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Hubrecht publications

2012

Abo A, Clevers H., Modulating WNT receptor turnover for tissue repair., Nat Biotechnol. 2012 Sep;30(9):835-6.

Aguado-Fraile E, Ramos E, Sáenz-Morales D, Conde E, Blanco-Sánchez I, Stamatakis K, del Peso L, Cuppen E, Brüne B, Bermejo ML., miR-127 protects proximal tubule cells against ischemia/reperfusion: identification of kinesin family member 3B as miR-127 target., PLoS One. 2012;7(9):e44305.

Ariotti S, Beltman JB, Chodaczek G, Hoekstra ME, van Beek AE, Gomez-Eerland R, Ritsma L, van Rheenen J, Marée AF, Zal T, de Boer RJ, Haanen JB, Schumacher TN., Tissue-resident memory CD8+ T cells continuously patrol skin epithelia to quickly recognize local antigen., Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19739-44.

Bakker ER, Raghoebir L, Franken PF, Helvensteijn W, van Gurp L, Meijlink F, van der Valk MA, Rottier RJ, Kuipers EJ, van Veelen W, Smits R., Induced Wnt5a expression perturbs embryonic outgrowth and intestinal elongation, but is well-tolerated in adult mice., Dev Biol. 2012 Sep 1;369(1):91-100.

Barker N, Rookmaaker MB, Kujala P, Ng A, Leushacke M, Snippert H, van de Wetering M, Tan S, Van Es JH, Huch M, Poulsom R, Verhaar MC, Peters PJ, Clevers H., Lgr5(+ve) stem/progenitor cells contribute to nephron formation during kidney development., Cell Rep. 2012 Sep 27;2(3):540-52.

Barker N, van Oudenaarden A, Clevers H., Identifying the stem cell of the intestinal crypt: strategies and pitfalls., Cell Stem Cell. 2012 Oct 5;11(4):452-60.

Bialecka M, Cdx genes and the maintenance of tissue progenitors in the mouse, Thesis, Universiteit Utrecht, p 1-100

Bialecka M, Young T, Chuva de Sousa Lopes S, ten Berge D, Sanders A, Beck F, Deschamps J., Cdx2 contributes to the expansion of the early primordial germ cell population in the mouse., Dev Biol. 2012 Nov 15;371(2):227-34.

Blauw HM, Barnes CP, van Vught PW, van Rheenen W, Verheul M, Cuppen E, Veldink JH, van den Berg LH., SMN1 gene duplications are associated with sporadic ALS., Neurology. 2012 Mar 13;78(11):776-80.

Blauw HM, van Rheenen W, Koppers M, Van Damme P, Waibel S, Lemmens R, van Vught PW, Meyer T, Schulte C, Gasser T, Cuppen E, Pasterkamp RJ, Robberecht W, Ludolph AC, Veldink JH, van den Berg LH., NIPA1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis., Hum Mol Genet. 2012 Jun 1;21(11):2497-502.

Boj SF, van Es JH, Huch M, Li VS, José A, Hatzis P, Mokry M, Haegebarth A, van den Born M, Chambon P, Voshol P, Dor Y, Cuppen E, Fillat C, Clevers H., Diabetes Risk Gene and Wnt Effector Tcf7l2/TCF4 Controls Hepatic Response to Perinatal and Adult Metabolic Demand., Cell. 2012 Dec 21;151(7):1595-607.

Bonapace L, Wyckoff J, Oertner T, Van Rheenen J, Junt T, Bentires-Alj M., If You Don't Look, You Won't See: Intravital Multiphoton Imaging of Primary and Metastatic Breast Cancer., J Mammary Gland Biol Neoplasia. 2012 Jun;17(2):125-9.

Buganim Y, Faddah DA, Cheng AW, Itskovich E, Markoulaki S, Ganz K, Klemm SL, van Oudenaarden A, Jaenisch R., Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase., Cell. 2012 Sep 14;150(6):1209-22.

Buske P, Przybilla J, Loeffler M, Sachs N, Sato T, Clevers H, Galle J., On the biomechanics of stem cell niche formation in the gut - modelling growing organoids., FEBS J. 2012 Sep;279(18):3475-87.

Cheng C, Haasdijk R, Tempel D, van de Kamp EH, Herpers R, Bos F, Den Dekker WK, Blonden LA, de Jong R, Bürgisser PE, Chrifi I, Biessen EA, Dimmeler S, Schulte-Merker S, Duckers HJ., Endothelial Cell-Specific FGD5 Involvement in Vascular Pruning Defines Neovessel Fate in Mice., Circulation. 2012 Jun 26;125(25):3142-59.

Choorapoikayil S, Kuiper RV, de Bruin A, den Hertog J., Haploinsufficiency of the genes encoding the tumor suppressor Pten predisposes zebrafish to hemangiosarcoma., Dis Model Mech. 2012 Mar;5(2):241-7.

Clevers H, Nusse R., Wnt/β-Catenin Signaling and Disease., Cell. 2012 Jun 8;149(6):1192-205.

Clevers H., The Paneth cell, caloric restriction, and intestinal integrity., N Engl J Med. 2012 Oct 18;367(16):1560-1.

Cullen PJ, Korswagen HC., Sorting nexins provide diversity for retromer-dependent trafficking events., Nat Cell Biol. 2012 Jan;14(1):29-37.

de Laat W, Dekker J., 3C-based technologies to study the shape of the genome., Methods. 2012 Nov;58(3):189-91.

de Lau W, Kujala P, Schneeberger K, Middendorp S, Li VS, Barker N, Martens A, Hofhuis F, Dekoter RP, Peters PJ, Nieuwenhuis E, Clevers H., Peyer's Patch M cells derive from Lgr5+ stem cells require SpiB and are induced by RankL in cultured 'organoids', Mol Cell Biol. 2012 Sep;32(18):3639-47.

de Lau WB, Snel B, Clevers HC., The R-spondin protein family., Genome Biol. 2012 Mar 22;13(3):242.

de Pater E, Ciampricotti M, Priller F, Veerkamp J, Strate I, Smith K, Lagendijk AK, Schilling TF, Herzog W, Abdelilah-Seyfried S, Hammerschmidt M, Bakkers J., Bmp Signaling Exerts Opposite Effects on Cardiac Differentiation., Circ Res. 2012 Feb 17;110(4):578-87

de Visser KE, Ciampricotti M, Michalak E, Wei-Min Tan D, Speksnijder EN, Hau CS, Clevers H, Barker N, Jonkers J., Developmental stage-specific contribution of LGR5+ cells to basal and luminal epithelial lineages in the postnatal mammary gland., J Pathol. 2012 Nov;228(3):300-9.

de Wit E, de Laat W., A decade of 3C technologies: insights into nuclear organization., Genes Dev. 2012 Jan 1;26(1):11-24.

Dierickx P, Doevendans PA, Geijsen N, van Laake LW., Embryonic Template-Based Generation and Purification of Pluripotent Stem Cell-Derived Cardiomyocytes for Heart Repair., J Cardiovasc Transl Res. 2012 Oct;5(5):566-80.

Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G., microRNAs associated with the different human Argonaute proteins., Nucleic Acids Res. 2012 Oct;40(19):9850-62.

Farin HF, van Es JH, Clevers H., Redundant Sources of Wnt Regulate Intestinal Stem Cells and Promote Formation of Paneth Cells., Gastroenterology. 2012 Dec;143(6):1518-1529.

Ferreira PA, Ruela-de-Sousa RR, Queiroz KC, Souza AC, Milani R, Pilli RA, Peppelenbosch MP, den Hertog J, Ferreira CV., Knocking down low molecular weight protein tyrosine phosphatase (LMW-PTP) reverts chemoresistance through inactivation of Src and Bcr-Abl proteins., PLoS One. 2012;7(9):e44312.

Fiaz AW, Léon-Kloosterziel KM, Gort G, Schulte-Merker S, van Leeuwen JL, Kranenbarg S., Swim-Training Changes the Spatio-Temporal Dynamics of Skeletogenesis in Zebrafish Larvae (Danio rerio)., PLoS One. 2012;7(4):e34072.

Fuchs SA, Harakalova M, van Haaften G, van Hasselt PM, Cuppen E, Houwen RH., Application of exome sequencing in the search for genetic causes of rare disorders of copper metabolism., Metallomics. 2012 Jul 28;4(7):606-13.

Geijsen N., Epigenetic reprogramming: Prdm14 hits the accelerator., EMBO J. 2012 Apr 20;31(10):2247-8.

Gloerich M, Ten Klooster JP, Vliem MJ, Koorman T, Zwartkruis FJ, Clevers H, Bos JL., Rap2A links intestinal cell polarity to brush border formation., Nat Cell Biol. 2012 Aug;14(8):793-801.

Gommans WM, Berezikov E., Sample preparation for small RNA massive parallel sequencing., Methods Mol Biol. 2012;786:167-78.

Gommans WM, Berezikov E., Controlling miRNA regulation in disease., Methods Mol Biol. 2012;822:1-18.

Goudarzi M, Banisch TU, Mobin MB, Maghelli N, Tarbashevich K, Strate I, van den Berg J, Blaser H, Bandemer S, Paluch E, Bakkers J, Tolić-Nørrelykke IM, Raz E., Identification and regulation of a molecular module for bleb-based cell motility., Dev Cell. 2012 Jul 17;23(1):210-8

Guardavaccaro D, Clevers H., Wnt/β-Catenin and MAPK Signaling: Allies and Enemies in Different Battlefields., Sci Signal. 2012 Apr 10;5(219):pe15.

Harakalova M, van den Boogaard MJ, Sinke R, van Lieshout S, van Tuil MC, Duran K, Renkens I, Terhal PA, de Kovel C, Nijman IJ, van Haelst M, Knoers NV, van Haaften G, Kloosterman W, Hennekam RC, Cuppen E, Ploos van Amstel HK., X-exome sequencing identifies a HDAC8 variant in a large pedigree with X-linked intellectual disability, truncal obesity, gynaecomastia, hypogonadism and unusual face., J Med Genet. 2012 Aug;49(8):539-43.

Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL, Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA, Asselbergs FW, Breur HM, Swinke, Dominant missense mutations in ABCC9 cause Cantú syndrome., Nat Genet. 2012 May 18;44(7):793-6.

Harterink M, Korswagen HC., Dissecting the Wnt secretion pathway: key questions on the modification and intracellular trafficking of Wnt proteins., Acta Physiol (Oxf). 2012 Jan;204(1):8-16.

Hashimoto T, Perlot T, Rehman A, Trichereau J, Ishiguro H, Paolino M, Sigl V, Hanada T, Hanada R, Lipinski S, Wild B, Camargo SM, Singer D, Richter A, Kuba K, Fukamizu A, Schreiber S, Clevers H, Verrey F, Rosenstiel P, Penninger JM., ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation., Nature. 2012 Jul 25;487(7408):477-81.

Hochstenbach R, Poot M, Nijman IJ, Renkens I, Duran KJ, Van't Slot R, van Binsbergen E, van der Zwaag B, Vogel MJ, Terhal PA, Ploos van Amstel HK, Kloosterman WP, Cuppen E., Discovery of variants unmasked by hemizygous deletions., Eur J Hum Genet. 2012 Jul;20(7):748-53.

Holwerda S, de Laat W., Chromatin loops, gene positioning, and gene expression., Front Genet. 2012;3:217.

Hua G, Thin TH, Feldman R, Haimovitz-Friedman A, Clevers H, Fuks Z, Kolesnick R., Crypt Base Columnar Stem Cells in Small Intestines of Mice Are Radioresistant., Gastroenterology. 2012 Nov;143(5):1266-76.

Huang, HY., Functional analysis of Tudor-domain-containing proteins in the zebrafish germline, Thesis, Universiteit Utrecht, p 1-153

Huitema LF, Apschner A, Logister I, Spoorendonk KM, Bussmann J, Hammond CL, Schulte-Merker S., Entpd5 is essential for skeletal mineralization and regulates phosphate homeostasis in zebrafish., Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21372-7.

Huitema LF, Renn J, Logister I, Gray JK, Waltz SE, Flik G, Schulte-Merker S., Macrophage-stimulating protein and calcium homeostasis in zebrafish., FASEB J. 2012 Oct;26(10):4092-101.

Huveneers S, Oldenburg J, Spanjaard E, van der Krogt G, Grigoriev I, Akhmanova A, Rehmann H, de Rooij J., Vinculin associates with endothelial VE-cadherin junctions to control force-dependent remodeling., J Cell Biol. 2012 Mar 5;196(5):641-52.

Hyde AS, Farmer EL, Easley KE, van Lammeren K, Christoffels VM, Barycki JJ, Bakkers J, Simpson MA., UDP-glucose dehydrogenase polymorphisms from patients with congenital heart valve defects disrupt enzyme stability and quaternary assembly., J Biol Chem. 2012 Sep 21;287(39):32708-16.

Isik M., Functional Analysis of microRNA miR-34 in Caenorhabditis elegans, Thesis, Universiteit Utrecht, p 1-164

Itsara A, Vissers LE, Steinberg KM, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson RK, Jenkins RB, Veltman JA, Eichler EE., Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing., Am J Hum Genet. 2012 Apr 6;90(4):599-613.

Itzkovitz S, Blat IC, Jacks T, Clevers H, van Oudenaarden A., Optimality in the development of intestinal crypts., Cell. 2012 Feb 3;148(3):608-19.

Itzkovitz S, Lyubimova A, Blat IC, Maynard M, van Es J, Lees J, Jacks T, Clevers H, van Oudenaarden A., Single-molecule transcript counting of stem-cell markers in the mouse intestine., Nat Cell Biol. 2012 Jan;14(1):106-14.

Ji N, van Oudenaarden A., Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos., WormBook. 2012 Dec 13:1-16.

Junker JP, van Oudenaarden A., When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes., Mol Cell. 2012 Feb 24;45(4):437-8.

Kamminga LM, van Wolfswinkel JC, Luteijn MJ, Kaaij LJ, Bagijn MP, Sapetschnig A, Miska EA, Berezikov E, Ketting RF., Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans., PLoS Genet. 2012 Jul;8(7):e1002702.

Kemper K, Prasetyanti PR, De Lau W, Rodermond H, Clevers H, Medema JP., Monoclonal antibodies against Lgr5 identify human colorectal cancer stem cells., Stem Cells. 2012 Nov;30(11):2378-86.

Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CA, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V,, Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms., Cell Rep. 2012 Jun 28;1(6):648-55.

Knipscheer P, Räschle M, Schärer OD, Walter JC., Replication-coupled DNA interstrand cross-link repair in Xenopus egg extracts., Methods Mol Biol. 2012;920:221-43.

Koo BK, Spit M, Jordens I, Low TY, Stange DE, van de Wetering M, van Es JH, Mohammed S, Heck AJ, Maurice MM, Clevers H., Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors., Nature. 2012 Aug 30;488(7413):665-9.

Kruiswijk F, Yuniati L, Magliozzi R, Low TY, Lim R, Bolder R, Mohammed S, Proud CG, Heck AJ, Pagano M, Guardavaccaro D., Coupled Activation and Degradation of eEF2K Regulates Protein Synthesis in Response to Genotoxic Stress., Sci Signal. 2012 Jun 5;5(227):ra40.

Kuijk EW, van Tol LT, van de Velde H, Wubbolts R, Welling M, Geijsen N, Roelen BA., The roles of FGF and MAP kinase signaling in the segregation of the epiblast and hypoblast cell lineages in bovine and human embryos., Development. 2012 Mar;139(5):871-82.

Lagendijk AK, Moulton JD, Bakkers J., Revealing details: whole mount microRNA in situ hybridization protocol for zebrafish embryos and adult tissues., Biology Open 2012 1:566-569 June 15, 2012; 1 (6)

Lander AD, Kimble J, Clevers H, Fuchs E, Montarras D, Buckingham M, Calof AL, Trumpp A, Oskarsson T., What does the concept of the stem cell niche really mean today?, BMC Biol. 2012 Mar 9;10:19.

Li VS, Clevers H., n vitro expansion and transplantation of intestinal crypt stem cells., Gastroenterology. 2012 Jul;143(1):30-4.

Li VS, Ng SS, Boersema PJ, Low TY, Karthaus WR, Gerlach JP, Mohammed S, Heck AJ, Maurice MM, Mahmoudi T, Clevers H., Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex., Cell. 2012 Jun 8;149(6):1245-56.

Linsen SE, Cuppen E., Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing., Methods Mol Biol. 2012;822:205-17.

Loerke D, le Duc Q, Blonk I, Kerstens A, Spanjaard E, Machacek M, Danuser G, de Rooij J., Quantitative imaging of epithelial cell scattering identifies specific inhibitors of cell motility and cell-cell dissociation., Sci Signal. 2012 Jul 3;5(231):rs5.

Lum L, Clevers H., Cell biology. The unusual case of Porcupine., Science. 2012 Aug 24;337(6097):922-3.

Luteijn MJ, van Bergeijk P, Kaaij LJ, Almeida MV, Roovers EF, Berezikov E, Ketting RF., Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans., EMBO J. 2012 Jul 31;31(16):3422-30.

Middelkoop TC, Williams L, Yang PT, Luchtenberg J, Betist MC, Ji N, van Oudenaarden A, Kenyon C, Korswagen HC., The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts., Dev Biol. 2012 Jan 15;361(2):338-48.

Moindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A., 3D chromatin conformation correlates with replication timing and is conserved in resting cells., Nucleic Acids Res. 2012 Oct;40(19):9470-81.

Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E., Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes., Nucleic Acids Res. 2012 Jan;40(1):148-58

Mul JD, Begg DP, Alsters SI, van Haaften G, Duran KJ, D'Alessio DA, Le Roux CW, Woods SC, Sandoval DA, Blakemore AI, Cuppen E, van Haelst MM, Seeley RJ., Effect of vertical sleeve gastrectomy in melanocortin receptor 4-deficient rats., Am J Physiol Endocrinol Metab. 2012 Jul;303(1):E103-10.

Mul JD, van Boxtel R, Bergen DJ, Brans MA, Brakkee JH, Toonen PW, Garner KM, Adan RA, Cuppen E., Melanocortin Receptor 4 Deficiency Affects Body Weight Regulation, Grooming Behavior, and Substrate Preference in the Rat., Obesity (Silver Spring). 2012 Mar;20(3):612-21.

Muñoz J, Stange DE, Schepers AG, van de Wetering M, Koo BK, Itzkovitz S, Volckmann R, Kung KS, Koster J, Radulescu S, Myant K, Versteeg R, Sansom OJ, van Es JH, Barker N, van Oudenaarden A, Mohammed S, Heck AJ, Clevers H., The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers., EMBO J. 2012 Jun 12;31(14):3079-91.

Munsky B, Neuert G, van Oudenaarden A., Using gene expression noise to understand gene regulation., Science. 2012 Apr 13;336(6078):183-7.

Nadra K, Médard JJ, Mul JD, Han GS, Grès S, Pende M, Metzger D, Chambon P, Cuppen E, Saulnier-Blache JS, Carman GM, Desvergne B, Chrast R., Cell autonomous lipin 1 function is essential for development and maintenance of white and brown adipose tissue., Mol Cell Biol. 2012 Dec;32(23):4794-810.

Nieuwenhuis MH, Douma KF, Bleiker EM, Aaronson NK, Clevers H, Vasen HF., Clinical evidence for an association between familial adenomatous polyposis (FAP) and type II diabetes., Int J Cancer. 2012 Sep 15;131(6):1488-9.

Northrup E, Zschemisch NH, Eisenblätter R, Glage S, Wedekind D, Cuppen E, Dorsch M, Hedrich HJ., The ter Mutation in the Rat Dnd1 Gene Initiates Gonadal Teratomas and Infertility in Both Genders., PLoS One. 2012;7(5):e38001.

Ostergaard P, Simpson MA, Mendola A, Vasudevan P, Connell FC, van Impel A, Moore AT, Loeys BL, Ghalamkarpour A, Onoufriadis A, Martinez-Corral I, Devery S, Leroy JG, van Laer L, Singer A, Bialer MG, McEntagart M, Quarrell O, Brice G, Trembath RC, Schulte-, Mutations in KIF11 Cause Autosomal-Dominant Microcephaly Variably Associated with Congenital Lymphedema and Chorioretinopathy., Am J Hum Genet. 2012 Feb 10;90(2):356-62.

Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, McMahon AP., Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning., Genes Dev. 2012 Dec 15;26(24):2802-16.

Ping Z, Lim R, Bashir T, Pagano M, Guardavaccaro D., APC/C (Cdh1) controls the proteasome-mediated degradation of E2F3 during cell cycle exit., Cell Cycle. 2012 May 15;11(10).

Poell JB, van Haastert RJ, de Gunst T, Schultz IJ, Gommans WM, Verheul M, Cerisoli F, van Noort PI, Prevost GP, Schaapveld RQ, Cuppen E., A Functional Screen Identifies Specific MicroRNAs Capable of Inhibiting Human Melanoma Cell Viability., PLoS One. 2012;7(8):e43569.

Poell JB., Functional screens for cancer-modulating microRNAs, Thesis, Universiteit Utrecht, p 1-152

Ritsma L, Steller EJ, Beerling E, Loomans CJ, Zomer A, Gerlach C, Vrisekoop N, Seinstra D, van Gurp L, Schäfer R, Raats DA, de Graaff A, Schumacher TN, de Koning EJ, Rinkes IH, Kranenburg O, van Rheenen J., Intravital microscopy through an abdominal imaging window reveals a pre-micrometastasis stage during liver metastasis., Sci Transl Med. 2012 Oct 31;4(158):158ra145.

Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J., Rap1 Can Bypass the FAK-Src-Paxillin Cascade to Induce Cell Spreading and Focal Adhesion Formation., PLoS One. 2012;7(11):e50072.

Runtuwene, V.J., Functional characterization of Protein-Tyrosine Phosphatases in zebrafish development using image analysis, Leiden University, pp. 1-176

Schasfoort RB, de Lau W, van der Kooi A, Clevers H, Engbers GH., Method for estimating the single molecular affinity., Anal Biochem. 2012 Feb 15;421(2):794-6.

Schepers A, Clevers H., Wnt signaling, stem cells, and cancer of the gastrointestinal tract., Cold Spring Harb Perspect Biol. 2012 Apr 1;4(4).

Schepers A., Characterizing intestinal stem cells - An important part of the puzzle -, Thesis, Universiteit Utrecht, p 1-115

Schepers AG, Snippert HJ, Stange DE, van den Born M, van Es JH, van de Wetering M, Clevers H., Lineage tracing reveals Lgr5+ stem cell activity in mouse intestinal adenomas., Science. 2012 Aug 10;337(6095):730-5.

Schneider J, Skelton RL, Von Stetina SE, Middelkoop TC, van Oudenaarden A, Korswagen HC, Miller DM 3rd., UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit., Development. 2012 Jun;139(12):2234-45.

Schuijers J, Clevers H., Adult mammalian stem cells: the role of Wnt, Lgr5 and R-spondins., EMBO J. 2012 May 22;31(12):2685-96.

Shaked H, Hofseth LJ, Chumanevich A, Chumanevich AA, Wang J, Wang Y, Taniguchi K, Guma M, Shenouda S, Clevers H, Harris CC, Karin M., Chronic epithelial NF-κB activation accelerates APC loss and intestinal tumor initiation through iNOS up-regulation., Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14007-12.

Simanov D, Mellaart-Straver I, Sormacheva I, Berezikov E., The Flatworm Macrostomum lignano Is a Powerful Model Organism for Ion Channel and Stem Cell Research., EMBO J. 2012 Aug 15;31(16):3422-30.

Simonis M, Atanur SS, Linsen SE, Guryev V, Ruzius FP, Game L, Lansu N, de Bruijn E, van Heesch S, Jones SJ, Pravenec M, Aitman TJ, Cuppen E., Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel., Genome Biol. 2012 Apr 27;13(4):R31.

Slavov N, Airoldi EM, van Oudenaarden A, Botstein D., A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes., Mol Biol Cell. 2012 May;23(10):1986-97.

Slavov N, van Oudenaarden A., How to regulate a gene: to repress or to activate?, Mol Cell. 2012 Jun 8;46(5):551-2.

Splinter E, de Wit E, van de Werken HJ, Klous P, de Laat W., Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation., Methods. 2012 Nov;58(3):221-30.

Staal FJ, Clevers H., Tales of the unexpected: tcf1 functions as a tumor suppressor for leukemias., Immunity. 2012 Nov 16;37(5):761-3.

Stange D.E., Defining and mining the intestinal stem cell signature, Universiteit Utrecht, pp. 1-136

Stassen JH, Seidl MF, Vergeer PW, Nijman IJ, Snel B, Cuppen E, VAN DEN Ackerveken G., Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing., Mol Plant Pathol. 2012 Sep;13(7):719-731.

Stringer EJ, Duluc I, Saandi T, Davidson I, Bialecka M, Sato T, Barker N, Clevers H, Pritchard CA, Winton DJ, Wright NA, Freund JN, Deschamps J, Beck F., Cdx2 determines the fate of postnatal intestinal endoderm., Development. 2012 Feb;139(3):465-74.

Tee JM, Sartori da Silva M, Rygiel A, Muncan V, Bink R, van den Brink G, van Tijn P, Zivkovic D, Kodach L, Guardavaccaro D, Diks S, Peppelenbosch M., asb11 is a regulator of embryonic and adult regenerative myogenesis., Stem Cells Dev. 2012 Nov 20;21(17):3091-103.

Teklenburg G, Weimar CH, Fauser BC, Macklon N, Geijsen N, Heijnen CJ, Chuva de Sousa Lopes SM, Kuijk EW., Cell Lineage Specific Distribution of H3K27 Trimethylation Accumulation in an In Vitro Model for Human Implantation., PLoS One. 2012;7(3):e32701.

Tempel D, de Boer M, van Deel ED, Haasdijk RA, Duncker DJ, Cheng C, Schulte-Merker S, Duckers HJ., Apelin Enhances Cardiac Neovascularization After Myocardial Infarction By Recruiting Aplnr+ Circulating Cells., Circ Res. 2012 Aug 17;111(5):585-98.

Tessadori F, van Weerd JH, Burkhard SB, Verkerk AO, de Pater E, Boukens BJ, Vink A, Christoffels VM, Bakkers J., Identification and functional characterization of cardiac pacemaker cells in zebrafish., PLoS One. 2012;7(10):e47644.

Tiemessen MM, Baert MR, Schonewille T, Brugman MH, Famili F, Salvatori DC, Meijerink JP, Ozbek U, Clevers H, van Dongen JJ, Staal FJ., The nuclear effector of wnt-signaling, tcf1, functions as a T-cell-specific tumor suppressor for development of lymphomas., PLoS Biol. 2012 Nov;10(11):e1001430.

Twiss F, Le Duc Q, Van Der Horst S, Tabdili H, Van Der Krogt G, Wang N, Rehmann H, Huveneers S, Leckband DE, De Rooij J., Vinculin-dependent Cadherin mechanosensing regulates efficient epithelial barrier formation., Biol Open. 2012 Nov 15;1(11):1128-40.

van de Werken HJ, de Vree PJ, Splinter E, Holwerda SJ, Klous P, de Wit E, de Laat W., 4C technology: protocols and data analysis., Methods Enzymol. 2012;513:89-112.

van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W., Robust 4C-seq data analysis to screen for regulatory DNA interactions., Nat Methods. 2012 Oct;9(10):969-72.

van den Boogaard M, Wong LY, Tessadori F, Bakker ML, Dreizehnter LK, Wakker V, Bezzina CR, 't Hoen PA, Bakkers J, Barnett P, Christoffels VM., Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer., J Clin Invest. 2012 Jul 2;122(7):2519-30.

van Eekelen M, Runtuwene V, Masselink W, den Hertog J., Pair-Wise Regulation of Convergence and Extension Cell Movements by Four Phosphatases via RhoA., PLoS One. 2012;7(4):e35913.

van Es JH, Haegebarth A, Kujala P, Itzkovitz S, Koo BK, Boj SF, Korving J, van den Born M, van Oudenaarden A, Robine S, Clevers H., A critical role for the Wnt effector TCF4 in adult intestinal homeostatic self-renewal, Mol Cell Biol. 2012 May;32(10):1918-27.

van Es JH, Sato T, van de Wetering M, Lyubimova A, Nee AN, Gregorieff A, Sasaki N, Zeinstra L, van den Born M, Korving J, Martens AC, Barker N, van Oudenaarden A, Clevers H., Dll1+ secretory progenitor cells revert to stem cells upon crypt damage., Nat Cell Biol. 2012 Oct;14(10):1099-104.

van Rooijen C, Simmini S, Bialecka M, Neijts R, van de Ven C, Beck F, Deschamps J., Evolutionarily conserved requirement of Cdx for post-occipital tissue emergence., Development. 2012 Jul;139(14):2576-83.

van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A., Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast., Cell. 2012 Sep 14;150(6):1170-81.

Vermaat JS, Nijman IJ, Koudijs MJ, Gerritse FL, Scherer S, Mokry M, Roessingh W, Lansu N, de Bruijn E, van Hillegersberg R, Van Diest PJ, Cuppen E, Voest EE., Primary colorectal cancers and their subsequent hepatic metastases are genetically different: implications for selection of patients for targeted treatment., Clin Cancer Res. 2012 Feb 1;18(3):688-99.

Weijts BG, Bakker WJ, Cornelissen PW, Liang KH, Schaftenaar FH, Westendorp B, de Wolf CA, Paciejewska M, Scheele CL, Kent L, Leone G, Schulte-Merker S, de Bruin A., E2F7 and E2F8 promote angiogenesis through transcriptional activation of VEGFA in cooperation with HIF1., EMBO J. 2012 Oct 3;31(19):3871-84.

Weil TT, Parton RM, Herpers B, Soetaert J, Veenendaal T, Xanthakis D, Dobbie IM, Halstead JM, Hayashi R, Rabouille C, Davis I., Drosophila patterning is established by differential association of mRNAs with P bodies., Nat Cell Biol. 2012 Dec;14(12):1305-15.

Welstead GG, Creyghton MP, Bilodeau S, Cheng AW, Markoulaki S, Young RA, Jaenisch R., X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner., Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):13004-9.

Westendorp B, Mokry M, Groot Koerkamp MJ, Holstege FC, Cuppen E, de Bruin A., E2F7 represses a network of oscillating cell cycle genes to control S-phase progression., Nucleic Acids Res. 2012 Apr;40(8):3511-23.

Wilkinson RN, Koudijs MJ, Patient RK, Ingham PW, Schulte-Merker S, van Eeden FJ., Hedgehog signaling via a calcitonin receptor-like receptor can induce arterial differentiation independently of VEGF signaling in zebrafish., Blood. 2012 Jul 12;120(2):477-88.

Wong VW, Stange DE, Page ME, Buczacki S, Wabik A, Itami S, van de Wetering M, Poulsom R, Wright NA, Trotter MW, Watt FM, Winton DJ, Clevers H, Jensen KB., Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling., Nat Cell Biol. 2012 Mar 4;14(4):401-8.

Yui S, Nakamura T, Sato T, Nemoto Y, Mizutani T, Zheng X, Ichinose S, Nagaishi T, Okamoto R, Tsuchiya K, Clevers H, Watanabe M., Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5(+) stem cell., Nat Med. 2012 Mar 11;18(4):618-23.