Hubrecht publications

2006   2007   2008   2009   2010

2010
Ashton GH, Morton JP, Myant K, Phesse TJ, Ridgway RA, Marsh V, Wilkins JA, Athineos D, Muncan V, Kemp R, Neufeld K, Clevers H, Brunton V, Winton DJ, Wang X, Sears RC, Clarke AR, Frame MC, Sansom OJ.
Focal adhesion kinase is required for intestinal regeneration and tumorigenesis downstream of Wnt/c-Myc signaling.
Dev Cell. 2010 Aug 17;19(2):259-69

Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ.
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome Res. 2010 Apr 29;20(6):791-803

Barker N, Huch M, Kujala P, van de Wetering M, Snippert HJ, van Es JH, Sato T, Stange DE, Begthel H, van den Born M, Danenberg E, van den Brink S, Korving J, Abo A, Peters PJ, Wright N, Poulsom R, Clevers H.
Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro.
Cell Stem Cell. 2010 Jan 8;6(1):25-36

Barker N, Clevers H.
Lineage tracing in the intestinal epithelium.
Curr Protoc Stem Cell Biol. 2010 May;Chapter 5:Unit5A.4

Barker N, Clevers H.
Leucine-rich repeat-containing G-protein-coupled receptors as markers of adult stem cells.
Gastroenterology. 2010 May;138(5):1681-96

Barker N, Bartfeld S, Clevers H.
Tissue-resident adult stem cell populations of rapidly self-renewing organs.
Cell Stem Cell. 2010 Dec 3;7(6):656-70

Beqqali A, Monshouwer-Kloots J, Monteiro R, Welling M, Bakkers J, Ehler E, Verkleij A, Mummery C, Passier R.
CHAP is a newly identified Z-disc protein essential for heart and skeletal muscle function.
J Cell Sci. 2010 Apr 1;123(Pt 7):1141-50

Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC.
Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
Nat Genet. 2010 Jan;42(1):6-9

Bialecka M, Wilson V, Deschamps J.
Cdx mutant axial progenitor cells are rescued by grafting to a wild type environment.
Dev Biol. 2010 Nov 1;347(1):228-34

Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ.
In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.
Mol Cell Proteomics. 2010 Jan;9(1):84-99.

Bongers G, Maussang D, Muniz LR, Noriega VM, Fraile-Ramos A, Barker N, Marchesi F, Thirunarayanan N, Vischer HF, Qin L, Mayer L, Harpaz N, Leurs R, Furtado GC, Clevers H, Tortorella D, Smit MJ, Lira SA.
The cytomegalovirus-encoded chemokine receptor US28 promotes intestinal neoplasia in transgenic mice.
J Clin Invest. 2010 Nov 1;120(11):3969-78.

Buecker C, Geijsen N.
Different flavors of pluripotency, molecular mechanisms, and practical implications.
Cell Stem Cell. 2010 Nov 5;7(5):559-64.

Buecker C, Chen HH, Polo JM, Daheron L, Bu L, Barakat TS, Okwieka P, Porter A, Gribnau J, Hochedlinger K, Geijsen N.
A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells.
Cell Stem Cell. 2010 Jun 4;6(6):535-46.

Bussmann J, Bos FL, Urasaki A, Kawakami K, Duckers HJ, Schulte-Merker S.
Arteries provide essential guidance cues for lymphatic endothelial cells in the zebrafish trunk.
Development. 2010 Aug;137(16):2653-7.

Cole AM, Myant K, Reed KR, Ridgway RA, Athineos D, Van den Brink GR, Muncan V, Clevers H, Clarke AR, Sicinski P, Sansom OJ.
Cyclin D2-cyclin-dependent kinase 4/6 is required for efficient proliferation and tumorigenesis following Apc loss.
Cancer Res. 2010 Oct 15;70(20):8149-58.

Cole AM, Ridgway RA, Derkits SE, Parry L, Barker N, Clevers H, Clarke AR, Sansom OJ.
p21 loss blocks senescence following Apc loss and provokes tumourigenesis in the renal but not the intestinal epithelium.
EMBO Mol Med. 2010 Nov;2(11):472-86.

Corrêa RL, Steiner FA, Berezikov E, Ketting RF.
MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.
PLoS Genet. 2010 Apr 8;6(4):e1000903.

Cuppen E.
DNA isolation from rat tail or ear.
Cold Spring Harb Protoc. 2010 May;2010(5):pdb.prot5434.

da Costa Martins PA, Salic K, Gladka MM, Armand AS, Leptidis S, el Azzouzi H, Hansen A, Coenen-de Roo CJ, Bierhuizen MF, van der Nagel R, van Kuik J, de Weger R, de Bruin A, Condorelli G, Arbones ML, Eschenhagen T, De Windt LJ.
MicroRNA-199b targets the nuclear kinase Dyrk1a in an auto-amplification loop promoting calcineurin/NFAT signalling.
Nat Cell Biol. 2010 Dec;12(12):1220-7.

de Mulder K, Berezikov E.
Tracing the evolution of tissue identity with microRNAs.
Genome Biol. 2010 Mar 30;11(3):111.

de Pater E
Growth of the Zebrafish Heart.
Thesis, Universiteit Utrecht, pp. 1-141

Faro A
Heads and Tails of endoderm development & adult tissue homeostasis in zebrafish.
Thesis, Universiteit Utrecht, pp. 1-177

Geudens I, Herpers R, Hermans K, Segura I, Ruiz de Almodovar C, Bussmann J, De Smet F, Vandevelde W, Hogan BM, Siekmann A, Claes F, Moore JC, Pistocchi AS, Loges S, Mazzone M, Mariggi G, Bruyère F, Cotelli F, Kerjaschki D, Noël A, Foidart JM, Gerhardt H, Ny A, Langenberg T, Lawson ND, Duckers HJ, Schulte-Merker S, Carmeliet P, Dewerchin M.
Role of delta-like-4/Notch in the formation and wiring of the lymphatic network in zebrafish.
Arterioscler Thromb Vasc Biol. 2010 Sep;30(9):1695-702.

Gjini E
Regulation of Angiogenesis and Lymphangiogenesis in Zebrafish.
Thesis, Universiteit Utrecht, pp. 1-106

Gregorieff A, Clevers H.
In situ hybridization to identify gut stem cells.
Curr Protoc Stem Cell Biol. 2010 Jan;Chapter 2:Unit 2F.1.

Groen EJ, van Es MA, van Vught PW, Spliet WG, van Engelen-Lee J, de Visser M, Wokke JH, Schelhaas HJ, Ophoff RA, Fumoto K, Pasterkamp RJ, Dooijes D, Cuppen E, Veldink JH, van den Berg LH.
FUS mutations in familial amyotrophic lateral sclerosis in the Netherlands.
Arch Neurol. 2010 Feb;67(2):224-30.

Hermans K, Claes F, Vandevelde W, Zheng W, Geudens I, Orsenigo F, De Smet F, Gjini E, Anthonis K, Ren B, Kerjaschki D, Autiero M, Ny A, Simons M, Dewerchin M, Schulte-Merker S, Dejana E, Alitalo K, Carmeliet P.
Role of synectin in lymphatic development in zebrafish and frogs.
Blood. 2010 Oct 28;116(17):3356-66.

Herpers RLJM
Genetic regulation of vascular development – building the Zebrafish Vascular Tree.
Thesis, Erasmus Universiteit Rotterdam, pp. 1-125

Hollestelle A, Nagel JH, Smid M, Lam S, Elstrodt F, Wasielewski M, Ng SS, French PJ, Peeters JK, Rozendaal MJ, Riaz M, Koopman DG, Ten Hagen TL, de Leeuw BH, Zwarthoff EC, Teunisse A, van der Spek PJ, Klijn JG, Dinjens WN, Ethier SP, Clevers H, Jochemsen AG, den Bakker MA, Foekens JA, Martens JW, Schutte M.
Distinct gene mutation profiles among luminal-type and basal-type breast cancer cell lines.
Breast Cancer Res Treat. 2010 May;121(1):53-64.

Homberg J, Nijman IJ, Kuijpers S, Cuppen E.
Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats.
BMC Genet. 2010 May 7;11:37.

Homberg JR, la Fleur SE, Cuppen E.
Serotonin transporter deficiency increases abdominal fat in female, but not male rats.
Obesity (Silver Spring). 2010 Jan;18(1):137-45.

in der Rieden PM, Vilaspasa FL, Durston AJ.
Xwnt8 directly initiates expression of labial Hox genes.
Dev Dyn. 2010 Jan;239(1):126-39.

Isik M, Korswagen HC, Berezikov E.
Expression patterns of intronic microRNAs in Caenorhabditis elegans.
Silence. 2010 Feb 1;1(1):5.

Jakobsson L, Franco CA, Bentley K, Collins RT, Ponsioen B, Aspalter IM, Rosewell I, Busse M, Thurston G, Medvinsky A, Schulte-Merker S, Gerhardt H.
Endothelial cells dynamically compete for the tip cell position during angiogenic sprouting.
Nat Cell Biol. 2010 Oct;12(10):943-53.

Jalink K, van Rheenen J.
Nano-imaging of membrane topography affects interpretations in cell biology.
Nat Methods. 2010 Jul;7(7):486.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Bioinformatics. 2010 Apr 15;26(8):1000-6.

Kaaij LJ, Ketting RF.
Dcr1 tracked down.
Dev Cell. 2010 Jan 19;18(1):6-7.

Kamminga LM, Luteijn MJ, den Broeder MJ, Redl S, Kaaij LJ, Roovers EF, Ladurner P, Berezikov E, Ketting RF.
Hen1 is required for oocyte development and piRNA stability in zebrafish.
EMBO J. 2010 Nov 3;29(21):3688-700.

Ketting RF.
MicroRNA biogenesis and function. An overview.
Adv Exp Med Biol. 2010;700:1-14.

Kosinski C, Stange DE, Xu C, Chan AS, Ho C, Yuen ST, Mifflin RC, Powell DW, Clevers H, Leung SY, Chen X.
Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development.
Gastroenterology. 2010 Sep;139(3):893-903.

Lagendijk AK, Smith KA, Bakkers J.
Genetics of congenital heart defects: a candidate gene approach.
Trends Cardiovasc Med. 2010 May;20(4):124-8.

le Duc Q, Shi Q, Blonk I, Sonnenberg A, Wang N, Leckband D, de Rooij J.
Vinculin potentiates E-cadherin mechanosensing and is recruited to actin-anchored sites within adherens junctions in a myosin II-dependent manner.
J Cell Biol. 2010 Jun 28;189(7):1107-15. Erratum in: J Cell Biol. 2010 Nov 15;191(4):891.

Li L, Clevers H.
Coexistence of quiescent and active adult stem cells in mammals.
Science. 2010 Jan 29;327(5965):542-5.

Linsen SE, de Wit E, de Bruijn E, Cuppen E.
Small RNA expression and strain specificity in the rat.
BMC Genomics. 2010 Apr 19;11:249.

Linsen SEV
Small RNA evolution and distribution patterns based on digital gene expression profiling.
Thesis, Universiteit Utrecht, pp. 1-135

Lyddon R, Cuppen E, Haroutunian V, Siever LJ, Dracheva S.
No link of serotonin 2C receptor editing to serotonin transporter genotype.
Neuroreport. 2010 Dec 8;21(17):1080-4.

Mahmoudi T, Boj SF, Hatzis P, Li VS, Taouatas N, Vries RG, Teunissen H, Begthel H, Korving J, Mohammed S, Heck AJ, Clevers H.
The leukemia-associated Mllt10/Af10-Dot1l are Tcf4/β-catenin coactivators essential for intestinal homeostasis.
PLoS Biol. 2010 Nov 16;8(11):e1000539.

Mallo M, Wellik DM, Deschamps J.
Hox genes and regional patterning of the vertebrate body plan.
Dev Biol. 2010 Aug 1;344(1):7-15.

Martins PA, Salic K, Gladka MM, Armand AS, Leptidis S, el Azzouzi H, Hansen A, Coenen-de Roo CJ, Bierhuizen MF, van der Nagel R, van Kuik J, de Weger R, de Bruin A, Condorelli G, Arbones ML, Eschenhagen T, De Windt LJ.
MicroRNA-199b targets the nuclear kinase Dyrk1a in an auto-amplification loop promoting calcineurin/NFAT signalling.
Nat Cell Biol. 2010 Dec;12(12):1220-7.

Menke V, van Es JH, de Lau W, van den Born M, Kuipers EJ, Siersema PD, de Bruin RW, Kusters JG, Clevers H.
Conversion of metaplastic Barrett's epithelium into post-mitotic goblet cells by gamma-secretase inhibition.
Dis Model Mech. 2010 Jan-Feb;3(1-2):104-10.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Science. 2010 Dec 24;330(6012):1787-97.

Mokry M, Hatzis P, de Bruijn E, Koster J, Versteeg R, Schuijers J, van de Wetering M, Guryev V, Clevers H, Cuppen E.
Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
PLoS One. 2010 Nov 30;5(11):e15092.

Mokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, Cuppen E.
Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
Nucleic Acids Res. 2010 Jun;38(10):e116.

Mul JD, Yi CX, van den Berg SA, Ruiter M, Toonen PW, van der Elst MC, Voshol PJ, Ellenbroek BA, Kalsbeek A, la Fleur SE, Cuppen E.
Pmch expression during early development is critical for normal energy homeostasis.
Am J Physiol Endocrinol Metab. 2010 Mar;298(3):E477-88.

Mul JD
Rat models in obesity research: functions for PMCH nd LPIN1 in energy homeostasis regulation.
Thesis, Universiteit Utrecht, pp. 1-168

Ng SS
Unravelling the molecular mechanisms of the canonical Wnt signalling pathway.
Thesis, Universiteit Utrecht, pp. 1-142

Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E.
Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples.
Nat Methods. 2010 Nov;7(11):913-5.

Oerlemans MI, Goumans MJ, van Middelaar B, Clevers H, Doevendans PA, Sluijter JP.
Active Wnt signaling in response to cardiac injury.
Basic Res Cardiol. 2010 Sep;105(5):631-41.

Pedrioli DM, Karpanen T, Dabouras V, Jurisic G, van de Hoek G, Shin JW, Marino D, Kälin RE, Leidel S, Cinelli P, Schulte-Merker S, Brändli AW, Detmar M.
miR-31 functions as a negative regulator of lymphatic vascular lineage-specific differentiation in vitro and vascular development in vivo.
Mol Cell Biol. 2010 Jul;30(14):3620-34.

Pontier DB
Double-strand break repair and G4 DNA stability in Caenorhabditis elegans.
Thesis, Universiteit Utrecht, pp. 1-142

Qiu W, Wang X, Leibowitz B, Liu H, Barker N, Okada H, Oue N, Yasui W, Clevers H, Schoen RE, Yu J, Zhang L.
Chemoprevention by nonsteroidal anti-inflammatory drugs eliminates oncogenic intestinal stem cells via SMAC-dependent apoptosis.
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):20027-32.

Quyn AJ, Appleton PL, Carey FA, Steele RJ, Barker N, Clevers H, Ridgway RA, Sansom OJ, Näthke IS.
Spindle orientation bias in gut epithelial stem cell compartments is lost in precancerous tissue.
Cell Stem Cell. 2010 Feb 5;6(2):175-81.

Roukens MG, Alloul-Ramdhani M, Baan B, Kobayashi K, Peterson-Maduro J, van Dam H, Schulte-Merker S, Baker DA.
Control of endothelial sprouting by a Tel-CtBP complex.
Nat Cell Biol. 2010 Oct;12(10):933-42.

Sartori da Silva MA, Tee JM, Paridaen J, Brouwers A, Runtuwene V, Zivkovic D, Diks SH, Guardavaccaro D, Peppelenbosch MP.
Essential Role for the d-Asb11 cul5 Box Domain for Proper Notch Signaling and Neural Cell Fate Decisions In Vivo.
PLoS One. 2010 Nov 19;5(11):e14023.

Silhankova M, Port F, Harterink M, Basler K, Korswagen HC.
Wnt signalling requires MTM-6 and MTM-9 myotubularin lipid-phosphatase function in Wnt-producing cells.
EMBO J. 2010 Dec 15;29(24):4094-105.

Snippert HJ, Haegebarth A, Kasper M, Jaks V, van Es JH, Barker N, van de Wetering M, van den Born M, Begthel H, Vries RG, Stange DE, Toftgård R, Clevers H.
Lgr6 marks stem cells in the hair follicle that generate all cell lineages of the skin.
Science. 2010 Mar 12;327(5971):1385-9.

Snippert HJ, van der Flier LG, Sato T, van Es JH, van den Born M, Kroon-Veenboer C, Barker N, Klein AM, van Rheenen J, Simons BD, Clevers H.
Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells.
Cell. 2010 Oct 1;143(1):134-44.

Snoeren E, Chan J, Bovens A, Cuppen E, Waldinger M, Olivier B, Oosting R.
Serotonin transporter null mutation and sexual behavior in female rats: 5-HT1A receptor desensitization.
J Sex Med. 2010 Jul;7(7):2424-34.

Sue Ng S, Mahmoudi T, Li VS, Hatzis P, Boersema PJ, Mohammed S, Heck AJ, Clevers H.
MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway.
Biol Chem. 2010 Feb-Mar;391(2-3):171-80.

Tauriello DV, Haegebarth A, Kuper I, Edelmann MJ, Henraat M, Canninga-van Dijk MR, Kessler BM, Clevers H, Maurice MM.
Loss of the tumor suppressor CYLD enhances Wnt/beta-catenin signaling through K63-linked ubiquitination of Dvl.
Mol Cell. 2010 Mar 12;37(5):607-19.

Tee JM
Cell Fate Determination in Zebrafish Embryonic and Adult Muscle Development.
Thesis, Universiteit Utrecht, pp. 1-153

Tournoij E
Platelet Activation in Vascular Disease: from Animal Studies to Clinical Consequences.
Thesis, Universiteit Utrecht, pp. 1-113

Tournoij E, Weber GJ, Akkerman JW, de Groot PG, Zon LI, Moll FL, Schulte-Merker S.
Mlck1a is expressed in zebrafish thrombocytes and is an essential component of thrombus formation.
J Thromb Haemost. 2010 Mar;8(3):588-95.

Vacaru AM, den Hertog J.
Catalytically active membrane-distal phosphatase domain of receptor protein-tyrosine phosphatase alpha is required for Src activation.
FEBS J. 2010 Mar;277(6):1562-70.

Vacaru AM
RPTPa-mediated activation of Src.
Thesis, Universiteit Utrecht, pp. 1-125

Vacaru AM, den Hertog J.
Serine dephosphorylation of receptor protein tyrosine phosphatase alpha in mitosis induces Src binding and activation.
Mol Cell Biol. 2010 Jun;30(12):2850-61.

van Arensbergen J, Garcia-Hurtado J, Moran I, Maestro M, Xu X, Van de Casteele M, Skoudy A, Palassini M, Heimberg H, Ferrer J.
Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program.
Genome Res. 2010 Jun;20(6):722-32.

van Boxtel R, Cuppen E.
Rat traps: filling the toolbox for manipulating the rat genome.
Genome Biol. 2010 Sep 29;11(9):217.

van Boxtel R
Rat reverse genetics: generation and characterization of chemically induced rat mutants.
Thesis, Universiteit Utrecht, pp. 1-161

van Boxtel R, Gould MN, Cuppen E, Smits BM.
ENU mutagenesis to generate genetically modified rat models.
Methods Mol Biol. 2010;597:151-67.

van den Akker WM, Durston AJ, Spaink HP
Identification of hoxb1b downstream genes: hoxb1b has a regulatory factor controlling transcriptional networks and cell movement during zebrafish gastrulation.
Int J Dev Biol. 2010;54(1):55-62.

van Eekelen M, Runtuwene V, Overvoorde J, den Hertog J.
RPTPalpha and PTPepsilon signaling via Fyn/Yes and RhoA is essential for zebrafish convergence and extension cell movements during gastrulation.
Dev Biol. 2010 Apr 15;340(2):626-39.

van Eekelen M, Overvoorde J, van Rooijen C, den Hertog J.
Identification and expression of the family of classical protein-tyrosine phosphatases in zebrafish.
PLoS One. 2010 Sep 3;5(9):e12573.

van Rooijen E, Voest EE, Logister I, Bussmann J, Korving J, van Eeden FJ, Giles RH, Schulte-Merker S.
von Hippel-Lindau tumor suppressor mutants faithfully model pathological hypoxia-driven angiogenesis and vascular retinopathies in zebrafish.
Dis Model Mech. 2010 May-Jun;3(5-6):343-53.

van Wolfswinkel JC, Ketting RF.
The role of small non-coding RNAs in genome stability and chromatin organization.
J Cell Sci. 2010 Jun 1;123(Pt 11):1825-39.

Verheyen EM, Clevers H.
Wnts as self-renewal factors: mammary stem cells and beyond.
Cell Stem Cell. 2010 Jun 4;6(6):494-5.

Verzi MP, Hatzis P, Sulahian R, Philips J, Schuijers J, Shin H, Freed E, Lynch JP, Dang DT, Brown M, Clevers H, Liu XS, Shivdasani RA.
TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions.
Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15157-62.

Vreugdenhil E, Berezikov E.
Fine-tuning the brain: MicroRNAs.
Front Neuroendocrinol. 2010 Apr;31(2):128-33.

Vries RG, Huch M, Clevers H.
Stem cells and cancer of the stomach and intestine.
Mol Oncol. 2010 Oct;4(5):373-84.

Wansleeben C, Feitsma H, Montcouquiol M, Kroon C, Cuppen E, Meijlink F.
Planar cell polarity defects and defective Vangl2 trafficking in mutants for the COPII gene Sec24b.
Development. 2010 Apr;137(7):1067-73.

Wansleeben C, Feitsma H, Tertoolen L, Kroon C, Guryev V, Cuppen E, Meijlink F.
A novel mutant allele of Ncx1: a single amino acid substitution leads to cardiac dysfunction.
Int J Dev Biol. 2010;54(10):1465-71.

Wansleeben C
A mutagenesis screen in the mouse: Identification of novel gene functions in embryonic development.
Thesis, Universiteit Utrecht, pp. 1-110

Witschi R, Johansson T, Morscher G, Scheurer L, Deschamps J, Zeilhofer HU.
Hoxb8-Cre mice: A tool for brain-sparing conditional gene deletion.
Genesis. 2010 Oct 1;48(10):596-602.

2009
Adamovic, T., McAllister, D., Guryev, V., Wang, X., Andrae, J.W., Cuppen, E., Jacob, H.J., Sugg, S.L. (2009) Microalterations of inherently unstable genomic regions in rat mammary carcinomas as revealed by long oligonucleotide array-based comparative genomic hybridization. Cancer Res. 69: 5159-5167.

Alders, M., Hogan, B.M., Gjini, E., Salehl, F., al Gazali, L., Hennekam, E.A., Holmberg, E.E., Mannens, M.M., Mulder, M.F., Offerhaus, G.J., Prescott, T.E., Schroor, E.J., Verheij, J.B., Witte, M., Zwijnenburg, P.J., Vikkula, J.M., Schulte-Merker, S., Hennekam, R.C. (2009) Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans. Nat. Genet. 41(12):1272-4.

Bakkers, J., Verhoeven, M.C., Abdelilah-Seyfried, S. (2009) Shaping the zebrafish heart: from left-right axis specification to epithelial tissue morphogenesis. Dev. Biol. 330: 213-220.

Barker, N., Ridgway, R.A., van Es, J.H., van de Wetering, M., Begthel, H., van den Born, M., Danenberg, E., Clarke, A.R., Sansom, O.J., Clevers, H. (2009) Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457:608-611.

Begus-Nahrmann, Y., Lechel, A., Obenauf, A.C., Nalapareddy, K., Peit, E., Hoffmann, E., Schlaudraff, F., Liss, B., Schirmacher, P., Kestler, H., Danenberg, E., Barker, N., Clevers, H., Speicher, M.R., Rudolph, K.L. (2009) p53 deletion impairs clearance of chromosomal-instable stem cells in aging telomere-dysfunctional mice. Nat. Genet. 41: 1138-1143.

Beqqali, A., van Eldik, W., Mummery, C., Passier, R. (2009) Human stem cells as a model for cardiac differentiation and disease. Cell. Mol. Life Sci. 66: 800-813.

Boonen, R.A.C.M., van Tijn, P., Zivkovic, D. (2009) Wnt signaling in Alzheimer’s disease: up or down, that is the question. Ageing Res. Rev. 8: 71-82.

Brittijn, S.A., Duivesteijn, S.J., Belmamoune, M., Bertens, L.F.M., Bitter, W., de Bruijn, J.D., Champagne, D., Cuppen, E., Flik, G., Vandenbroucke-Grauls, C.M., Janssen, R.A.J., de Jong, I.M., de Kloet, E.R., Kros, A., Meijer, A.H., Metz, J.R., van der Sar, A.M., Schaaf, M.J.M., Schulte-Merker, S., Spaink, H.P., Tak, P.P., Verbeek, F.J., Vervoordeldonk, M.J., Vonk, F.F., Witte, F., Yuan, H., Richardson, M.K. (2009) Zebrafish development and regeneration: new tools for  biomedical research. Int. J. Dev. Biol. 53: 835-850.

Brouwer, K. (2009) DNA repair mechanisms in C. elegans. Thesis, Univ. Utrecht, pp. 1-128.

Bussmann, J. (2009) Genetic analysis and in vivo imaging of vascular development in the zebrafish. Thesis, Univ. Utrecht, pp. 1-100.

Chen, G., Korfhagen, T.R., Xu, Y., Kitzmiller, J., Wert, S.E., Maeda, Y., Gregorieff, A., Clevers, H., Whitsett, J.A. (2009) SPDEF is required for Mouse pulmonary goblet cell differentiation and regulates a network of genes associated with mucus production. J. Clin. Invest. 119: 2914-2924.

Claycomb, J.M., Batista, P.J., Pang, K.M., Gu, W., Vasale, J.J., van Wolfswinkel, J.C., Chaves, D.A., Shirayama, M., Mitani, S., Ketting, R.F., Conte Jr., D., Mello, C.C. (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139: 123-134.

Clevers, H. (2009) Eyeing up new Wnt pathway players. Cell 139: 227-229.

Clevers, H. (2009) Inflammatory bowel disease, stress, and the endoplasmic reticulum. N. Engl. J. Med. 360: 726-727.

Clevers, H. (2009) Searching for adult stem cells in the intestine. EMBO Mol. Med. 1: 255-259.

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de Pater, E., Clijsters, L., Marques, S.R., Lin, Y.F., Garavito-Aguilar, Z.V., Yelon, D., Bakkers, J. (2009) Distinct phases of cardiomyocyte differentiation regulate growth of the zebrafish heart. Development 136: 1633-1641.

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Faro, A., Boj, S.F., Ambrosio, R., van den Broek, O., Korving, J., Clevers, H. (2009) T-cell factor 4 (tcf7l2) is the main effector of Wnt signaling during zebrafish intestine organogenesis. Zebrafish 6: 59-68.

Faro, A., Boj, S.F., Clevers, H. (2009) Fishing for intestinal cancer models: unraveling gastrointestinal homeostatis and tumorigenesis in zebrafish. Zebrafish. 6(4):361-76.

Fu, H., Cai, J., Clevers, H., Fast, E., Gray, S., Greenberg, R., Jain, M.K., Ma, Q., Qiu, M., Rowitch, D.H., Taylor, C.M., Stiles, C.D. (2009) A genome-wide screen for spatially restricted expression patterns identifies transcription factors that regulate glial development. J. Neurosci. 29: 11399-11408.

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Guryev, V., Cuppen, E. (2009) Next generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation. FEBS Lett. 583: 1668-1173

Haegebarth, A., Clevers, H. (2009) Wnt signaling, Lgr5, and stem cells in the intestine and skin. Am. J. Pathol. 174: 715-721.

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2008
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Brugmann, S.A., Goodnough, L.H., Gregorieff, A., Leucht, P., ten Berge, D., Fuerer, C., Clevers, H., Nusse, R., Helms, J.A. (2007) Wnt signaling mediates regional specification in the vertebrate face. Development 134: 3282-3295.

Canté-Barrett, K. (2007) Selection in the thymus: pathway divergence and the commitment to life or death. Thesis, Univ. Utrecht, pp. 1-106.

Carretero, J., Medina, P.P., Blanco, R., Smit, L., Tang, M., Roncador, G., Maestre, L., Conde, E., Lopez-Rios, F., Clevers, H.C., Sanchez-Cespedes, M. (2007) Dysfunctional AMPK activity, signalling through mTOR and survival in response to energetic stress in LKB1-deficient lung cancer. Oncogene 26: 1616-1625.

Carvalho, R.L.C., Itoh, F., Goumans, M.J., Lebrin, F., Kato, M., Takahashi, S., Ema, M., Itoh, S., van Rooijen, M., Bertolino, P., ten Dijke, P., Mummery, C.L. (2007) Compensatory signalling induced in the yolk sac vasculature by deletion of TGFß receptors in mice. J. Cell Sci. 120: 4269-4277.

Chocron, S., Verhoeven, M.C., Rentzsch, F., Hammerschmidt, M., Bakkers, J. (2007) Zebrafish Bmp4 regulates left-right asymmetry at two distinct developmental time points. Dev. Biol. 305: 577-588.

Coudreuse, D., Korswagen, H.C. (2007) The making of Wnt: new insights into Wnt maturation, sorting and secretion. Development 134: 3-12.

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Daley, G.Q., Ahrlund-Richter, L., Auerbach, J.M., Benvenisty, N., Charo, R.A., Chen, G., Deng, H., Goldstein, L.S., Hudson, K.L., Hyun, I., Junn, S.C., Love, J., Lee, E.H., McLaren, A., Mummery, C.L., Nakatsuji, N., Racowsky, C., Rooke, H., Rossant, J., Schöler, H.R., Solbakk, J.H., Taylor, P., Trounson, A.O., Weissman, I.L., Wilmut, I., Yu, J., Zoloth, L. (2007) Ethics. The ISSCR guidelines for human embryonic stem cell research. Science 315: 603-604.

Danalache, B.A., Paquin, J., Wang, D., Grygorczyk, R., Moore, J.C., Mummery, C.L., Gutkowska, J., Jankowski, M. (2007) Nitric oxide signaling in oxytocin-mediated cardiomyogenesis. Stem Cells 25: 679-688.

de Lau, W., Barker, N., Clevers, H. (2007) WNT signaling in the normal intestine and colorectal cancer. Front. Biosci. 12: 471-491.

de Leng, W.W.J., Jansen, M., Keller, J.J., de Gijsel, M., Milne, A.N.A., Morsink, F.H.M., Weterman, M.A.J., Iacobuzio-Donahue, C.A., Clevers, H.C., Giardiello, F.M., Offerhaus, G.J. (2007) Peutz-Jeghers syndrome polyps are polyclonal with expanded progenitor cell compartment. Gut 56: 1475-1476.

Deschamps, J. (2007) Ancestral and recently recruited global control of the Hox genes in development. Curr. Opin. Genet. Dev. 17: 422-427.

Evans, S.M., Mummery, C., Doevendans, P.A. (2007) Progenitor cells for cardiac repair. Semin. Cell Devel. Biol. 18: 153-160.

Feitsma, H., Leal, M.C., Moens, P.B., Cuppen, E., Schulz, R.W. (2007) Mlh1 deficiency in zebrafish results in male sterility and aneuploid as well as triploid progeny in females. Genetics 175: 1561-1569.

Fielitz, J., van Rooij, E., Spencer, J.A., Shelton, J.M., Latif, S., van der Nagel, R., Bezprozvannaya, S., de Windt, L., Richardson, J.A., Bassel-Duby, R., Olson, E.N. (2007) Loss of muscle-specific RING-finger 3 predisposes the heart to cardiac rupture after myocardial infartction. Proc. Natl. Acad. Sci 104: 4377-4382.

Filipczyk, A.A., Laslett, A.L., Mummery, C., Pera, M.F. (2007) Differentiation is coupled to changes in the cell cycle regulatory apparatus of human embryonic stem cells. Stem Cell Res. 1: 46-60.

Filipczyk, A.A., Passier, R., Rochat, A., Mummery, C.L. (2007) Regulation of cardiomyocyte differentiation of embryonic stem cells by extracellular signalling. Cell. Mol. Life Sci. 64: 704-718.

Frische, E.W., Pellis-van Berkel, W., van Haaften, G., Cuppen, E., Plasterk, R.H.A., Tijsterman, M., Bos, J.L., Zwartkruis, F.J.T. (2007) RAP-1 and the RAL-1/exocyst pathway coordinate hypodermal cell organization in Caenorhabditis elegans. EMBO J. 26: 5083-5092.

Gregorieff, A., Clevers, H. (2007) Giving APCmin tumours a SPARC. Gut 56: 1341-1343.

Heck, A.J.R., Mummery, C., Whetton, A., Oh, S., Lee, B., Pera, M., Lemischka, I., Krijgsveld, J. (2007) Proteome biology of stem cells. Stem Cell Res. 1: 7-8.

Holmes, A., Flett, A., Coudreuse, D., Korswagen, H.C., Pettitt, J. (2007) C. elegans disabled is required for cell-type specific endocytosis and is essential in animals lacking the AP-3 adaptor complex. J. Cell Sci. 120: 2741-2751.

Homberg, J.R., Olivier, J.D.A., Smits, B.M.G., Mul, J.D., Mudde, J., Verheul, M., Nieuwenhuizen, O.F.M., Cools, A.R., Ronken, E., Cremers, T., Schoffelmeer, A.N.M., Ellenbroek, B.A., Cuppen, E. (2007) Characterization of the serotonin transporter knockout rat: a selective change in the functioning of the serotonergic system. Neuroscience 146: 1662-1676.

Homberg, J.R., Pattij, T., Janssen, M.C.W., Ronken, E., de Boer, S.F., Schoffelmeer, A.N.M., Cuppen, E. (2007) Serotonin transporter deficiency in rats improves inhibitory control but not behavioural flexibility. Eur. J. Neurosci. 26: 2066-2073.

Homberg, J.R., Schiepers, O.J.G., Schoffelmeer, A.N.M., Cuppen, E., Vanderschuren, L.J.M.J. (2007) Acute and constitutive increases in central serotonin levels reduce social play behaviour in peri-adolescent rats. Psychopharmacology 195: 175-182.

Hornsten, A., Lieberthal, J., Fadia, S., Malins, R., Ha, L., Xu, X., Daigle, L., Markowitz, M., O’Connor, G., Plasterk, R., Li, C. (2007) APL-1, a Caenorhabditis elegans protein related to the human beta-amyloid precursor protein, is essential for viability. Proc. Natl. Acad. Sci. 104: 1971-1976.

Houwing, S., Kamminga, L.M., Berezikov, E., Cronembold, D., Girard, A., van den Elst, H., Filippov, D.V., Blaser, H., Raz, E., Moens, C.B., Plasterk, R.H.A., Hannon, G.J., Draper, B.W., Ketting, R.F. (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129: 69-82.

Jopling, C., den Hertog, J. (2007) Essential role for Csk upstream of Fyn and Yes in zebrafish gastrulation. Mech. Dev. 124: 129-136.

Jopling, C., van Geemen, D., den Hertog, J. (2007) Shp2 knockdown and Noonan/LEOPARD mutant Shp2-induced gastrulation defects. PLoS Genet. 3: e225.

Kammenga, J.E., Doroszuk, A., Riksen, J.A.G., Hazendonk, E., Spiridon, L., Petrescu, A.J., Tijsterman, M., Plasterk, R.H.A., Bakker, J. (2007) A Caenorhabditis elegans wild type defies the temperature-size rule owing to a single nucleotide polymorphism in tra-3. PLoS Genet. 3: e34.

Kapsimali, M., Kloosterman, W.P., de Bruijn, E., Rosa, F., Plasterk, R.H.A., Wilson, S.W. (2007) MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biol. 8: R173.

Kessler, B.M., Fortunati, E., Melis, M., Pals, C.E.G.M., Clevers, H., Maurice, M.M. (2007) Proteome changes induced by knock-down of the deubiquitylating enzyme HAUSP/USP7. J. Proteome Res. 6: 4163-4172.

Ketting, R.F. (2007) A dead end for microRNAs. Cell 131: 1226-1227.

Kim, K.P., Thurston, A., Mummery, C., Ward-van Oostwaard, D., Priddle, H., Allegrucci, C., Denning, C., Young, L. (2007) Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines. Genome Res. 17: 1731-1742.

Kloosterman, W.P. (2007) The expression and function of microRNAs in vertebrate embryonic development. Thesis, Univ. Utrecht, pp. 1-126.

Kloosterman, W.P., Lagendijk, A.K., Ketting, R.F., Moulton, J.D., Plasterk, R.H.A. (2007) Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development. PLoS Biol. 5: e203.

Knoll, R., Postel, R., Wang, J., Kratzner, R., Hennecke, G., Vacaru, A.M., Vakeel, P., Schubert, C., Murthy, K., Rana, B.K., Kube, D., Knoll, G., Schafer, K., Hayashi, T., Holm, T., Kimura, A., Schork, N., Toliat, M.R., Nurnberg, P., Schultheiss, H.P., Schaper, W., Schaper, J., Bos, E., den Hertog, J., van Eeden, F.J.M., Peters, P.J., Hasenfuss, G., Chien, K.R., Bakkers, J. (2007) Laminin-alpha4 and integrin-linked kinase mutations cause human cardiomyopathy via simultaneous defects in cardiomyocytes and endothelial cells. Circulation 116: 515-525.

Kojima, Y., Miyoshi, H., Clevers, H.C., Oshima, M., Aoki, M., Taketo, M.M. (2007) Suppression of tubulin polymerisation by the LKB1-microtubule-associated protein/microtubule affinity-regulating kinasa signaling. J. Biol. Chem. 282: 23532-23540.

Korswagen, H.C. (2007) Wnt signaling in C. elegans: new insights into the regulation of POP-1/TCF-mediated activation and repression. In: Advances in Developmental Biology 17, Wnt signaling in embryonic development. Ed. Sokol, S.Y., Elsevier, San Diego, pp. 95-110

Koudijs, M.J. (2007) Consequences of aberrant hedgehog signaling during zebrafish development. Thesis, Univ. Utrecht, pp. 1-128.

Lemeer, S., Jopling, C., Naji, F., Ruijtenbeek, R., Slijper, M., Heck, A.J.R., den Hertog, J. (2007) Protein-tyrosine kinase activity profiling in knock down zebrafish embryos. PLoS One 2: e581.

Lemeer, S., Ruijtenbeek, R., Pinkse, M.W.H., Jopling, C., Heck, A.J.R., den Hertog, J., Slijper, M. (2007) Endogenous phosphotyrosine signaling in zebrafish embryos. Mol. Cell. Proteomics 6: 2088-2099.

Longman, D., Plasterk, R.H.A., Johnstone, I.L., Caceres, J.F. (2007) Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev. 21: 1075-1085.

Mainguy, G., Koster, J., Woltering, J., Jansen, H., Durston, A. (2007) Extensive polycistronism and antisense transcription in the mammalian hox clusters. PLoS ONE 2: e356.

Malaterre, J., Carpinelli, M., Ernst, M., Alexander, W., Cooke, M., Sutton, S., Dworkin, S., Heath, J.K., Frampton, J., McArthur, G., Clevers, H., Hilton, D., Mantamadiotis, T., Ramsay, R.G. (2007) c-Myb is required for progenitor cell homeostatis in colonic crypts. Proc. Natl. Acad. Sci. 104: 3829-3834.

Meijs, M.F.L., de Windt, L.J., de Jonge, N., Cramer, M.J., Bots, M.L., Mali, W.P.Th., Doevendans, P.A. (2007) Left ventricular hypertrophy: a shift in paradigm. Curr. Med. Chem. 14: 157-171.

Mori-Akiyama, Y., van den Born, M., van Es, J.H., Hamilton, S.R., Adams, H.P., Zhang, J., Clevers, H., de Crombrugghe, B. (2007) SOX9 is required for the differentiation of paneth cells in the intestinal epithelium. Gastroenterology 133: 539-546.

Mummery, C. (2007) Cardiomyocytes from human embryonic stem cells: more than heart repair alone. Bioessays 29: 572-579.

Mummery, C. (2007) Genetic selection of cardiomyocytes from human embryonic stem cells. Mol. Ther. 15: 1908-1909.

Mummery, C., Passier, R., Denning, C. (2007) Directed differentiation of human embryonic stem cells into cardiomyocytes. In: Human embryonic stem cells: the practical handbook. Eds. Sullivan, S., Cowan, C.A., Eggan, K., John Wiley & Sons Ltd, Chichester, pp. 213-228.

Mummery, C., van der Heyden, M.A.G., de Boer, T.P., Passier, R., Ward, D., van den Brink, S., van Rooijen, M., van de Stolpe, A. (2007) Cardiomyocytes from human and mouse embryonic stem cells. In: Methods in Molecular Medicine – Tissue Engineering 2nd edition. Eds. Hauser, H., Fussenegger, M., Humana Press Inc., Totowa, NJ, pp. 249-272.

Muncan, V. (2007) Wnt signaling and c-Myc in intestinal epithelium. Thesis, Univ. Utrecht, pp. 1-112.

Muncan, V., Faro, A., Haramis, A.P.G., Hurlstone, A.F.L., Wienholds, E., van Es, J., Korving, J., Begthel, H., Zivkovic, D., Clevers, H. (2007) T-cell factor 4 (Tcf712) maintains proliferative compartments in zebrafish intestine. EMBO Rep. 8: 966-973.

Naseem, R.H., Meeson, A.P., Dimaio, J.M., White, M.D., Kallhoff, J., Humphries, C., Goetsch, S.C., de Windt, L.J., Williams, M.A., Garry, M.G., Garry, D.J. (2007) Reparative myocardial mechanisms in adult C57BL/6 and MRL mice following injury. Physiol. Genomics 30: 44-52.

Oosterveen, T., Coudreuse, D.Y.M., Yang, P.T., Fraser, E., Bergsma, J., Dale, T.C., Korswagen, H.C. (2007) Two functionally distinct Axin-like proteins regulate canonical Wnt signaling in C. elegans. Dev. Biol. 308: 438-448.

Oving, I.M. (2007) Wnt signaling: its transcriptional output in the intestinal crypt and in colon cancer. Thesis, Univ. Utrecht, pp. 1-108.

Penttinen, P., Jaehrling, J., Damdimopoulos, A.E., Inzunza, J., Lemmen, J.G., van der Saag, P., Pettersson, K., Gauglitz, G., Makela, S., Pongratz, I. (2007) Diet-derived polyphenol metabolite enterolactone is a tissue-specific estrogen receptor activator. Endocrinology 148: 4875-4886.

Quaedackers, M.E., van den Brink, C.E., van der Saag, P.T., Tertoolen, L.G.J. (2007) Direct interaction between estrogen receptor alpha and NF-kappaB in the nucleus of living cells. Mol. Cell. Endocrinol. 273: 42-50.

Rodriguez, F. (2007) Functional characterization of RPTP Dep1 in the zebrafish. Thesis, Univ. Utrecht, pp. 1-146.

Sabates-Bellver, J., van der Flier, L.G., de Palo, M., Cattaneo, E., Maake, C., Rehrauer, H., Laczko, E., Kurowski, M.A., Bujnicki, J.M., Menigatti, M., Luz, J., Ranalli, T.V., Gomes, V., Pastorelli, A., Faggiani, R., Anti, M., Jiricny, J., Clevers, H., Marra, G. (2007) Transcriptome profile of human colorectal adenomas. Mol. Cancer Res. 5: 1263-1275.

Sansom, O.J., Meniel, V.S., Muncan, V., Phesse, T.J., Wilkins, J.A., Reed, K.R., Vass, J.K., Athineos, D., Clevers, H., Clarke, A.R. (2007). Myc deletion rescues Apc deficiency in the small intestine. Nature 446: 676-679.

Sijen, T., Steiner, F.A., Thijssen, K.L., Plasterk, R.H.A. (2007) Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315: 244-247.

Silahtaroglu, A.N., Nolting, D., Dyrskjot, L., Berezikov, E., Moller, M., Tommerup, N., Kauppinen, S. (2007) Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat. Protoc. 2: 2520-2528.

Silhankova, M., Korswagen, H.C. (2007) Migration of neuronal cells along the anterior-posterior body axis of C. elegans: Wnts are in control. Curr. Opin. Genet. Dev. 17: 320-325.

Soete, G. (2007) Cell fate determination in the Caenorhabditis elegans epidermal lineages. Thesis, Univ. Utrecht, pp. 1-138.

Soete, G., Betist, M.C., Korswagen, H.C. (2007) Regulation of Caenorhabditis elegans body size and male tail development by the novel gene lon-8. BMC Dev. Biol. 7: 20.

Steiner, F.A. (2007) Small RNAs and Argonaute proteins: key players in post-transcriptional gene silencing. Thesis, Univ. Utrecht, pp. 1-118.

Steiner, F.A., Hoogstrate, S.W., Okihara, K.L., Thijssen, K.L., Ketting, R.F., Plasterk, R.H.A., Sijen, T. (2007) Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 14: 927-933.

Teunissen, B.E.J., Smeets, P.J.H., Willemsen, P.H.M., de Windt, L.J., van der Vusse, G.J., van Bilsen, M. (2007) Activation of PPARdelta inhibits cardiac fibroblast proliferation and the transdifferentiation into myofibroblasts. Cardiovasc. Res. 75: 519-529.

Thum, T., Galuppo, P., Wolf, C., Fiedler, J., Kneitz, S., van Laake, L.W., Doevendans, P.A., Mummery, C.L., Borlak, J., Haverich, A., Gross, C., Engelhardt, S., Ertl, G., Bauersachs, J. (2007) MicroRNAs in the human heart: a clue to fetal gene reprogramming in heart failure. Circulation 116: 258-267.

Tops, B.B.J. (2007) The biogenesis and function of small RNAs in C. elegans. Thesis, Univ. Utrecht, pp. 1-150.

van Bezooijen, R.L., de Ruiter, M.C., Vilain, N., Monteiro, R.M., Visser, A., van der Wee-Pals, L., van Munsteren, C.J., Hogendoorn, P.C.W., Aguet, M., Mummery, C.L., Papapoulos, S.E., ten Dijke, P., Lowik, C.W.G.M. (2007) SOST expression is restricted to the great arteries during embryonic and neonatal cardiovascular development. Dev. Dyn. 236: 606-612.

van den Akker, W.M.R., Brox, A., Puelles, L., Durston, A.J., Medina, L. (2007) Comparative functional analysis provides evidence for a crucial role for the homeobox gene Nkx2.1/Titf-1 in forebrain evolution. J. Comp. Neurol. 506: 211-223.

van der Flier, L.G., Sabates-Bellver, J., Oving, I., Haegebarth, A., de Palo, M., Anti, M., van Gijn, M.E., Suijkerbuijk, S., van de Wetering, M., Marra, G., Clevers, H. (2007) The intestinal Wnt/TCF signature. Gastroenterology 132: 628-632.

van Empel, V. (2007) Apoptosis-inducing factors in cardiac cell death and cell survival. Thesis, Univ. Utrecht, pp. 1-122.

van Hoof, D., Pinkse, M.W.H., Ward-van Oostwaard, D., Mummery, C.L., Heck, A.J.R., Krijgsveld, J. (2007) An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nat. Methods 4: 677-678.

van Laake, L.W., Passier, R., Monshouwer-Kloots, J., Nederhoff, M.G., Ward-van Oostwaard, D., Field, L.J., van Echteld, C.J., Doevendans, P.A., Mummery, C.L. (2007) Monitoring of cell therapy and assessment of cardiac function using magnetic resonance imaging in a mouse model of myocardial infarction. Nat. Protoc. 2: 2551-2567.

van Laake, L.W., Passier, R., Monshouwer-Kloots, J., Verkleij, A.J., Lips, D.J., Freund, C., den Ouden, K., Ward-van Oostwaard, D., Korving, J., Tertoolen, L.G., van Echteld, C.J., Doevendans, P.A., Mummery, C.L. (2007) Human embryonic stem cell-derived cardiomyocytes survive and mature in the mouse heart and transiently improve function after myocardial infarction. Stem Cell Res. 1: 9-24.

van Noort, M., Weerkamp, F., Clevers, H.C., Staal, F.J.T. (2007) Wnt signaling and phosphorylation status of ß-catenin: importance of the correct antibody tools. Blood 110: 2778-2779.

van Oort, R.J. (2007) The transcription factor myocyte enhancer factor-2 (MEF2) in cardiac hypertrophy and heart failure. Thesis, Univ. Utrecht, pp. 1-118.

von der Hardt, S., Bakkers, J., Inbal, A., Carvalho, L., Solnica-Krezel, L., Heisenberg, C.P., Hammerschmidt, M. (2007) The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion. Curr. Biol. 17: 475-487.

Vooijs, M., Ong, C.T., Hadland, B., Huppert, S., Liu, Z., Korving, J., van den Born, M., Stappenbeck, T., Wu, Y., Clevers, H., Kopan, R. (2007) Mapping the consequence of Notch1 proteolysis in vivo with NIP-CRE. Development 134: 535-544.

Wehkamp, J., Wang, G., Kubler, I., Nuding, S., Gregorieff, A., Schnabel, A., Kays, R.J., Fellermann, K., Burk, O., Schwab, M., Clevers, H., Bevins, C.L., Stange, E.F. (2007) The paneth cell alpha-defensin deficiency of ileal Crohn’s disease is linked to Wnt/Tcf-4. J. Immunol. 179: 3109-3118.

Windahl, S.H., Lagerquist, M.K., Andersson, N., Jochems, C., Kallkopf, A., Hakansson, C., Inzunza, J., Gustafsson, J.A., van der Saag, P.T., Carlsten, H., Pettersson, K., Ohlsson, C. (2007) Identification of target cells for the genomic effects of estrogens in bone. Endocrinology 148: 5688-5695.

Yang, J., Groen, A., Lemeer, S., Jans, A., Slijper, M., Roe, S.M., den Hertog, J., Barford, D. (2007) Reversible oxidation of the membrane distal domain of receptor PTPalpha is mediated by a cyclic sulfenamide. Biochemistry 46: 709-719.

2006
Ason, B., Darnell, D.K., Wittbrodt, B., Berezikov, E., Kloosterman, W.P., Wittbrodt, J., Antin, P.B., Plasterk, R.H.A. (2006) Differences in vertebrate microRNA expression. Proc. Natl. Acad. Sci. 103: 14385-14389.

Barker, N., Clevers, H. (2006) Mining the Wnt pathway for cancer therapeutics. Nat. Rev. Drug Discov. 5: 997-1014.

Beqqali, A., Kloots, J., Ward-van Oostwaard, D., Mummery, C., Passier, R. (2006) Genome-wide transcriptional profiling of human embryonic stem cells differentiating to cardiomyocytes. Stem Cells 24: 1956-1967.

Berezikov, E., Cuppen, E., Plasterk, R.H.A. (2006) Approaches to microRNA discovery. Nat. Genet. 38: S2-S7.

Berezikov, E., Thuemmler, F., van Laake, L.W., Kondova, I., Bontrop, R., Cuppen, E., Plasterk, R.H.A. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38: 1375-1377.

Berezikov, E., van Tetering, G., Verheul, M., van de Belt, J., van Laake, L., Vos, J., Verloop, R., van de Wetering, M., Guryev, V., Takada, S., van Zonneveld, A.J., Mano, H., Plasterk, R., Cuppen, E. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 16: 1289-1298.

Bijlsma, M.F., Spek, C.A., Zivkovic, D., van de Water, S., Rezaee, F., Peppelenbosch, M.P. (2006) Repression of smoothened by patched-dependent (pro-)vitamin D3 secretion. PLoS Biol. 4: e232.

Chuva de Sousa Lopes, S.M., Hassink, R.J., Feijen, A., van Rooijen, M.A., Doevendans, P.A., Tertoolen, L., Brutel de la Riviere, A., Mummery, C.L. (2006) Patterning the heart, a template for human cardiomyocyte development. Dev. Dyn. 235: 1994-2002.

Chuva de Sousa Lopes, S.M., Mummery, C.L. (2006) Differentiation in early development. In: Essentials of Stem Cell Biology. Ed. Lanza, R., San Diego, Elsevier Academic Press, pp. 101-110.

Chuva de Sousa Lopes, S.M., Mummery, C.L., Thorsteinsdottir, S. (2006) Implantation and placentation. In: Cell signaling and growth factors in development: from molecules to organogenesis. Eds. Unsicker, K., Krieglstein, K., Weinheim, Wiley Verlag GmbH & Co., pp. 73-105.

Clevers, H. (2006) Colon cancer - understanding how NSAIDs work. N. Engl. J. Med. 354: 761-763.

Clevers, H. (2006) Wnt/ß-catenin signaling in development and disease. Cell 127: 469-480.

Clevers, H., Batlle, E. (2006) EphB/EphrinB receptors and Wnt signaling in colorectal cancer. Cancer Res. 66: 2-5.

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