppen, E., Offerhaus, G. J. & Voest, E. E., Jun 2015, In : Nature Biotechnology. 35, 6, p. 3399-403 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Efficient cryopreservation of human pluripotent stem cells by surface-based vitrification

Neubauer, J. C., Beier, A. F., Geijsen, N. & Zimmermann, H., 2015, In : Methods in Molecular Biology. 1257, p. 321-8 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Efficient intracellular delivery of native proteins

D'Astolfo, D. S., Pagliero, R. J., Pras, A., Karthaus, W. R., Clevers, H., Prasad, V., Lebbink, R. J., Rehmann, H. & Geijsen, N., 23 Apr 2015, In : Cell. 161, 3, p. 674-90 17 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Erfelijke ouderdomsdiabetes bij jongeren

Translated title of the contribution: Maturity-onset diabetes of the youngvan der Tuin, K., Hannema, S. E., Houdijk, E. C. A. M. M., Losekoot, M., de Koning, E. J. P. & Breuning, M. H., 2015, In : Nederlands Tijdschrift voor Geneeskunde. 159, p. A9247

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Exosomal microRNA clusters are important for the therapeutic effect of cardiac progenitor cells

Sluijter, J. P. G. & van Rooij, E., 16 Jan 2015, In : Circulation Research. 116, 2, p. 219-21 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Factors shaping the 3D genome

Zhu, Y., 07 Jul 2015, Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access

F-box proteins, cell cycle and cancer

Kim, J., 13 Jan 2015, utrecht: Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access

Frizzled7 functions as a wnt receptor in intestinal epithelial lgr5(+) stem cells

Flanagan, D. J., Phesse, T. J., Barker, N., Schwab, R. H. M., Amin, N., Malaterre, J., Stange, D. E., Nowell, C. J., Currie, S. A., Saw, J. T. S., Beuchert, E., Ramsay, R. G., Sansom, O. J., Ernst, M., Clevers, H. & Vincan, E., 12 May 2015, In : Stem Cell Reports. 4, 5, p. 759-67 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access