• Netherlands

  • Netherlands

Research Output

2015

Rat genome variation and complex traits

Hermsen, R. M. T., 21 Jan 2015, Utrecht University.

Research output: PhD ThesisPhD thesis

Open Access

Rat genome variation and complex traits

Hermsen, R. M. T., 21 Jan 2015, Utrecht University.

Research output: PhD ThesisPhD thesis

Rb and FZR1/Cdh1 determine CDK4/6-cyclin D requirement in C. elegans and human cancer cells

The, I., Ruijtenberg, S., Bouchet, B. P., Cristobal, A., Prinsen, M. B. W., van Mourik, T., Koreth, J., Xu, H., Heck, A. J. R., Akhmanova, A., Cuppen, E., Boxem, M., Muñoz, J. & van den Heuvel, S., 2015, In : Nature Communications. 6, p. 5906

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Recurrent Mutations in the Basic Domain of TWIST2 Cause Ablepharon Macrostomia and Barber-Say Syndromes

Marchegiani, S., Davis, T., Tessadori, F., van Haaften, G., Brancati, F., Hoischen, A., Huang, H., Valkanas, E., Pusey, B., Schanze, D., Venselaar, H., Vulto-van Silfhout, A. T., Wolfe, L. A., Tifft, C. J., Zerfas, P. M., Zambruno, G., Kariminejad, A., Sabbagh-Kermani, F., Lee, J., Tsokos, M. G. & 27 others, Lee, C-C. R., Ferraz, V., da Silva, E. M., Stevens, C. A., Roche, N., Bartsch, O., Farndon, P., Bermejo-Sanchez, E., Brooks, B. P., Maduro, V., Dallapiccola, B., Ramos, F. J., Chung, H-Y. B., Le Caignec, C., Martins, F., Jacyk, W. K., Mazzanti, L., Brunner, H. G., Bakkers, J., Lin, S., Malicdan, M. C. V., Boerkoel, C. F., Gahl, W. A., de Vries, B. B. A., van Haelst, M. M., Zenker, M. & Markello, T. C., 02 Jul 2015, In : American Journal of Human Genetics. 97, 1, p. 99-110 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Repairing organs: lessons from intestine and liver

Gehart, H. & Clevers, H., 16 May 2015, In : Trends in Genetics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Sambamba: fast processing of NGS alignment formats

Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P., 19 Feb 2015, In : Bioinformatics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

SEC16 in COPII coat dynamics at ER exit sites

Sprangers, J. & Rabouille, C., Feb 2015, In : Biochemical Society Transactions. 43, 1, p. 97-103 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Sequential cancer mutations in cultured human intestinal stem cells

Drost, J., van Jaarsveld, R. H., Ponsioen, B., Zimberlin, C., van Boxtel, R., Buijs, A., Sachs, N., Overmeer, R. M., Offerhaus, G. J., Begthel, H., Korving, J., van de Wetering, M., Schwank, G., Logtenberg, M., Cuppen, E., Snippert, H. J., Medema, J. P., Kops, G. J. P. L. & Clevers, H., 07 May 2015, In : Nature. 521, 7550, p. 43-7 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Simultaneous detection of clinically relevant mutations and amplifications for routine cancer pathology

Hoogstraat, M., Hinrichs, J. W. J., Besselink, N. J. M., Radersma-van Loon, J. H., de Voijs, C. M. A., Peeters, T., Nijman, I. J., de Weger, R. A., Voest, E. E., Willems, S. M., Cuppen, E. & Koudijs, M. J., Jan 2015, In : Journal of Molecular Diagnostics. 17, 1, p. 10-8 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Grün, D., Lyubimova, A., Kester, L., Wiebrands, K., Basak, O., Sasaki, N., Clevers, H. & van Oudenaarden, A., 19 Aug 2015, In : Nature.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Single-cell transcriptomics enters the age of mass production

Junker, J. P. & van Oudenaarden, A., 21 May 2015, In : Molecular Cell. 58, 4, p. 563-4 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Slamf receptors: Modulators of Phagocyte Immune Responses

Van Driel, B. J., 2015, Utrecht University. 120 p.

Research output: PhD ThesisPhD thesis

Open Access

SnapShot: Growing Organoids from Stem Cells

Sato, T. & Clevers, H., 18 Jun 2015, In : Cell. 161, 7, p. 1700-1700.e1

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Spatially resolved transcriptomics and beyond

Crosetto, N., Bienko, M. & van Oudenaarden, A., Jan 2015, In : Nature Reviews Genetics. 16, 1, p. 57-66 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

STEM CELLS. What is an adult stem cell?

Clevers, H., 11 Dec 2015, In : Science Magazine. 350, 6266, p. 1319-20 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Structure-guided design of selective Epac1 and Epac2 agonists

Schwede, F., Bertinetti, D., Langerijs, C. N., Hadders, M. A., Wienk, H., Ellenbroek, J. H., de Koning, E. J. P., Bos, J. L., Herberg, F. W., Genieser, H-G., Janssen, R. A. J. & Rehmann, H., Jan 2015, In : PLoS Biology. 13, 1, p. e1002038

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools

Semrau, S. & van Oudenaarden, A., 13 Nov 2015, In : Annual Review of Cell and Developmental Biology. 31, p. 317-45 29 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Targeting development of incretin-producing cells increases insulin secretion

Petersen, N., Reimann, F., van Es, J. H., van den Berg, B. M., Kroone, C., Pais, R., Jansen, E., Clevers, H., Gribble, F. M. & de Koning, E. J. P., Jan 2015, In : Journal of Clinical Investigation. 125, 1, p. 379-85 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R. & Huminiecki, L., Dec 2015, In : PLoS Biology. 13, 12, p. e1002315

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The gut microbiota keeps enteric glial cells on the move; prospective roles of the gut epithelium and immune system

Kabouridis, P. S., Lasrado, R., McCallum, S., Chng, S. H., Snippert, H. J., Clevers, H., Pettersson, S. & Pachnis, V., 02 Nov 2015, In : Gut Microbes. 6, 6, p. 398-403 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, C., Forrest, A. R. R. & Wagner, G. P., 2015, In : Nature Communications. 6, p. 6066

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

The von Hippel-Lindau tumor suppressor regulates programmed cell death 5-mediated degradation of Mdm2

Essers, P. B., Klasson, T. D., Pereboom, T. C., Mans, D. A., Nicastro, M., Boldt, K., Giles, R. H. & MacInnes, A. W., 05 Feb 2015, In : Oncogene. 34, 6, p. 771-9 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Thirty Years of Pancreas Transplantation at Leiden University Medical Center: Long-Term Follow-Up in a Large Eurotransplant Center

Kopp, W. H., Verhagen, M. J. J., Blok, J. J., Huurman, V. A. L., de Fijter, J. W., de Koning, E. J., Putter, H., Baranski, A. G., Schaapherder, A. F. M., Braat, A. E. & Ringers, J., 20 Feb 2015, In : Cell Transplantation.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

TORC2 mediates the heat stress response in Drosophila by promoting the formation of stress granules

Jevtov, I., Zacharogianni, M., van Oorschot, M. M., van Zadelhoff, G., Aguilera-Gomez, A., Vuillez, I., Braakman, I., Hafen, E., Stocker, H. & Rabouille, C., 15 Jul 2015, In : Journal of Cell Science. 128, 14, p. 2497-508 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Toward effective software solutions for big biology

Prins, P., de Ligt, J., Tarasov, A., Jansen, R. C., Cuppen, E. & Bourne, P. E., Jul 2015, In : Nature Biotechnology. 33, 7, p. 686-7 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Towards personalized therapy in pediatric acute lymphoblastic leukemia: RAS mutations and prednisolone resistance

Ariës, I. M., van den Dungen, R. E., Koudijs, M. J., Cuppen, E., Voest, E., Molenaar, J. J., Caron, H. N., Pieters, R. & den Boer, M. L., Apr 2015, In : Haematologica. 100, 4, p. e132-6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Austenaa, L. M. I., Barozzi, I., Simonatto, M., Masella, S., Della Chiara, G., Ghisletti, S., Curina, A., de Wit, E., Bouwman, B. A. M., de Pretis, S., Piccolo, V., Termanini, A., Prosperini, E., Pelizzola, M., de Laat, W. & Natoli, G., 05 Nov 2015, In : Molecular Cell. 60, 3, p. 460-74 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Translational regulation shapes the molecular landscape of complex disease phenotypes

Schafer, S., Adami, E., Heinig, M., Rodrigues, K. E. C., Kreuchwig, F., Silhavy, J., van Heesch, S., Simaite, D., Rajewsky, N., Cuppen, E., Pravenec, M., Vingron, M., Cook, S. A. & Hubner, N., 2015, In : Nature Communications. 6, p. 7200

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Unraveling the mechano-responsive mechanisms at Focal Adherens Junctions

Oldenburg, J., 2015, Utrecht University. 145 p.

Research output: PhD ThesisPhD thesis

Open Access

Utilization of organs from donors after circulatory death for vascularized pancreas and islet of Langerhans transplantation: recommendations from an expert group

Berney, T., Boffa, C., Augustine, T., Badet, L., de Koning, E., Pratschke, J., Socci, C. & Friend, P., 04 Sep 2015, In : Transplant international : official journal of the European Society for Organ Transplantation.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers

Galli, G. G., Carrara, M., Yuan, W-C., Valdes-Quezada, C., Gurung, B., Pepe-Mooney, B., Zhang, T., Geeven, G., Gray, N. S., de Laat, W., Calogero, R. A. & Camargo, F. D., 15 Oct 2015, In : Molecular Cell. 60, 2, p. 328-37 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

2014

A20 controls intestinal homeostasis through cell-specific activities

Vereecke, L., Vieira-Silva, S., Billiet, T., van Es, J. H., Mc Guire, C., Slowicka, K., Sze, M., van den Born, M., De Hertogh, G., Clevers, H., Raes, J., Rutgeerts, P., Vermeire, S., Beyaert, R. & van Loo, G., 2014, In : Nature Communications. 5, p. 5103

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A bone to pick with zebrafish: chemistry and genetics of osteogenesis

Mackay, E., 25 Nov 2014, Utrecht: Utrecht University. 128 p.

Research output: PhD ThesisPhD thesis

A common genetic variant within SCN10A modulates cardiac SCN5A expression

van den Boogaard, M., Smemo, S., Burnicka-Turek, O., Arnolds, D. E., van de Werken, H. J. G., Klous, P., McKean, D., Muehlschlegel, J. D., Moosmann, J., Toka, O., Yang, X. H., Koopmann, T. T., Adriaens, M. E., Bezzina, C. R., de Laat, W., Seidman, C., Seidman, J. G., Christoffels, V. M., Nobrega, M. A., Barnett, P. & 1 others, Moskowitz, I. P., 01 Apr 2014, In : Journal of Clinical Investigation. 124, 4, p. 1844-52 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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A comparative study of nucleostemin family members in zebrafish reveals specific roles in ribosome biogenesis

Essers, P. B., Pereboom, T. C., Goos, Y. J., Paridaen, J. T. & Macinnes, A. W., 15 Jan 2014, In : Developmental Biology. 385, 2, p. 304-15 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Adult stem cells in the small intestine are intrinsically programmed with their location-specific function

Middendorp, S., Schneeberger, K., Wiegerinck, C. L., Mokry, M., Akkerman, R. D. L., van Wijngaarden, S., Clevers, H. & Nieuwenhuis, E. E. S., May 2014, In : Stem Cells. 32, 5, p. 1083-91 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A fisheye view on lymphangiogenesis

van Impel, A. & Schulte-Merker, S., 2014, In : Advances in anatomy, embryology, and cell biology. 214, p. 153-65 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A large permissive regulatory domain exclusively controls Tbx3 expression in the cardiac conduction system

van Weerd, J. H., Badi, I., van den Boogaard, M., Stefanovic, S., van de Werken, H. J. G., Gomez-Velazquez, M., Badia-Careaga, C., Manzanares, M., de Laat, W., Barnett, P. & Christoffels, V. M., 01 Aug 2014, In : Circulation Research. 115, 4, p. 432-41 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

An atlas of active enhancers across human cell types and tissues

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O. & 29 others, Jørgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Müller, F., Forrest, A. R. R., Carninci, P. & Rehli, M., 27 Mar 2014, In : Nature. 507, 7493, p. 455-61 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning

Junker, J. P., Peterson, K. A., Nishi, Y., Mao, J., McMahon, A. P. & van Oudenaarden, A., 24 Nov 2014, In : Developmental Cell. 31, 4, p. 448-60 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A promoter-level mammalian expression atlas

Forrest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J. L., Haberle, V., Lassman, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U. & 30 others, Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Clevers, H. C. & Mummery, C. L., 27 Mar 2014, In : Nature. 507, 7493, p. 462-70 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia

Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., Rombouts, E. J., van Duin, M., Döhner, K., Beverloo, H. B., Bradner, J. E., Döhner, H., Löwenberg, B., Valk, P. J. M., Bindels, E. M. J., de Laat, W. & 1 others, Delwel, R., 10 Apr 2014, In : Cell. 157, 2, p. 369-81 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A stress assembly that confers cell viability by preserving ERES components during amino-acid starvation

Zacharogianni, M., Gomez, A. A., Veenendaal, T., Smout, J. & Rabouille, C., 2014, In : eLife. 3

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A systems-wide screen identifies substrates of the SCFβTrCP ubiquitin ligase

Low, T. Y., Peng, M., Magliozzi, R., Mohammed, S., Guardavaccaro, D. & Heck, A. J. R., 16 Dec 2014, In : Science Signaling. 7, 356, p. rs8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A unified nomenclature and amino acid numbering for human PTEN

Pulido, R., Baker, S. J., Barata, J. T., Carracedo, A., Cid, V. J., Chin-Sang, I. D., Davé, V., den Hertog, J., Devreotes, P., Eickholt, B. J., Eng, C., Furnari, F. B., Georgescu, M-M., Gericke, A., Hopkins, B., Jiang, X., Lee, S-R., Lösche, M., Malaney, P., Matias-Guiu, X. & 19 others, Molina, M., Pandolfi, P. P., Parsons, R., Pinton, P., Rivas, C., Rocha, R. M., Rodríguez, M. S., Ross, A. H., Serrano, M., Stambolic, V., Stiles, B., Suzuki, A., Tan, S-S., Tonks, N. K., Trotman, L. C., Wolff, N., Woscholski, R., Wu, H. & Leslie, N. R., 01 Jul 2014, In : Science Signaling. 7, 332, p. pe15

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A versatile spectrophotometric protein tyrosine phosphatase assay based on 3-nitrophosphotyrosine containing substrates

van Ameijde, J., Overvoorde, J., Knapp, S., den Hertog, J., Ruijtenbeek, R. & Liskamp, R. M. J., 01 Mar 2014, In : Analytical Biochemistry. 448, p. 9-13 5 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Biased competition between Lgr5 intestinal stem cells driven by oncogenic mutation induces clonal expansion

Snippert, H. J., Schepers, A. G., van Es, J. H., Simons, B. D. & Clevers, H., Jan 2014, In : EMBO Reports. 15, 1, p. 62-9 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Ccbe1 regulates Vegfc-mediated induction of Vegfr3 signaling during embryonic lymphangiogenesis

Le Guen, L., Karpanen, T., Schulte, D., Harris, N. C., Koltowska, K., Roukens, G., Bower, N. I., van Impel, A., Stacker, S. A., Achen, M. G., Schulte-Merker, S. & Hogan, B. M., Mar 2014, In : Development. 141, 6, p. 1239-49 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A. R. R. & Suzuki, H., 2014, In : Scientific Reports. 4, p. 5228

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cell intrinsic modulation of Wnt signaling controls neuroblast migration in C. elegans

Mentink, R. A., Middelkoop, T. C., Rella, L., Ji, N., Tang, C. Y., Betist, M. C., van Oudenaarden, A. & Korswagen, H. C., 27 Oct 2014, In : Developmental Cell. 31, 2, p. 188-201 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review