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2020

Alcohol-derived DNA crosslinks are repaired by two distinct mechanisms

Hodskinson, M. R., Bolner, A., Sato, K., Kamimae-Lanning, A. N., Rooijers, K., Witte, M., Mahesh, M., Silhan, J., Petek, M., Williams, D. M., Kind, J., Chin, J. W., Patel, K. J. & Knipscheer, P., Mar 2020, In : Nature. 579, 7800, p. 603-608 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity

Calandrini, C., Schutgens, F., Oka, R., Margaritis, T., Candelli, T., Mathijsen, L., Ammerlaan, C., van Ineveld, R. L., Derakhshan, S., de Haan, S., Dolman, E., Lijnzaad, P., Custers, L., Begthel, H., Kerstens, H. H. D., Visser, L. L., Rookmaaker, M., Verhaar, M., Tytgat, G. A. M., Kemmeren, P. & 11 others, de Krijger, R. R., Al-Saadi, R., Pritchard-Jones, K., Kool, M., Rios, A. C., van den Heuvel-Eibrink, M. M., Molenaar, J. J., van Boxtel, R., Holstege, F. C. P., Clevers, H. & Drost, J., 11 Mar 2020, In : Nature Communications. 11, 1, p. 1310

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Degree and site of chromosomal instability define its oncogenic potential

Hoevenaar, W. H. M., Janssen, A., Quirindongo, A. I., Ma, H., Klaasen, S. J., Teixeira, A., van Gerwen, B., Lansu, N., Morsink, F. H. M., Offerhaus, G. J. A., Medema, R. H., Kops, G. J. P. L. & Jelluma, N., 20 Mar 2020, In : Nature Communications. 11, 1, p. 1501

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR-Cas9 precision genome editing

Artegiani, B., Hendriks, D., Beumer, J., Kok, R., Zheng, X., Joore, I., Chuva de Sousa Lopes, S., van Zon, J., Tans, S. & Clevers, H., Mar 2020, In : Nature Cell Biology. 22, 3, p. 321-331 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance

Ringel, T., Frey, N., Ringnalda, F., Janjuha, S., Cherkaoui, S., Butz, S., Srivatsa, S., Pirkl, M., Russo, G., Villiger, L., Rogler, G., Clevers, H., Beerenwinkel, N., Zamboni, N., Baubec, T. & Schwank, G., 05 Mar 2020, In : Cell Stem Cell. 26, 3, p. 431-440.e8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients

Castelijns, B., Baak, M. L., Timpanaro, I. S., Wiggers, C. R. M., Vermunt, M. W., Shang, P., Kondova, I., Geeven, G., Bianchi, V., de Laat, W., Geijsen, N. & Creyghton, M. P., 16 Jan 2020, In : Nature Communications. 11, 1, p. 301

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

HSF2BP negatively regulates homologous recombination in DNA interstrand crosslink repair

Sato, K., Brandsma, I., van Rossum-Fikkert, S. E., Verkaik, N., Oostra, A. B., Dorsman, J. C., van Gent, D. C., Knipscheer, P., Kanaar, R. & Zelensky, A. N., 18 Mar 2020, In : Nucleic Acids Research. 48, 5, p. 2442-2456 15 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

L-Cell Differentiation Is Induced by Bile Acids Through GPBAR1 and Paracrine GLP-1 and Serotonin Signaling

Lund, M. L., Sorrentino, G., Egerod, K. L., Kroone, C., Mortensen, B., Knop, F. K., Reimann, F., Gribble, F. M., Drucker, D. J., de Koning, E. J. P., Schoonjans, K., Bäckhed, F., Schwartz, T. W. & Petersen, N., Apr 2020, In : Diabetes. 69, 4, p. 614-623 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

LKB1 Represses ATOH1 via PDK4 and Energy Metabolism and Regulates Intestinal Stem Cell Fate

Gao, Y., Yan, Y., Tripathi, S., Pentinmikko, N., Amaral, A., Päivinen, P., Domènech-Moreno, E., Andersson, S., Wong, I. P. L., Clevers, H., Katajisto, P. & Mäkelä, T. P., Apr 2020, In : Gastroenterology. 158, 5, p. 1389-1401.e10

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Long-Term Expansion of Pancreatic Islet Organoids from Resident Procr+ Progenitors

Wang, D., Wang, J., Bai, L., Pan, H., Feng, H., Clevers, H. & Zeng, Y. A., 19 Mar 2020, In : Cell. 180, 6, p. 1198-1211.e19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

Vermeulen, C., Allahyar, A., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., Valdes-Quezada, C., Renkens, I., Straver, R., Kloosterman, W. P., de Ridder, J. & de Laat, W., Feb 2020, In : Nature Protocols. 15, 2, p. 364-397 34 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Organoid cultures from normal and cancer-prone human breast tissues preserve complex epithelial lineages

Rosenbluth, J. M., Schackmann, R. C. J., Gray, G. K., Selfors, L. M., Li, C. M-C., Boedicker, M., Kuiken, H. J., Richardson, A., Brock, J., Garber, J., Dillon, D., Sachs, N., Clevers, H. & Brugge, J. S., 06 Apr 2020, In : Nature Communications. 11, 1, p. 1711

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Quantification of mRNA translation in live cells using single-molecule imaging

Khuperkar, D., Hoek, T. A., Sonneveld, S., Verhagen, B. M. P., Boersma, S. & Tanenbaum, M. E., Apr 2020, In : Nature Protocols. 15, 4, p. 1371-1398 28 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Rewiring E2 enzymes

Sato, K. & Knipscheer, P., Mar 2020, In : Nature Chemical Biology. 16, 3, p. 227-229 3 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Battich, N., Beumer, J., de Barbanson, B., Krenning, L., Baron, C. S., Tanenbaum, M. E., Clevers, H. & van Oudenaarden, A., 06 Mar 2020, In : Science. 367, 6482, p. 1151-1156 6 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Snake Venom Gland Organoids

Post, Y., Puschhof, J., Beumer, J., Kerkkamp, H. M., de Bakker, M. A. G., Slagboom, J., de Barbanson, B., Wevers, N. R., Spijkers, X. M., Olivier, T., Kazandjian, T. D., Ainsworth, S., Iglesias, C. L., van de Wetering, W. J., Heinz, M. C., van Ineveld, R. L., van Kleef, R. G. D. M., Begthel, H., Korving, J., Bar-Ephraim, Y. E. & 11 others, Getreuer, W., Rios, A. C., Westerink, R. H. S., Snippert, H. J. G., van Oudenaarden, A., Peters, P. J., Vonk, F. J., Kool, J., Richardson, M. K., Casewell, N. R. & Clevers, H., 23 Jan 2020, In : Cell. 180, 2, p. 233-247.e21

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The potential and challenges of patient-derived organoids in guiding the multimodality treatment of upper gastrointestinal malignancies

Busslinger, G. A., Lissendorp, F., Franken, I. A., van Hillegersberg, R., Ruurda, J. P., Clevers, H. & de Maat, M. F. G., Apr 2020, In : Open Biology. 10, 4, p. 190274

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

β-Cell Stress Shapes CTL Immune Recognition of Preproinsulin Signal Peptide by Posttranscriptional Regulation of Endoplasmic Reticulum Aminopeptidase 1

Thomaidou, S., Kracht, M. J. L., van der Slik, A., Laban, S., de Koning, E. J., Carlotti, F., Hoeben, R. C., Roep, B. O. & Zaldumbide, A., Apr 2020, In : Diabetes. 69, 4, p. 670-680 11 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

2019

4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Krijger, P. H. L., Geeven, G., Bianchi, V., Hilvering, C. R. E. & de Laat, W., 26 Jul 2019, In : Methods.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

ABCC9-related Intellectual disability Myopathy Syndrome is a KATP channelopathy with loss-of-function mutations in ABCC9

Smeland, M. F., McClenaghan, C., Roessler, H. I., Savelberg, S., Hansen, G. Å. M., Hjellnes, H., Arntzen, K. A., Müller, K. I., Dybesland, A. R., Harter, T., Sala-Rabanal, M., Emfinger, C. H., Huang, Y., Singareddy, S. S., Gunn, J., Wozniak, D. F., Kovacs, A., Massink, M., Tessadori, F., Kamel, S. M. & 5 others, Bakkers, J., Remedi, M. S., Van Ghelue, M., Nichols, C. G. & van Haaften, G., 01 Oct 2019, In : Nature Communications. 10, 1, p. 4457

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A de novo variant in the human HIST1H4J gene causes a syndrome analogous to the HIST1H4C-associated neurodevelopmental disorder

Tessadori, F., Rehman, A. U., Giltay, J. C., Xia, F., Streff, H., Duran, K., Bakkers, J., Lalani, S. R. & van Haaften, G., 05 Dec 2019, In : European Journal of Human Genetics.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Advances in β-cell replacement therapy for the treatment of type 1 diabetes

Vantyghem, M-C., de Koning, E. J. P., Pattou, F. & Rickels, M. R., 05 Oct 2019, In : The Lancet. 394, 10205, p. 1274-1285 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Afferent Neuropeptide Y projections to the ventral tegmental area in normal-weight male Wistar rats

Gumbs, M. C. R., Vuuregge, A. H., Eggels, L., Unmehopa, U. A., Lamuadni, K., Mul, J. D. & la Fleur, S. E., 2019, In : Journal of Comparative Neurology. 527, p. 2659-2674

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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A Human Hematopoietic Niche Model Supporting Hematopoietic Stem and Progenitor Cells In Vitro

Braham, M. V. J., Li Yim, A. S. P., Garcia Mateos, J., Minnema, M. C., Dhert, W. J. A., Öner, F. C., Robin, C. & Alblas, J., May 2019, In : Advanced healthcare materials. 8, 10, p. e1801444

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

AML Subtype Is a Major Determinant of the Association between Prognostic Gene Expression Signatures and Their Clinical Significance

Wiggers, C. R. M., Baak, M. L., Sonneveld, E., Nieuwenhuis, E. E. S., Bartels, M. & Creyghton, M. P., 10 Sep 2019, In : Cell Reports. 28, 11, p. 2866-2877.e5

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

Man, J. C. K., Mohan, R. A., Boogaard, M. V. D., Hilvering, C. R. E., Jenkins, C., Wakker, V., Bianchi, V., Laat, W. D., Barnett, P., Boukens, B. J. & Christoffels, V. M., 30 Oct 2019, In : Nature Communications. 10, 1, p. 4943

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A new perspective on fungal metabolites: identification of bioactive compounds from fungi using zebrafish embryogenesis as read-out

Hoeksma, J., Misset, T., Wever, C., Kemmink, J., Kruijtzer, J., Versluis, K., Liskamp, R. M. J., Boons, G. J., Heck, A. J. R., Boekhout, T. & den Hertog, J., 26 Nov 2019, In : Scientific Reports. 9, 1, p. 17546

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

An FBXW7-ZEB2 axis links EMT and tumour microenvironment to promote colorectal cancer stem cells and chemoresistance

Li, N., Babaei-Jadidi, R., Lorenzi, F., Spencer-Dene, B., Clarke, P., Domingo, E., Tulchinsky, E., Vries, R. G. J., Kerr, D., Pan, Y., He, Y., Bates, D. O., Tomlinson, I., Clevers, H. & Nateri, A. S., 19 Feb 2019, In : Oncogenesis. 8, 3, p. 13

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity

Kopper, O., de Witte, C. J., Lõhmussaar, K., Valle-Inclan, J. E., Hami, N., Kester, L., Balgobind, A. V., Korving, J., Proost, N., Begthel, H., van Wijk, L. M., Revilla, S. A., Theeuwsen, R., van de Ven, M., van Roosmalen, M. J., Ponsioen, B., Ho, V. W. H., Neel, B. G., Bosse, T., Gaarenstroom, K. N. & 11 others, Vrieling, H., Vreeswijk, M. P. G., van Diest, P. J., Witteveen, P. O., Jonges, T., Bos, J. L., van Oudenaarden, A., Zweemer, R. P., Snippert, H. J. G., Kloosterman, W. P. & Clevers, H., May 2019, In : Nature Medicine. 25, 5, p. 838-849 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A Protein Disulfide Isomerase Controls Neuronal Migration through Regulation of Wnt Secretion

Torpe, N., Gopal, S., Baltaci, O., Rella, L., Handley, A., Korswagen, H. C. & Pocock, R., 19 Mar 2019, In : Cell Reports. 26, 12, p. 3183-3190.e5

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A rectal cancer organoid platform to study individual responses to chemoradiation

Ganesh, K., Wu, C., O'Rourke, K. P., Szeglin, B. C., Zheng, Y., Sauvé, C-E. G., Adileh, M., Wasserman, I., Marco, M. R., Kim, A. S., Shady, M., Sanchez-Vega, F., Karthaus, W. R., Won, H. H., Choi, S-H., Pelossof, R., Barlas, A., Ntiamoah, P., Pappou, E., Elghouayel, A. & 30 others, Strong, J. S., Chen, C-T., Harris, J. W., Weiser, M. R., Nash, G. M., Guillem, J. G., Wei, I. H., Kolesnick, R. N., Veeraraghavan, H., Ortiz, E. J., Petkovska, I., Cercek, A., Manova-Todorova, K. O., Saltz, L. B., Lavery, J. A., DeMatteo, R. P., Massagué, J., Paty, P. B., Yaeger, R., Chen, X., Patil, S., Clevers, H., Berger, M. F., Lowe, S. W., Shia, J., Romesser, P. B., Dow, L. E., Garcia-Aguilar, J., Sawyers, C. L. & Smith, J. J., Oct 2019, In : Nature Medicine. 25, 10, p. 1607-1614 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Assessment of the Most Optimal Control Tissue for Intracranial Aneurysm Gene Expression Studies

Laarman, M. D., Kleinloog, R., Bakker, M. K., Rinkel, G. J. E., Bakkers, J. & Ruigrok, Y. M., Oct 2019, In : Stroke. 50, 10, p. 2933-2936 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Association between person and disease related factors and the planned diabetes care in people who receive person-centered type 2 diabetes care: An implementation study

van Vugt, H. A., de Koning, E. J. P. & Rutten, G. E. H. M., 2019, In : PLoS One. 14, 7, p. e0219702

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A transcriptomic roadmap to α- and β-cell differentiation in the embryonic pancreas

van Gurp, L., Muraro, M. J., Dielen, T., Seneby, L., Dharmadhikari, G., Gradwohl, G., van Oudenaarden, A. & de Koning, E. J. P., 24 Jun 2019, In : Development (Cambridge). 146, 12

Research output: Contribution to journal/periodicalArticleScientificpeer-review

A Versatile Biosynthetic Hydrogel Platform for Engineering of Tissue Analogues

Klotz, B. J., Oosterhoff, L. A., Utomo, L., Lim, K. S., Vallmajo-Martin, Q., Clevers, H., Woodfield, T. B. F., Rosenberg, A. J. W. P., Malda, J., Ehrbar, M., Spee, B. & Gawlitta, D., Oct 2019, In : Advanced healthcare materials. 8, 19, p. e1900979

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

A ZNRF3-dependent Wnt/β-catenin signaling gradient is required for adrenal homeostasis

Basham, K. J., Rodriguez, S., Turcu, A. F., Lerario, A. M., Logan, C. Y., Rysztak, M. R., Gomez-Sanchez, C. E., Breault, D. T., Koo, B-K., Clevers, H., Nusse, R., Val, P. & Hammer, G. D., 01 Feb 2019, In : Genes & Development. 33, 3-4, p. 209-220 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Cancer modeling meets human organoid technology

Tuveson, D. & Clevers, H., 07 Jun 2019, In : Science. 364, 6444, p. 952-955 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Baron, C. S., Barve, A., Muraro, M. J., van der Linden, R., Dharmadhikari, G., Lyubimova, A., de Koning, E. J. P. & van Oudenaarden, A., 03 Oct 2019, In : Cell. 179, 2, p. 527-542.e19

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Cellular stress leads to the formation of membraneless stress assemblies in eukaryotic cells

van Leeuwen, W. & Rabouille, C., Sep 2019, In : Traffic. 20, 9, p. 623-638 16 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm-Associated Regions to Potential Candidate Genes

07 May 2019, In : Journal of the American Heart Association. 8, 9, p. e011201

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Gerlach, J. P., van Buggenum, J. A. G., Tanis, S. E. J., Hogeweg, M., Heuts, B. M. H., Muraro, M. J., Elze, L., Rivello, F., Rakszewska, A., van Oudenaarden, A., Huck, W. T. S., Stunnenberg, H. G. & Mulder, K. W., 06 Feb 2019, In : Scientific Reports. 9, 1, p. 1469

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Conserved NPPB+ Border Zone Switches From MEF2- to AP-1-Driven Gene Program

van Duijvenboden, K., de Bakker, D. E. M., Man, J. C. K., Janssen, R., Günthel, M., Hill, M. C., Hooijkaas, I. B., van der Made, I., van der Kraak, P. H., Vink, A., Creemers, E. E., Martin, J. F., Barnett, P., Bakkers, J. & Christoffels, V. M., 09 Sep 2019, In : Circulation. 140, 10, p. 864-879 16 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

COPII vesicles and the expansion of the phagophore

Rabouille, C., 29 Jan 2019, In : eLife. 8

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Correction: Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics (doi: 10.1242/dev.166728)

Attardi, A., Fulton, T., Florescu, M., Shah, G., Muresan, L., Lenz, M. O., Lancaster, C., Huisken, J., van Oudenaarden, A. & Steventon, B., 22 Jan 2019, In : Development (Cambridge). 146, 2

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

CRISPR Craze to Transform Cardiac Biology

van Kampen, S. J. & van Rooij, E., Sep 2019, In : Trends in Molecular Medicine. 25, 9, p. 791-802 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., Tiana, G., Smallwood, S. A., de Laat, W. & Giorgetti, L., Jun 2019, In : Nature Structural & Molecular Biology. 26, 6, p. 471-480 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Defining Adult Stem Cell Function at Its Simplest: The Ability to Replace Lost Cells through Mitosis

Post, Y. & Clevers, H., 01 Aug 2019, In : Cell Stem Cell. 25, 2, p. 174-183 10 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells

Han, S., Fink, J., Jörg, D. J., Lee, E., Yum, M. K., Chatzeli, L., Merker, S. R., Josserand, M., Trendafilova, T., Andersson-Rolf, A., Dabrowska, C., Kim, H., Naumann, R., Lee, J-H., Sasaki, N., Mort, R. L., Basak, O., Clevers, H., Stange, D. E., Philpott, A. & 3 others, Kim, J. K., Simons, B. D. & Koo, B-K., 05 Sep 2019, In : Cell Stem Cell. 25, 3, p. 342-356.e7

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Ectopic Activation of the Spindle Assembly Checkpoint Signaling Cascade Reveals Its Biochemical Design

Chen, C., Whitney, I. P., Banerjee, A., Sacristan, C., Sekhri, P., Kern, D. M., Fontan, A., Kops, G. J. P. L., Tyson, J. J., Cheeseman, I. M. & Joglekar, A. P., 07 Jan 2019, In : Current Biology. 29, 1, p. 104-119.e10

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

van Es, J. H., Wiebrands, K., López-Iglesias, C., van de Wetering, M., Zeinstra, L., van den Born, M., Korving, J., Sasaki, N., Peters, P. J., van Oudenaarden, A. & Clevers, H., 16 Dec 2019, In : Proceedings of the National Academy of Sciences of the United States of America.

Research output: Contribution to journal/periodicalArticleScientificpeer-review