Jan M Ruijter

Jan M Ruijter

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Jan M Ruijter

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

FASEB J 2019 Dec 2;33(12):14542-14555. Epub 2019 Nov 2.

Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center (AMC), Amsterdam, The Netherlands.

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http://dx.doi.org/10.1096/fj.201901604RDOI Listing
December 2019

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

Forensic Sci Int Genet 2019 05 31;40:e243-e244. Epub 2019 Jan 31.

Ars Cogniscendi Centre for Legal and Forensic medicine, Wezep, the Netherlands; Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1016/j.fsigen.2019.01.011DOI Listing
May 2019

Considerations for Measurement of Embryonic Organ Growth.

Anat Rec (Hoboken) 2019 01 5;302(1):49-57. Epub 2018 Oct 5.

Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/ar.23908DOI Listing
January 2019

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

Neurobiol Aging 2018 12 18;72:62-71. Epub 2018 Aug 18.

Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01974580183029
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http://dx.doi.org/10.1016/j.neurobiolaging.2018.08.011DOI Listing
December 2018

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

Biomol Detect Quantif 2017 Dec 1;14:7-18. Epub 2017 Nov 1.

Academic Medical Center, Department of Medical Biology, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.bdq.2017.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727009PMC
December 2017

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

Clin Anat 2017 Sep 19;30(6):799-804. Epub 2017 Jun 19.

Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, 1105, AZ Amsterdam, The Netherlands.

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http://doi.wiley.com/10.1002/ca.22917
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http://dx.doi.org/10.1002/ca.22917DOI Listing
September 2017

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

Arterioscler Thromb Vasc Biol 2017 09 13;37(9):e116-e130. Epub 2017 Jul 13.

From the Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (S.P., M.S., F.R., Q.D.G., J.M.R., M.J.B.v.d.H.); Cardiovascular Imaging Laboratory, Centro Nacional de Investigación Cardiovascular, Madrid, Spain (L.J.J.B., L.F.R.); and Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigación Cardiovascular, Madrid, Spain (J.-L.d.l.P.).

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http://dx.doi.org/10.1161/ATVBAHA.117.309089DOI Listing
September 2017

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

Sci Rep 2017 09 15;7(1):11714. Epub 2017 Sep 15.

Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, Netherlands.

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http://dx.doi.org/10.1038/s41598-017-11696-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5601907PMC
September 2017

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

Int J Legal Med 2017 Jul 10;131(4):1155-1163. Epub 2017 Feb 10.

Department of Biomedical Engineering and Physics, Academic Medical Centre, University of Amsterdam, P.O. Box 22660, 1100 DD, Amsterdam, The Netherlands.

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http://link.springer.com/10.1007/s00414-017-1548-z
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http://dx.doi.org/10.1007/s00414-017-1548-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491564PMC
July 2017

Luminescence of thermally altered human skeletal remains.

Int J Legal Med 2017 Jul 23;131(4):1165-1177. Epub 2017 Feb 23.

Department of Anatomy, Embryology and Physiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00414-017-1546-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491595PMC
July 2017

Reference genes for gene expression studies in the mouse heart.

Sci Rep 2017 02 2;7(1):24. Epub 2017 Feb 2.

Department of Anatomy, Embryology and Physiology, Academic Medical Center, Amsterdam, The Netherlands.

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http://www.nature.com/articles/s41598-017-00043-9
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http://dx.doi.org/10.1038/s41598-017-00043-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428317PMC
February 2017

Pivotal role of glutamine synthetase in ammonia detoxification.

Hepatology 2017 01 12;65(1):281-293. Epub 2016 Nov 12.

Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/hep.28852DOI Listing
January 2017

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

Nucleic Acids Res 2016 Mar 3;44(5):e42. Epub 2015 Nov 3.

Department of Anatomy, Embryology & Physiology, Academic Medical Centre, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv1144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797259PMC
March 2016

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

Biomol Detect Quantif 2015 Sep 30;5:10-4. Epub 2015 Jul 30.

Department of Anatomy, Embryology and Physiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.bdq.2015.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822202PMC
September 2015

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

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

Department of Anatomy, Embryology and Physiology, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/wsbm.1285DOI Listing
June 2015

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

BMC Bioinformatics 2015 Jun 20;16:197. Epub 2015 Jun 20.

Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, 69117, Germany.

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http://dx.doi.org/10.1186/s12859-015-0637-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474546PMC
June 2015

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

PLoS One 2014 17;9(6):e99844. Epub 2014 Jun 17.

Department of Anatomy, Embryology & Physiology, Academic Medical Centre, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099844PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4061025PMC
February 2015

Gene regulatory elements of the cardiac conduction system.

Brief Funct Genomics 2014 Jan 22;13(1):28-38. Epub 2013 Aug 22.

Department of Anatomy, Embryology & Physiology, Academic Medical Centre, L2-108, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands. Tel.: + 31 20 5667821; Fax: + 31 20 6976177;

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http://dx.doi.org/10.1093/bfgp/elt031DOI Listing
January 2014

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

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

Department of Anatomy, Embryology & Physiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00604-013-1155-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167442PMC
January 2014

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

Methods 2013 Jan 3;59(1):32-46. Epub 2012 Sep 3.

Department of Anatomy, Embryology & Physiology, Academic Medical Center, Meibergdreef 15, 1100AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.ymeth.2012.08.011DOI Listing
January 2013

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

Prog Histochem Cytochem 2013 Jan 10;47(4):211-333. Epub 2012 Nov 10.

Center for Applied Biomedical Research, S. Orsola-Malpighi University Hospital, Via Massarenti 9, I-40138 Bologna, Italy.

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http://dx.doi.org/10.1016/j.proghi.2012.09.001DOI Listing
January 2013

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

Dev Biol 2012 Aug 14;368(2):203-13. Epub 2012 May 14.

Heart Failure Research Center, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.ydbio.2012.05.001DOI Listing
August 2012

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

Europace 2011 Jul 26;13(7):968-75. Epub 2011 Jan 26.

Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/europace/eur011DOI Listing
July 2011

Bone structure changes in iliac crest grafts combined with implants.

Clin Implant Dent Relat Res 2010 Dec;12(4):289-96

Department of Oral & Maxillofacial Surgery, Prosthodontics and Special Dental Care, University Medical Center, Utrecht, The Netherlands.

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http://dx.doi.org/10.1111/j.1708-8208.2009.00169.xDOI Listing
December 2010

Dentofacial characteristics of patients with hypodontia.

Clin Oral Investig 2010 Aug 10;14(4):467-77. Epub 2009 Jul 10.

Department of Oral-Maxillofacial Surgery, Prosthodontics and Special Dental Care, University Medical Centre Utrecht, PO Box 85.060, 3508 AB Utrecht, The Netherlands.

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http://dx.doi.org/10.1007/s00784-009-0308-yDOI Listing
August 2010

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

Methods 2010 Apr 6;50(4):313-22. Epub 2010 Feb 6.

Departments of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.

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http://dx.doi.org/10.1016/j.ymeth.2010.02.003DOI Listing
April 2010

Glutamine synthetase deficiency in murine astrocytes results in neonatal death.

Glia 2010 Apr;58(6):741-54

AMC Liver Center and Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/glia.20960DOI Listing
April 2010

Tubulin polymerization modifies cardiac sodium channel expression and gating.

Cardiovasc Res 2010 Mar 26;85(4):691-700. Epub 2009 Oct 26.

Department of Clinical and Experimental Cardiology, Heart Failure Research Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/cvr/cvp352DOI Listing
March 2010

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

Nucleic Acids Res 2009 Dec;37(22):7349-59

Heart Failure Research Center, Department of Anatomy and Embryology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkp819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794177PMC
December 2009

Exercise-induced ECG changes in Brugada syndrome.

Circ Arrhythm Electrophysiol 2009 Oct 24;2(5):531-9. Epub 2009 Aug 24.

Heart Failure Research Center and Department of Cardiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.

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https://www.ahajournals.org/doi/10.1161/CIRCEP.109.862441
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http://dx.doi.org/10.1161/CIRCEP.109.862441DOI Listing
October 2009

Msx1 and Msx2 are functional interacting partners of T-box factors in the regulation of Connexin43.

Cardiovasc Res 2008 Jun 19;78(3):485-93. Epub 2008 Feb 19.

Department of Anatomy and Embryology, Heart Failure Research Centre, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/cvr/cvn049DOI Listing
June 2008

Statistical comparison of two or more SAGE libraries: one tag at a time.

Methods Mol Biol 2008 ;387:151-68

Department of Human Genetics, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/978-1-59745-454-4_12DOI Listing
April 2008

Scaling of gene expression data allowing the comparison of different gene expression platforms.

Methods Mol Biol 2008 ;387:169-83

Department of Neurogenetics, Academic Medical Center, Amsterdam, The Netherlands.

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http://link.springer.com/content/pdf/10.1007/978-1-59745-454
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http://dx.doi.org/10.1007/978-1-59745-454-4_13DOI Listing
April 2008

Regionalized sequence of myocardial cell growth and proliferation characterizes early chamber formation.

Circ Res 2006 Sep 3;99(5):545-52. Epub 2006 Aug 3.

Molecular and Experimental Cardiology Group, Academic Medical Centre, University of Amsterdam, the Netherlands.

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http://dx.doi.org/10.1161/01.RES.0000239407.45137.97DOI Listing
September 2006

Diagnostic value of flecainide testing in unmasking SCN5A-related Brugada syndrome.

J Cardiovasc Electrophysiol 2006 Aug 9;17(8):857-64. Epub 2006 Jun 9.

Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1111/j.1540-8167.2006.00531.xDOI Listing
August 2006

Comparison of Schwann cell and sciatic nerve transcriptomes indicates that mouse is a valid model for the human peripheral nervous system.

J Neurosci Res 2006 Aug;84(3):542-52

Neurogenetics Laboratory, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/jnr.20966DOI Listing
August 2006

Atrial and ventricular myosin heavy-chain expression in the developing chicken heart: strengths and limitations of non-radioactive in situ hybridization.

J Histochem Cytochem 2006 Jun 6;54(6):649-64. Epub 2006 Feb 6.

Academic Medical Center, Department of Anatomy & Embryology, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1369/jhc.5A6846.2006DOI Listing
June 2006

Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology.

Retrovirology 2006 Jan 6;3. Epub 2006 Jan 6.

Department of Anatomy and Embryology, Academic Medical Centre, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1742-4690-3-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1368993PMC
January 2006

Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips.

BMC Genomics 2005 Jun 14;6:91. Epub 2005 Jun 14.

Department of Neurogenetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-6-91DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1186021PMC
June 2005

Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries.

FASEB J 2005 Mar 3;19(3):404-6. Epub 2005 Jan 3.

Department of Neurogenetics, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1096/fj.04-2104fjeDOI Listing
March 2005

Effect of arginine deficiency on arginine-dependent post-translational protein modifications in mice.

Br J Nutr 2005 Feb;93(2):183-9

AMC Liver Center and Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Meibergdreef 69-71, 1105 BK, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1079/bjn20051334DOI Listing
February 2005

Quantification of viability in organotypic multicellular spheroids of human malignant glioma using lactate dehydrogenase activity: a rapid and reliable automated assay.

J Histochem Cytochem 2005 Jan;53(1):23-34

Academic Medical Centre, University of Amsterdam, Dept. of Neurosurgery, Room H2-230, PO Box 22660, 1100 DD Amsterdam, The Netherlands.

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http://dx.doi.org/10.1177/002215540505300104DOI Listing
January 2005

Hepatic response to right ventricular pressure overload.

Gastroenterology 2004 Oct;127(4):1210-21

AMC Liver Center, Academic Medical Center, University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1053/j.gastro.2004.07.057DOI Listing
October 2004

Structural requirements of the glucocorticoid-response unit of the carbamoyl-phosphate synthase gene.

Biochem J 2004 Sep;382(Pt 2):463-70

AMC Liver Center, Academic Medical Center, University of Amsterdam, Meibergdreef 69-71, 1105 BK, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1042/BJ20040471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1133802PMC
September 2004

Increased cardiac workload by closure of the ductus arteriosus leads to hypertrophy and apoptosis rather than to hyperplasia in the late fetal period.

Naunyn Schmiedebergs Arch Pharmacol 2004 Sep 31;370(3):193-202. Epub 2004 Aug 31.

Experimental and Molecular Cardiology Group, Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://link.springer.com/10.1007/s00210-004-0955-0
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http://dx.doi.org/10.1007/s00210-004-0955-0DOI Listing
September 2004

Molecular imaging of the embryonic heart: Fables and facts on 3D imaging of gene expression patterns.

Birth Defects Res C Embryo Today 2004 Sep;72(3):224-40

Department of Anatomy and Embryology, Experimental and Molecular Cardiology Group, Academic Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/bdrc.20018DOI Listing
September 2004

TBX5 overexpression stimulates differentiation of chamber myocardium in P19C16 embryonic carcinoma cells.

J Muscle Res Cell Motil 2003 ;24(2-3):211-8

Experimental and Molecular Cardiology Group, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1023/a:1026063409656DOI Listing
June 2004

Stereological measurement of porto-central gradients in gene expression in mouse liver.

Hepatology 2004 Feb;39(2):343-52

Department of Anatomy and Embryology and AMC Liver Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/hep.20068DOI Listing
February 2004

Pulmonary surfactant protein A, B, and C mRNA and protein expression in the nitrofen-induced congenital diaphragmatic hernia rat model.

Pediatr Res 2003 Nov 6;54(5):641-52. Epub 2003 Aug 6.

Department of Surgery, Sophia Children's Hospital, Erasmus Medical Center Rotterdam, 3015 GJ Rotterdam, The Netherlands.

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http://dx.doi.org/10.1203/01.PDR.0000086906.19683.42DOI Listing
November 2003

Expression analysis of subtractively enriched libraries (EASEL): a widely applicable approach to the identification of differentially expressed genes.

J Biochem Biophys Methods 2003 Jul;57(1):17-33

Experimental and Molecular Cardiology Group, Cardiovascular Research Institute Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0165-022x(03)00083-6DOI Listing
July 2003

Three-dimensional reconstruction of gene expression patterns during cardiac development.

Physiol Genomics 2003 May 13;13(3):187-95. Epub 2003 May 13.

Experimental and Molecular Cardiology Group, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1152/physiolgenomics.00182.2002DOI Listing
May 2003

Cardiomyocytes derived from embryonic stem cells resemble cardiomyocytes of the embryonic heart tube.

Cardiovasc Res 2003 May;58(2):399-409

Experimental and Molecular Cardiology Group, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0008-6363(03)00282-7DOI Listing
May 2003

Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data.

Neurosci Lett 2003 Mar;339(1):62-6

Department of Anatomy and Embryology K2-283, Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0304-3940(02)01423-4DOI Listing
March 2003

Upstream and intronic regulatory sequences interact in the activation of the glutamine synthetase promoter.

Eur J Biochem 2003 Jan;270(2):206-12

AMC Liver Center, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1046/j.1432-1033.2003.03424.xDOI Listing
January 2003

Statistical evaluation of SAGE libraries: consequences for experimental design.

Physiol Genomics 2002 Oct 29;11(2):37-44. Epub 2002 Oct 29.

Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1152/physiolgenomics.00042.2002DOI Listing
October 2002

Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions.

Anal Biochem 2002 Aug;307(1):63-9

Experimental and Molecular Cardiology Group, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0003-2697(02)00021-0DOI Listing
August 2002