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Items: 1 to 50 of 135

1.

Removal of artifact bias from qPCR results using DNA melting curve analysis.

Ruijter JM, Ruiz-Villalba A, van den Hoff AJJ, Gunst QD, Wittwer CT, van den Hoff MJB.

FASEB J. 2019 Nov 2:fj201901604R. doi: 10.1096/fj.201901604R. [Epub ahead of print]

PMID:
31682470
2.

Colourimetric analysis of thermally altered human bone samples.

Krap T, Ruijter JM, Nota K, Karel J, Burgers AL, Aalders MCG, Oostra RJ, Duijst W.

Sci Rep. 2019 Jun 20;9(1):8923. doi: 10.1038/s41598-019-45420-8.

3.

Comment on 'A DNA extraction method for small quantities of bone for high-qualitygenotyping' by Caputo et al.

Krap T, Busscher L, Ruijter JM, Oostra RJ, Duijst W.

Forensic Sci Int Genet. 2019 May;40:e243-e244. doi: 10.1016/j.fsigen.2019.01.011. Epub 2019 Jan 31. No abstract available.

PMID:
30770290
4.

Considerations for Measurement of Embryonic Organ Growth.

Prakash S, de Boer BA, Hagoort J, Gunst QD, Ruijter JM, van den Hoff MJB.

Anat Rec (Hoboken). 2019 Jan;302(1):49-57. doi: 10.1002/ar.23908. Epub 2018 Oct 5.

PMID:
30289204
5.

Interfering With DNA Decondensation as a Strategy Against Mycobacteria.

Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN.

Front Microbiol. 2018 Sep 5;9:2034. doi: 10.3389/fmicb.2018.02034. eCollection 2018.

6.

Paradoxical effects of mutant ubiquitin on Aβ plaque formation in an Alzheimer mouse model.

Verheijen BM, Stevens JAA, Gentier RJG, van 't Hekke CD, van den Hove DLA, Hermes DJHP, Steinbusch HWM, Ruijter JM, Grimm MOW, Haupenthal VJ, Annaert W, Hartmann T, van Leeuwen FW.

Neurobiol Aging. 2018 Dec;72:62-71. doi: 10.1016/j.neurobiolaging.2018.08.011. Epub 2018 Aug 18.

7.

Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review.

de Ronde MWJ, Ruijter JM, Moerland PD, Creemers EE, Pinto-Sietsma SJ.

Clin Chem. 2018 Sep;64(9):1308-1318. doi: 10.1373/clinchem.2017.285288. Epub 2018 Jun 14. Review.

8.

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers.

Kok MGM, de Ronde MWJ, Moerland PD, Ruijter JM, Creemers EE, Pinto-Sietsma SJ.

Biomol Detect Quantif. 2017 Dec 18;15:1-5. doi: 10.1016/j.bdq.2017.11.002. eCollection 2018 May.

9.

Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR).

Ruiz-Villalba A, van Pelt-Verkuil E, Gunst QD, Ruijter JM, van den Hoff MJ.

Biomol Detect Quantif. 2017 Nov 1;14:7-18. doi: 10.1016/j.bdq.2017.10.001. eCollection 2017 Dec.

10.

Maternal diabetes causes developmental delay and death in early-somite mouse embryos.

Zhao J, Hakvoort TBM, Ruijter JM, Jongejan A, Koster J, Swagemakers SMA, Sokolovic A, Lamers WH.

Sci Rep. 2017 Sep 15;7(1):11714. doi: 10.1038/s41598-017-11696-x.

11.

Deletion of Fstl1 (Follistatin-Like 1) From the Endocardial/Endothelial Lineage Causes Mitral Valve Disease.

Prakash S, Borreguero LJJ, Sylva M, Flores Ruiz L, Rezai F, Gunst QD, de la Pompa JL, Ruijter JM, van den Hoff MJB.

Arterioscler Thromb Vasc Biol. 2017 Sep;37(9):e116-e130. doi: 10.1161/ATVBAHA.117.309089. Epub 2017 Jul 13.

PMID:
28705792
12.

The effect of repeated freeze-thaw cycles on human muscle tissue visualized by postmortem computed tomography (PMCT).

Klop AC, Vester MEM, Colman KL, Ruijter JM, Van Rijn RR, Oostra RJ.

Clin Anat. 2017 Sep;30(6):799-804. doi: 10.1002/ca.22917. Epub 2017 Jun 19.

PMID:
28514529
13.

The dimensions of the tarsal sinus and canal in different foot positions and its clinical implications.

Kleipool RP, Blankevoort L, Ruijter JM, Kerkhoffs GMMJ, Oostra RJ.

Clin Anat. 2017 Nov;30(8):1049-1057. doi: 10.1002/ca.22908. Epub 2017 Jun 12.

PMID:
28514509
14.

Luminescence of thermally altered human skeletal remains.

Krap T, Nota K, Wilk LS, van de Goot FRW, Ruijter JM, Duijst W, Oostra RJ.

Int J Legal Med. 2017 Jul;131(4):1165-1177. doi: 10.1007/s00414-017-1546-1. Epub 2017 Feb 23.

15.

Practical data handling pipeline improves performance of qPCR-based circulating miRNA measurements.

de Ronde MWJ, Ruijter JM, Lanfear D, Bayes-Genis A, Kok MGM, Creemers EE, Pinto YM, Pinto-Sietsma SJ.

RNA. 2017 May;23(5):811-821. doi: 10.1261/rna.059063.116. Epub 2017 Feb 15.

16.

The geometrical precision of virtual bone models derived from clinical computed tomography data for forensic anthropology.

Colman KL, Dobbe JGG, Stull KE, Ruijter JM, Oostra RJ, van Rijn RR, van der Merwe AE, de Boer HH, Streekstra GJ.

Int J Legal Med. 2017 Jul;131(4):1155-1163. doi: 10.1007/s00414-017-1548-z. Epub 2017 Feb 10.

17.

Reference genes for gene expression studies in the mouse heart.

Ruiz-Villalba A, Mattiotti A, Gunst QD, Cano-Ballesteros S, van den Hoff MJ, Ruijter JM.

Sci Rep. 2017 Feb 2;7(1):24. doi: 10.1038/s41598-017-00043-9.

18.

Unexpected regulation of miRNA abundance during adaptation of early-somite mouse embryos to diabetic pregnancy.

Zhao J, Hakvoort TBM, Jongejan A, Ruijter JM, van Kampen AHC, Lamers WH.

Biochem Biophys Res Commun. 2017 Jan 22;482(4):1013-1018. doi: 10.1016/j.bbrc.2016.11.149. Epub 2016 Nov 28.

PMID:
27908722
19.

An interactive three-dimensional digital atlas and quantitative database of human development.

de Bakker BS, de Jong KH, Hagoort J, de Bree K, Besselink CT, de Kanter FE, Veldhuis T, Bais B, Schildmeijer R, Ruijter JM, Oostra RJ, Christoffels VM, Moorman AF.

Science. 2016 Nov 25;354(6315). pii: aag0053.

PMID:
27884980
20.

Pivotal role of glutamine synthetase in ammonia detoxification.

Hakvoort TB, He Y, Kulik W, Vermeulen JL, Duijst S, Ruijter JM, Runge JH, Deutz NE, Koehler SE, Lamers WH.

Hepatology. 2017 Jan;65(1):281-293. doi: 10.1002/hep.28852. Epub 2016 Nov 12.

PMID:
27641632
21.

Removal of between-run variation in a multi-plate qPCR experiment.

Ruijter JM, Ruiz Villalba A, Hellemans J, Untergasser A, van den Hoff MJ.

Biomol Detect Quantif. 2015 Jul 30;5:10-4. doi: 10.1016/j.bdq.2015.07.001. eCollection 2015 Sep.

22.

Identification of a regulatory domain controlling the Nppa-Nppb gene cluster during heart development and stress.

Sergeeva IA, Hooijkaas IB, Ruijter JM, van der Made I, de Groot NE, van de Werken HJ, Creemers EE, Christoffels VM.

Development. 2016 Jun 15;143(12):2135-46. doi: 10.1242/dev.132019. Epub 2016 Apr 5.

23.

EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures.

van Duijvenboden K, de Boer BA, Capon N, Ruijter JM, Christoffels VM.

Nucleic Acids Res. 2016 Mar 18;44(5):e42. doi: 10.1093/nar/gkv1144. Epub 2015 Nov 3.

24.

RDML-Ninja and RDMLdb for standardized exchange of qPCR data.

Ruijter JM, Lefever S, Anckaert J, Hellemans J, Pfaffl MW, Benes V, Bustin SA, Vandesompele J, Untergasser A; RDML consortium.

BMC Bioinformatics. 2015 Jun 20;16:197. doi: 10.1186/s12859-015-0637-6.

25.

Integrating multi-scale knowledge on cardiac development into a computational model of ventricular trabeculation.

de Boer BA, Le Garrec JF, Christoffels VM, Meilhac SM, Ruijter JM.

Wiley Interdiscip Rev Syst Biol Med. 2014 Nov-Dec;6(6):389-97. doi: 10.1002/wsbm.1285. Epub 2014 Oct 6.

PMID:
25286050
26.

Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry, targeted sequence, type of DNA input and PCR efficiency.

Ruijter JM, Lorenz P, Tuomi JM, Hecker M, van den Hoff MJ.

Mikrochim Acta. 2014;181(13-14):1689-1696. Epub 2014 Jan 14.

27.

OccuPeak: ChIP-Seq peak calling based on internal background modelling.

de Boer BA, van Duijvenboden K, van den Boogaard M, Christoffels VM, Barnett P, Ruijter JM.

PLoS One. 2014 Jun 17;9(6):e99844. doi: 10.1371/journal.pone.0099844. eCollection 2014.

28.

Cardiomyocyte-specific miRNA-30c over-expression causes dilated cardiomyopathy.

Wijnen WJ, van der Made I, van den Oever S, Hiller M, de Boer BA, Picavet DI, Chatzispyrou IA, Houtkooper RH, Tijsen AJ, Hagoort J, van Veen H, Everts V, Ruijter JM, Pinto YM, Creemers EE.

PLoS One. 2014 May 2;9(5):e96290. doi: 10.1371/journal.pone.0096290. eCollection 2014.

29.

Gene regulatory elements of the cardiac conduction system.

van Duijvenboden K, Ruijter JM, Christoffels VM.

Brief Funct Genomics. 2014 Jan;13(1):28-38. doi: 10.1093/bfgp/elt031. Epub 2013 Aug 22. Review.

PMID:
23969024
30.

Augmented mandibular bone structurally adapts to functional loading.

Verhoeven JW, Ruijter JM, Koole R, de Putter C, Terlou M, Cune MS.

Int J Oral Maxillofac Surg. 2013 Dec;42(12):1515-21. doi: 10.1016/j.ijom.2013.03.016. Epub 2013 Jun 20.

PMID:
23791249
31.

Image cytometry: protocols for 2D and 3D quantification in microscopic images.

Chieco P, Jonker A, De Boer BA, Ruijter JM, Van Noorden CJ.

Prog Histochem Cytochem. 2013 Jan;47(4):211-333. doi: 10.1016/j.proghi.2012.09.001. Epub 2012 Nov 10. Review.

PMID:
23146330
32.

Measurement and 3D-visualization of cell-cycle length using double labelling with two thymidine analogues applied in early heart development.

de Boer BA, van den Berg G, Soufan AT, de Boer PA, Hagoort J, van den Hoff MJ, Moorman AF, Ruijter JM.

PLoS One. 2012;7(10):e47719. doi: 10.1371/journal.pone.0047719. Epub 2012 Oct 16.

33.

Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications.

Ruijter JM, Pfaffl MW, Zhao S, Spiess AN, Boggy G, Blom J, Rutledge RG, Sisti D, Lievens A, De Preter K, Derveaux S, Hellemans J, Vandesompele J.

Methods. 2013 Jan;59(1):32-46. doi: 10.1016/j.ymeth.2012.08.011. Epub 2012 Sep 3.

PMID:
22975077
34.

Growth of the developing mouse heart: an interactive qualitative and quantitative 3D atlas.

de Boer BA, van den Berg G, de Boer PA, Moorman AF, Ruijter JM.

Dev Biol. 2012 Aug 15;368(2):203-13. doi: 10.1016/j.ydbio.2012.05.001. Epub 2012 May 14.

35.

Facilitatory and inhibitory effects of SCN5A mutations on atrial fibrillation in Brugada syndrome.

Amin AS, Boink GJ, Atrafi F, Spanjaart AM, Asghari-Roodsari A, Molenaar RJ, Ruijter JM, Wilde AA, Tan HL.

Europace. 2011 Jul;13(7):968-75. doi: 10.1093/europace/eur011. Epub 2011 Jan 26.

PMID:
21273195
36.

The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format.

de Boer BA, Soufan AT, Hagoort J, Mohun TJ, van den Hoff MJ, Hasman A, Voorbraak FP, Moorman AF, Ruijter JM.

Development. 2011 Jan;138(1):159-67. doi: 10.1242/dev.051086.

37.

Glutamine synthetase deficiency in murine astrocytes results in neonatal death.

He Y, Hakvoort TB, Vermeulen JL, Labruyère WT, De Waart DR, Van Der Hel WS, Ruijter JM, Uylings HB, Lamers WH.

Glia. 2010 Apr 15;58(6):741-54. doi: 10.1002/glia.20960.

PMID:
20140959
38.

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value.

Tuomi JM, Voorbraak F, Jones DL, Ruijter JM.

Methods. 2010 Apr;50(4):313-22. doi: 10.1016/j.ymeth.2010.02.003. Epub 2010 Feb 6.

PMID:
20138998
39.

Glutamine synthetase in muscle is required for glutamine production during fasting and extrahepatic ammonia detoxification.

He Y, Hakvoort TB, Köhler SE, Vermeulen JL, de Waart DR, de Theije C, ten Have GA, van Eijk HM, Kunne C, Labruyere WT, Houten SM, Sokolovic M, Ruijter JM, Deutz NE, Lamers WH.

J Biol Chem. 2010 Mar 26;285(13):9516-24. doi: 10.1074/jbc.M109.092429. Epub 2010 Jan 11.

40.

Tubulin polymerization modifies cardiac sodium channel expression and gating.

Casini S, Tan HL, Demirayak I, Remme CA, Amin AS, Scicluna BP, Chatyan H, Ruijter JM, Bezzina CR, van Ginneken AC, Veldkamp MW.

Cardiovasc Res. 2010 Mar 1;85(4):691-700. doi: 10.1093/cvr/cvp352. Epub 2009 Oct 26.

PMID:
19861310
41.

Exercise-induced ECG changes in Brugada syndrome.

Amin AS, de Groot EA, Ruijter JM, Wilde AA, Tan HL.

Circ Arrhythm Electrophysiol. 2009 Oct;2(5):531-9. doi: 10.1161/CIRCEP.109.862441. Epub 2009 Aug 24.

PMID:
19843921
42.

More than a decade of developmental gene expression atlases: where are we now?

de Boer BA, Ruijter JM, Voorbraak FP, Moorman AF.

Nucleic Acids Res. 2009 Dec;37(22):7349-59. doi: 10.1093/nar/gkp819. Review. Erratum in: Nucleic Acids Res. 2010 May;38(9):3147.

43.

Epicardium and myocardium separate from a common precursor pool by crosstalk between bone morphogenetic protein- and fibroblast growth factor-signaling pathways.

van Wijk B, van den Berg G, Abu-Issa R, Barnett P, van der Velden S, Schmidt M, Ruijter JM, Kirby ML, Moorman AF, van den Hoff MJ.

Circ Res. 2009 Aug 28;105(5):431-41. doi: 10.1161/CIRCRESAHA.109.203083. Epub 2009 Jul 23.

44.

Serial noninvasive assessment of apoptosis during right ventricular disease progression in rats.

Campian ME, Verberne HJ, Hardziyenka M, de Bruin K, Selwaness M, van den Hoff MJ, Ruijter JM, van Eck-Smit BL, de Bakker JM, Tan HL.

J Nucl Med. 2009 Aug;50(8):1371-7. doi: 10.2967/jnumed.108.061366. Epub 2009 Jul 17.

45.

Dentofacial characteristics of patients with hypodontia.

Créton M, Cune MS, de Putter C, Ruijter JM, Kuijpers-Jagtman AM.

Clin Oral Investig. 2010 Aug;14(4):467-77. doi: 10.1007/s00784-009-0308-y. Epub 2009 Jul 10.

PMID:
19590908
46.

Bone structure changes in iliac crest grafts combined with implants.

Verhoeven JW, Ruijter JM, Koole R, de Putter C, Cune MS.

Clin Implant Dent Relat Res. 2010 Dec;12(4):289-96. doi: 10.1111/j.1708-8208.2009.00169.x.

PMID:
19438961
47.

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data.

Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, Moorman AF.

Nucleic Acids Res. 2009 Apr;37(6):e45. doi: 10.1093/nar/gkp045. Epub 2009 Feb 22.

48.

A caudal proliferating growth center contributes to both poles of the forming heart tube.

van den Berg G, Abu-Issa R, de Boer BA, Hutson MR, de Boer PA, Soufan AT, Ruijter JM, Kirby ML, van den Hoff MJ, Moorman AF.

Circ Res. 2009 Jan 30;104(2):179-88. doi: 10.1161/CIRCRESAHA.108.185843. Epub 2008 Dec 4.

49.

The human neonatal small intestine has the potential for arginine synthesis; developmental changes in the expression of arginine-synthesizing and -catabolizing enzymes.

Köhler ES, Sankaranarayanan S, van Ginneken CJ, van Dijk P, Vermeulen JL, Ruijter JM, Lamers WH, Bruder E.

BMC Dev Biol. 2008 Nov 10;8:107. doi: 10.1186/1471-213X-8-107.

50.

Fever-induced QTc prolongation and ventricular arrhythmias in individuals with type 2 congenital long QT syndrome.

Amin AS, Herfst LJ, Delisle BP, Klemens CA, Rook MB, Bezzina CR, Underkofler HA, Holzem KM, Ruijter JM, Tan HL, January CT, Wilde AA.

J Clin Invest. 2008 Jul;118(7):2552-61. doi: 10.1172/JCI35337.

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