J.M. Ruijter PhD publications

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Publications PhD J.M. Ruijter

Position
Assistant Professor
Main activities
Education, Research
Specialisation
Cardiac growth and development / Analysis of quantitative PCR data
Focus of research

In previous years I have developed methods for 3D analysis and visualization of gene expression patterns and morphogenetic parameters during embryogenesis and for the analysis of quantitative PCR (LinRegPCR) and transcript count (SAGEstat and Gtest) data. The programs resulting from this work were made available and are frequently downloaded; papers related to LinRegPCR are cited  over 2500 times. In the field of cardiac development this has lead to new methods for analysis and visualization of morphogenetic parameters and gene expression patterns in 3D-space, which have helped the departmental research lines to become world leading. In the EU-funded CHeartED project these methods were used to genetically annotate and identify components of the developing heart. In the EU-funded CardioNeT project, the methods for 3D measurement of growth and differentiation of the heart are applied to determine the function of several regulators of development in mouse models of normal and abnormal growth. In the NHS funded  COBRA3 program, the regeneration capacity of the normal and congenetally malformed hearts will be compared. The research efforts in these projects will stay focussed on 3D quantification of gene expression and cardiac morphogenesis data in series of developmental stages of different transgenic mouse models. To determine the basis of congenital malformations, transgenic lineage markers will be included to trace the cellular and developmental origin of the different cardiac compartments. Furthermore, I will further develop and update the LinRegPCR program for analysis of qPCR data. The introduction of several massive parallel sequencing modalities, has renewed the interest in comparison and statistical analysis of transcript counts which has lead to the publicationof a peak calling program (OccuPeak) and a method for predicting regulatory regions inthe genome by combining the information in diverse genomic datasets. My group currently further develops these tools to improve the analysis of sequencing data generated in cardiac development and arrhythmia projects.
 

Amsterdam UMC Research Institutes
AMC departments
All publications

2019

  • Krap Tristan, Ruijter Jan M., Nota Kevin, Karel Joyce, Burgers A. Lieke, Aalders Maurice C. G., Oostra Roelof-Jan, Duijst Wilma Colourimetric analysis of thermally altered human bone samples Scientific reports 2019;9 (1) [PubMed]
  • Krap Tristan, Busscher Loes, Ruijter Jan M., Oostra Roelof-Jan, Duijst Wilma Comment on ‘A DNA extraction method for small quantities of bone for high-qualitygenotyping’ by Caputo et al Forensic science international. Genetics 2019;40:e243-e244 [PubMed]
  • Prakash Stuti, de Boer Bouke A., Hagoort Jaco, Gunst Quinn D., Ruijter Jan M., van den Hoff Maurice J. B. Considerations for Measurement of Embryonic Organ Growth Anatomical record 2019;302 (1):49-57 [PubMed]
  • van Duijvenboden Karel Deciphering the regulome of the heart 2019. 221p. ISBN 9789463752862. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Christoffels V. M.; Co-supervisor: Ruijter J. M.)
  • Ruijter Jan M., Ruiz-Villalba Adrian, van den Hoff Axel J. J., Gunst Quinn D., Wittwer Carl T., van den Hoff Maurice J. B. Removal of artifact bias from qPCR results using DNA melting curve analysis FASEB journal 2019;33 (12):14542-14555 [PubMed]

2018

  • Scutigliani Enzo M., Scholl Edwin R., Grootemaat Anita E., Khanal Sadhana, Kochan Jakub A., Krawczyk Przemek M., Reits Eric A., Garzan Atefeh, Ngo Huy X., Green Keith D., Garneau-Tsodikova Sylvie, Ruijter Jan M., van Veen Henk A., van der Wel Nicole N. Interfering with DNA decondensation as a strategy against mycobacteria Frontiers in microbiology 2018;9 (SEP) [PubMed]
  • Verheijen Bert M., Stevens Jo A. A., Gentier Romina J. G., van ‘t Hekke Christian D., van den Hove Daniel L. A., Hermes Denise J. H. P., Steinbusch Harry W. M., Ruijter Jan M., Grimm Marcus O. W., Haupenthal Viola J., Annaert Wim, Hartmann Tobias, van Leeuwen Fred W. Paradoxical effects of mutant ubiquitin on Aβ plaque formation in an Alzheimer mouse model Neurobiology of aging 2018;72:62-71 [PubMed]
  • Kok M. G. M., de Ronde M. W. J., Moerland P. D., Ruijter J. M., Creemers E. E., Pinto-Sietsma S. J. Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers Biomolecular Detection and Quantification 2018;15:1-5 [PubMed]
  • de Ronde Maurice W. J., Ruijter Jan M., Moerland Perry D., Creemers Esther E., Pinto-Sietsma Sara-Joan Study design and qPCR data analysis guidelines for reliable circulating miRNA biomarker experiments: A review Clinical chemistry 2018;64 (9):1308-1318 [PubMed]

2017

  • Ruiz-Villalba Adrián, van Pelt-Verkuil Elizabeth, Gunst Quinn D., Ruijter Jan M., van den Hoff Maurice J. B. Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR) Biomolecular Detection and Quantification 2017;14:7-18 [PubMed]
  • Prakash Stuti, Borreguero Luis J. J., Sylva Marc, Flores Ruiz Lorena, Rezai Fereshte, Gunst Quinn D., de la Pompa José-Luis, Ruijter Jan M., van den Hoff Maurice J. B. Deletion of Fstl1 (Follistatin-Like 1) From the Endocardial/Endothelial Lineage Causes Mitral Valve Disease Arteriosclerosis, thrombosis, and vascular biology 2017;37 (9):E116-E130 [PubMed]
  • Krap Tristan, Nota Kevin, Wilk Leah S., van de Goot Franklin R. W., Ruijter Jan M., Duijst Wilma, Oostra Roelof-Jan Luminescence of thermally altered human skeletal remains International journal of legal medicine 2017;131 (4):1165-1177 [PubMed]
  • Zhao Jing, Hakvoort Theodorus B. M., Ruijter Jan M., Jongejan Aldo, Koster Jan, Swagemakers Sigrid M. A., Sokolovic Aleksandar, Lamers Wouter H. Maternal diabetes causes developmental delay and death in early-somite mouse embryos Scientific reports 2017;7 (1) [PubMed]
  • Hakvoort Theodorus B. M., He Youji, Kulik Wim, Vermeulen Jacqueline L. M., Duijst Suzanne, Ruijter Jan M., Runge Jurgen H., Deutz Nicolaas E. P., Koehler S. Eleonore, Lamers Wouter H. Pivotal Role of Glutamine Synthetase in Ammonia Detoxification Hepatology (Baltimore, Md.) 2017;65 (1):281-293 [PubMed]
  • de Ronde Maurice W. J., Ruijter Jan M., Lanfear David, Bayes-Genis Antoni, Kok Maayke G. M., Creemers Esther E., Pinto Yigal M., Pinto-Sietsma Sara-Joan Practical data handling pipeline improves performance of qPCR-based circulating miRNA measurements RNA (New York, N.Y.) 2017;23 (5):811-821 [PubMed]
  • Ruiz-Villalba Adrián, Mattiotti Andrea, Gunst Quinn D., Cano-Ballesteros Sara, van den Hoff Maurice J. B., Ruijter Jan M. Reference genes for gene expression studies in the mouse heart Scientific reports 2017;7 (1) [PubMed]
  • Kleipool R. P., Blankevoort L., Ruijter J. M., Kerkhoffs G. M. M. J., Oostra R. J. The dimensions of the tarsal sinus and canal in different foot positions and its clinical implications Clinical anatomy (New York, N.Y.) 2017;30 (8):1049-1057 [PubMed]
  • Klop Anthony C., Vester Marloes E. M., Colman Kerri L., Ruijter Jan M., van Rijn Rick R., Oostra Roelof-Jan The effect of repeated freeze-thaw cycles on human muscle tissue visualized by postmortem computed tomography (PMCT) Clinical anatomy (New York, N.Y.) 2017;30 (6):799-804 [PubMed]
  • Colman Kerri L., Dobbe Johannes G. G., Stull Kyra E., Ruijter Jan M., Oostra Roelof-Jan, van Rijn Rick R., van der Merwe Alie E., de Boer Hans H., Streekstra Geert J. The geometrical precision of virtual bone models derived from clinical computed tomography data for forensic anthropology International journal of legal medicine 2017;131 (4):1155-1163 [PubMed]
  • Colman Kerri L., Dobbe Johannes G. G., Stull Kyra E., Ruijter Jan M., Oostra Roelof Jan, van Rijn Rick R., van der Merwe Alie E., de Boer Hans H., Streekstra Geert J. THE PRECISION OF VIRTUAL PELVISES DERIVED FROM CLINICAL CTIMAGES FOR FORENSIC ANTHROPOLOGY: IAFS 2017: 21st Triennial Meeting of the International Association of Forensic Sciences 2017 Forensic science international 2017;277 (Suppl. 1):92-93 [PubMed]
  • Zhao J., Hakvoort T. B. M., Jongejan A., Ruijter J. M., van Kampen A. H. C., Lamers W. H. Unexpected regulation of miRNA abundance during adaptation of early-somite mouse embryos to diabetic pregnancy Biochemical and biophysical research communications 2017;482 (4):1013-1018 [PubMed]

2016

  • de Bakker Bernadette S., de Jong Kees H., Hagoort Jaco, de Bree Karel, Besselink Clara T., de Kanter Froukje E. C., Veldhuis Tyas, Bais Babette, Schildmeijer Reggie, Ruijter Jan M., Oostra Roelof-Jan, Christoffels Vincent M., Moorman Antoon F. M. An interactive three-dimensional digital atlas and quantitative database of human development Science 2016;354 (6315):1019 aag0053-+ [PubMed]
  • van Duijvenboden Karel, de Boer Bouke A., Capon Nicolas, Ruijter Jan M., Christoffels Vincent M. EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures Nucleic acids research 2016;44 (5):e42 [PubMed]
  • Sergeeva Irina A., Hooijkaas Ingeborg B., Ruijter Jan M., van der Made Ingeborg, de Groot Nina E., van de Werken Harmen J. G., Creemers Esther E., Christoffels Vincent M. Identification of a regulatory domain controlling the Nppa-Nppb gene cluster during heart development and stress Development (Cambridge, England) 2016;143 (12):2135-2146 [PubMed]

2015

  • Ruijter Jan M., Lefever Steve, Anckaert Jasper, Hellemans Jan, Pfaffl Michael W., Benes Vladimir, Bustin Stephen A., Vandesompele Jo, Untergasser Andreas RDML-Ninja and RDMLdb for standardized exchange of qPCR data BMC bioinformatics 2015;16:197 [PubMed]
  • Ruijter Jan M., Ruiz Villalba Adrián, Hellemans Jan, Untergasser Andreas, van den Hoff Maurice J. B. Removal of between-run variation in a multi-plate qPCR experiment Biomolecular Detection and Quantification 2015;5:10-14 [PubMed]

2014

  • Wijnen Wino J., van der Made Ingeborg, van den Oever Stephanie, Hiller Monika, de Boer Bouke A., Picavet Daisy I., Chatzispyrou Iliana A., Houtkooper Riekelt H., Tijsen Anke J., Hagoort Jaco, van Veen Henk, Everts Vincent, Ruijter Jan M., Pinto Yigal M., Creemers Esther E. Cardiomyocyte-specific miRNA-30c over-expression causes dilated cardiomyopathy PLoS ONE 2014;9 (5):e96290 [PubMed]
  • Ruijter Jan M., Lorenz Peter, Tuomi Jari M., Hecker Michael, van den Hoff Maurice J. B. Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry, targeted sequence, type of DNA input and PCR efficiency MICROCHIMICA ACTA 2014;181 (13-14):1689-1696 [PubMed]
  • van Duijvenboden Karel, Ruijter Jan M., Christoffels Vincent M. Gene regulatory elements of the cardiac conduction system Briefings in functional genomics 2014;13 (1):28-38 [PubMed]
  • de Boer Bouke A., Le Garrec Jean-François, Christoffels Vincent M., Meilhac Sigolène M., Ruijter Jan M. Integrating multi-scale knowledge on cardiac development into a computational model of ventricular trabeculation Wiley interdisciplinary reviews. Systems biology and medicine 2014;6 (6):389-397 [PubMed]
  • de Boer Bouke A., van Duijvenboden Karel, van den Boogaard Malou, Christoffels Vincent M., Barnett Phil, Ruijter Jan M. OccuPeak: ChIP-Seq peak calling based on internal background modelling PLoS ONE 2014;9 (6):e99844 [PubMed]

2013

  • Verhoeven J. W., Ruijter J. M., Koole R., de Putter C., Terlou M., Cune M. S. Augmented mandibular bone structurally adapts to functional loading International journal of oral and maxillofacial surgery 2013;42 (12):1515-1521 [PubMed]
  • Ruijter Jan M., Pfaffl Michael W., Zhao Sheng, Spiess Andrej N., Boggy Gregory, Blom Jochen, Rutledge Robert G., Sisti Davide, Lievens Antoon, de Preter Katleen, Derveaux Stefaan, Hellemans Jan, Vandesompele Jo Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications Methods (San Diego, Calif.) 2013;59 (1):32-46 [PubMed]
  • Chieco Pasquale, Jonker Ard, de Boer Bouke A., Ruijter Jan M., van Noorden Cornelis J. F. Image cytometry: protocols for 2D and 3D quantification in microscopic images Progress in histochemistry and cytochemistry 2013;47 (4):211-333 [PubMed]

2012

  • de Boer Bouke A., van den Berg Gert, de Boer Piet A. J., Moorman Antoon F. M., Ruijter Jan M. Growth of the developing mouse heart: An interactive qualitative and quantitative 3D atlas Developmental biology 2012;368 (2):203-213 [PubMed]
  • de Boer Bouke A., van den Berg Gert, Soufan Alexandre T., de Boer Piet A. J., Hagoort Jaco, van den Hoff Maurice J. B., Moorman Antoon F. M., Ruijter Jan M. Measurement and 3D-Visualization of Cell-Cycle Length Using Double Labelling with Two Thymidine Analogues Applied in Early Heart Development PLoS ONE 2012;7 (10):e47719 [PubMed]

2011

  • Amin Ahmad S., Boink Gerard J. J., Atrafi Florence, Spanjaart Anne M., Asghari-Roodsari Alaleh, Molenaar Remco J., Ruijter Jan M., Wilde Arthur A. M., Tan Hanno L. Facilitatory and inhibitory effects of SCN5A mutations on atrial fibrillation in Brugada syndrome Europace : European pacing, arrhythmias, and cardiac electrophysiology 2011;13 (7):968-975 [PubMed]
  • de Boer Bouke A. Morphology, growth and patterning of the develloping heart. Methods and applications 2011. 160p. ISBN 9789490371982. [UvA Dissertations Online] University of Amsterdam. (Supervisors: Moorman A. F. M., Hasman A.; Co-supervisors: Ruijter J. M., Voorbraak F. P. J. M.)
  • de Boer Bouke A., Soufan Alexandre T., Hagoort Jaco, Mohun Timothy J., van den Hoff Maurice J. B., Hasman Arie, Voorbraak Frans P. J. M., Moorman Antoon F. M., Ruijter Jan M. The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format Development (Cambridge, England) 2011;138 (1):159-167 [PubMed]

2010

  • Tuomi Jari Michael, Voorbraak Frans, Jones Douglas L., Ruijter Jan M. Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value Methods (San Diego, Calif.) 2010;50 (4):313-322 [PubMed]
  • Verhoeven Jan Willem, Ruijter Jan M., Koole Ronald, de Putter Cornelis, Cune Marco S. Bone structure changes in iliac crest grafts combined with implants Clinical implant dentistry and related research 2010;12 (4):289-296 [PubMed]
  • Créton Marijn, Cune Marco S., de Putter Cornelis, Ruijter Jan M., Kuijpers-Jagtman Anne Marie Dentofacial characteristics of patients with hypodontia Clinical oral investigations 2010;14 (4):467-477 [PubMed]
  • He Youji, Hakvoort Theodorus B. M., Vermeulen Jacqueline L. M., Labruyère Wilhelmina T., de Waart D. Rudi, van der Hel W. Saskia, Ruijter Jan M., Uylings Harry B. M., Lamers Wouter H. Glutamine Synthetase Deficiency in Murine Astrocytes Results in Neonatal Death Glia 2010;58 (6):741-754 [PubMed]
  • He Youji, Hakvoort Theodorus B. M., Köhler S. Eleonore, Vermeulen Jacqueline L. M., de Waart D. Rudi, de Theije Chiel, ten Have Gabrie A. M., van Eijk Hans M. H., Kunne Cindy, Labruyere Wilhelmina T., Houten Sander M., Sokolovic Milka, Ruijter Jan M., Deutz Nicolaas E. P., Lamers Wouter H. Glutamine Synthetase in Muscle Is Required for Glutamine Production during Fasting and Extrahepatic Ammonia Detoxification Journal of biological chemistry 2010;285 (13):9516-9524 [PubMed]
  • de Boer Bouke A., Voorbraak Frans P. J. M., van den Berg Gert, Ruijter Jan M. Measurement of the shortest path length; Distance estimation within the 3D borders of a tissue of interest Image analysis and stereology 2010;29:53-60
  • Casini Simona, Tan Hanno L., Demirayak Ilker, Remme Carol Ann, Amin Ahmad S., Scicluna Brendon P., Chatyan Houssine, Ruijter Jan M., Bezzina Connie R., van Ginneken Antoni C. G., Veldkamp Marieke W. Tubulin polymerization modifies cardiac sodium channel expression and gating Cardiovascular research 2010;85 (4):691-700 [PubMed]

2009

  • van den Berg Gert, Abu-Issa Radwan, de Boer Bouke A., Hutson Mary R., de Boer Piet A. J., Soufan Alexandre T., Ruijter Jan M., Kirby Margaret L., van den Hoff Maurice J. B., Moorman Antoon F. M. A caudal proliferating growth center contributes to both poles of the forming heart tube Circulation research 2009;104 (2):179-188 [PubMed]
  • Ruijter J. M., Ramakers C., Hoogaars W. M. H., Karlen Y., Bakker O., van den Hoff M. J. B., Moorman A. F. M. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data Nucleic acids research 2009;37 (6):e45 [PubMed]
  • van Wijk Bram, van den Berg Gert, Abu-Issa Radwan, Barnett Phil, van der Velden Saskia, Schmidt Martina, Ruijter Jan M., Kirby Margaret L., Moorman Antoon F. M., van den Hoff Maurice J. B. Epicardium and Myocardium Separate From a Common Precursor Pool by Crosstalk Between Bone Morphogenetic Protein- and Fibroblast Growth Factor-Signaling Pathways Circulation research 2009;105 (5):431-U71 [PubMed]
  • Amin Ahmad S., de Groot Elisabeth A. A., Ruijter Jan M., Wilde Arthur A. M., Tan Hanno L. Exercise-Induced ECG Changes in Brugada Syndrome Circulation. Arrhythmia and electrophysiology 2009;2 (5):531-539 [PubMed]
  • de Boer Bouke A., Ruijter Jan M., Voorbraak Frans P. J. M., Moorman Antoon F. M. More than a decade of developmental gene expression atlases: where are we now? Nucleic acids research 2009;37 (22):7349-7359 [PubMed]
  • Campian Maria E., Verberne Hein J., Hardziyenka Maxim, de Bruin Kora, Selwaness Mariana, van den Hoff Maurice J. B., Ruijter Jan M., van Eck-Smit Berthe L. F., de Bakker Jacques M. T., Tan Hanno L. Serial Noninvasive Assessment of Apoptosis During Right Ventricular Disease Progression in Rats Journal of nuclear medicine 2009;50 (8):1371-1377 [PubMed]

2008

  • Amin Ahmad S., Herfst Lucas J., Delisle Brian P., Klemens Christine A., Rook Martin B., Bezzina Connie R., Underkofler Heather A. S., Holzem Katherine M., Ruijter Jan M., Tan Hanno L., January Craig T., Wilde Arthur A. M. Fever-induced QTc prolongation and ventricular arrhythmias in individuals with type 2 congenital long QT syndrome Journal of clinical investigation 2008;118 (7):2552-2561 [PubMed]
  • Boogerd Kees-Jan, Wong L. Y. Elaine, Christoffels Vincent M., Klarenbeek Meinke, Ruijter Jan M., Moorman Antoon F. M., Barnett Phil Msx1 and Msx2 are functional interacting partners of T-box factors in the regulation of Connexin43 Cardiovascular research 2008;78 (3):485-493 [PubMed]
  • van Ruissen Fred, Schaaf Gerben J., Kool Marcel, Baas Frank, Ruijter Jan M. Scaling of gene expression data allowing the comparison of different gene expression platforms Methods in molecular biology (Clifton, N.J.) 2008;387:169-183 [PubMed]
  • Schaaf Gerben J., van Ruissen Fred, van Kampen Antoine, Kool Marcel, Ruijter Jan M. Statistical comparison of two or more SAGE libraries: one tag at a time Methods in molecular biology (Clifton, N.J.) 2008;387:151-168 [PubMed]
  • Köhler Eleonore S., Sankaranarayanan Selvakumari, van Ginneken Christa J., van Dijk Paul, Vermeulen Jacqueline L. M., Ruijter Jan M., Lamers Wouter H., Bruder Elisabeth The human neonatal small intestine has the potential for arginine synthesis; developmental changes in the expression of arginine-synthesizing and -catabolizing enzymes BMC developmental biology 2008;8 (1):107 [PubMed]

2007

  • Stanulović Vesna S., Kyrmizi Irene, Kruithof-de Julio Marianna, Hoogenkamp Maarten, Vermeulen Jacqueline L. M., Ruijter Jan M., Talianidis Iannis, Hakvoort Theodorus B. M., Lamers Wouter H. Hepatic HNF4alpha deficiency induces periportal expression of glutamine synthetase and other pericentral enzymes Hepatology (Baltimore, Md.) 2007;45 (2):433-444 [PubMed]
  • Gorgels Theo G. M. F., van der Pluijm Ingrid, Brandt Renata M. C., Garinis George A., van Steeg Harry, van den Aardweg Gerard, Jansen Gerard H., Ruijter Jan M., Bergen Arthur A. B., van Norren Dirk, Hoeijmakers Jan H. J., van der Horst Gijsbertus T. J. Retinal degeneration and ionizing radiation hypersensitivity in a mouse model for Cockayne syndrome Molecular and cellular biology 2007;27 (4):1433-1441 [PubMed]
  • Schaaf Gerben J., van Ruissen Fred, van Kampen Antoine, Kool Marcel, Ruijter Jan M. Statistical Comparison of Two or More SAGE Libraries: One Tag at the Time Methods in molecular biology (Clifton, N.J.) 2007;397:151-168
  • Soufan A. T., van den Berg G., Moerland P. D., Massink M. M. G., van den Hoff M. J. B., Moorman A. F. M., Ruijter J. M. Three-dimensional measurement and visualization of morphogenesis applied to cardiac embryology Journal of microscopy 2007;225 (Part 3):269-274 [PubMed]
  • de Boer Bouke A., Ruijter Jan M., Voorbraak Frans P. J. M. Towards the automatic registration of histological sections into a 3D reference modelin: Mohammad Dastani, Edwin de Jong, editors. BNAIC'07. Proceedings of the Nineteenth Belgium/Netherlands Artificial Intelligence Conference. Utrecht: s.n.; 2007. p. 41-48

2006

  • Somi Semir, Klein André T. J., Houweling Arjan C., Ruijter Jan M., Buffing Anita A. M., Moorman Antoon F. M., van den Hoff Maurice J. B. Atrial and ventricular myosin heavy-chain expression in the developing chicken heart: strengths and limitations of non-radioactive in situ hybridization journal of histochemistry and cytochemistry 2006;54 (6):649-664 [PubMed]
  • van Straaten Henny W. M., He Youji, van Duist Marjan M., Labruyère Wil T., Vermeulen Jacqueline L. M., van Dijk Paul J., Ruijter Jan M., Lamers Wouter H., Hakvoort Theodorus B. M. Cellular concentrations of glutamine synthetase in murine organs Biochemistry and cell biology = Biochimie et biologie cellulaire 2006;84 (2):215-231 [PubMed]
  • ten Asbroek Anneloor L. M. A., van Ruissen Fred, Ruijter Jan M., Baas Frank Comparison of Schwann cell and sciatic nerve transcriptomes indicates that mouse is a valid model for the human peripheral nervous system Journal of neuroscience research 2006;84 (3):542-552 [PubMed]
  • Meregalli Paola G., Ruijter Jan M., Hofman Nynke, Bezzina Connie R., Wilde Arthur A. M., Tan Hanno L. Diagnostic value of flecainide testing in unmasking SCN5A-related Brugada syndrome Journal of cardiovascular electrophysiology 2006;17 (8):857-864 [PubMed]
  • Ruijter Jan M., Thygesen Helene H., Schoneveld Onard J. L. M., Das Atze T., Berkhout Ben, Lamers Wouter H. Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology Retrovirology 2006;3 (jan 6):2 [PubMed]
  • Firouzi Mehran, Kok Bart, Spiering Wilko, Busjahn Andreas, Bezzina Connie R., Ruijter Jan M., Koeleman Bobby P. C., Schipper Maria, Groenewegen W. Antoinette, Jongsma Habo J., de Leeuw Peter W. Polymorphisms in human connexin40 gene promoter are associated with increased risk of hypertension in men Journal of hypertension 2006;24 (2):325-330 [PubMed]
  • Soufan Alexandre T., van den Berg Gert, Ruijter Jan M., de Boer Piet A. J., van den Hoff Maurice J. B., Moorman Antoon F. M. Regionalized sequence of myocardial cell growth and proliferation characterizes early chamber formation Circulation research 2006;99 (5):545-552 [PubMed]
  • Stanulović V. S., Garcia de Veas Lovillo R. M., Labruyère W. T., Ruijter J. M., Hakvoort T. B. M., Lamers W. H. The 3'-UTR of the glutamine-synthetase gene interacts specifically with upstream regulatory elements, contains mRNA-instability elements and is involved in glutamine sensing Biochimie 2006;88 (9):1255-1264 [PubMed]
  • Soufan A. T. Three dimensional visualization & analysis of cardiac development 2006. 95p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Moorman A. F. M.; Co-supervisors: Ruijter J. M., van den Hoff M. J. B.)

2005

  • Gieling R. G. Changes in blood flow that affect hepatic gene expression 2005. 170p. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Lamers W. H.; Co-supervisor: Ruijter J. M.)
  • Kwikkers Karin L., Ruijter Jan M., Labruyère Wil T., McMahon Kathryn K., Lamers Wouter H. Effect of arginine deficiency on arginine-dependent post-translational protein modifications in mice British journal of nutrition 2005;93 (2):183-189 [PubMed]
  • van Ruissen Fred, Ruijter Jan M., Schaaf Gerben J., Asgharnegad Lida, Zwijnenburg Danny A., Kool Marcel, Baas Frank Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips BMC genomics 2005;6:91 [PubMed]
  • Schaaf Gerben J., Ruijter Jan M., van Ruissen Fred, Zwijnenburg Danny A., Waaijer Raymond, Valentijn Linda J., Benit-Deekman Jennifer, van Kampen Antoine H. C., Baas Frank, Kool Marcel Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries FASEB journal 2005;19 (3):404-406 [PubMed]
  • de Witt Hamer Philip C., Jonker Ard, Leenstra Sieger, Ruijter Jan M., van Noorden Cornelis J. F. Quantification of viability in organotypic multicellular spheroids of human malignant glioma using lactate dehydrogenase activity: A rapid and reliable automated assay journal of histochemistry and cytochemistry 2005;53 (1):23-34 [PubMed]
  • Kruithof-de Julio Marianna, Labruyère Wilhelmina T., Ruijter Jan M., Vermeulen Jacqueline L. M., Stanulović Vesna, Stallen Jan M. P., Baldysiak-Figiel Alicja, Gebhardt Rolf, Lamers Wouter H., Hakvoort Theodorus B. M. The RL-ET-14 cell line mediates expression of glutamine synthetase through the upstream enhancer/promoter region Journal of hepatology 2005;43 (1):126-131 [PubMed]

2004

  • Gieling Roben G., Ruijter Jan M., Maas Adri A. W., van den Bergh Weerman Marius A., Dingemans Koert P., ten Kate Fibo J. W., Lekanne dit Deprez Ronald H., Moorman Antoon F. M., Lamers Wouter H. Hepatic response to right ventricular pressure overload Gastroenterology 2004;127 (4):1210-1221 [PubMed]
  • van den Hoff Maurice J. B., Deprez Ronald H. Lekanne, Ruijter Jan M., de Boer Piet A. J., Tesink-Taekema Sabina, Buffing Anita A., Lamers Wouter H., Moorman Antoon F. M. Increased cardiac workload by closure of the ductus arteriosus leads to hypertrophy and apoptosis rather than to hyperplasia in the late fetal period Naunyn-Schmiedeberg s archives of pharmacology 2004;370 (3):193-202 [PubMed]
  • Ruijter Jan M., Soufan Alexandre T., Hagoort Jaco, Moorman Antoon F. M. Molecular imaging of the embryonic heart: Fables and facts on 3D imaging of gene expression patterns Birth defects research. Part C, Embryo today 2004;72 (3):224-240 [PubMed]
  • van Tuyl Minke, Blommaart Pietjan E., de Boer Piet A. J., Wert Susan E., Ruijter Jan M., Islam Saleem, Schnitzer Jay, Ellison Aaron R., Tibboel Dick, Moorman Antoon F. M., Lamers Wouter H. Prenatal exposure to thyroid hormone is necessary for normal postnatal development of murine heart and lungs Developmental biology 2004;272 (1):104-117 [PubMed]
  • Soufan Alexandre T., van den Hoff Maurice J. B., Ruijter Jan M., de Boer Piet A. J., Hagoort Jaco, Webb Sandra, Anderson Robert H., Moorman Antoon F. M. Reconstruction of the patterns of gene expression in the developing mouse heart reveals an architectural arrangement that facilitates the understanding of atrial malformations and arrhythmias Circulation research 2004;95 (12):1207-1215 [PubMed]
  • Ruijter Jan M., Gieling Roben G., Markman Marry M., Hagoort Jaco, Lamers Wouter H. Stereological measurement of porto-central gradients in gene expression in mouse liver Hepatology (Baltimore, Md.) 2004;39 (2):343-352 [PubMed]
  • Schoneveld Onard J. L. M., Gaemers Ingrid C., Das Atze T., Hoogenkamp Maarten, Renes Johan, Ruijter Jan M., Lamers Wouter H. Structural requirements of the glucocorticoid-response unit of the carbamoyl-phosphate synthase gene Biochemical journal 2004;382 (Part 2):463-470 [PubMed]

2003

  • Ramakers Christian, Ruijter Jan M., Deprez Ronald H. Lekanne, Moorman Antoon F. M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neuroscience letters 2003;339 (1):62-66 [PubMed]
  • Fijnvandraat Arnoud C., van Ginneken Antoni C. G., de Boer Piet A. J., Ruijter Jan M., Christoffels Vincent M., Moorman Antoon F. M., Lekanne Deprez Ronald H. Cardiomyocytes derived from embryonic stem cells resemble cardiomyocytes of the embryonic heart tube Cardiovascular research 2003;58 (2):399-409 [PubMed]
  • Lombardi M. Paola, van den Hoff Maurice J. B., Ruijter Jan M., Luijerink Marjanka, Buffing Anita A., Markman Marry W., Moorman Antoon F. M., Lekanne Deprez Ronald H. Expression analysis of subtractively enriched libraries (EASEL): a widely applicable approach to the identification of differentially expressed genes Journal of biochemical and biophysical methods 2003;57 (1):17-33 [PubMed]
  • van Kampen A. H. C., Ruijter J. M., van Schaik B. D. C., Caron H. N., Versteeg R. Gene expression informatics and analysisin: M. R. Barnes, I. C. Gray, editors. Bioinformatics for geneticists. Chichester: John Wiley & Sons; 2003. p. 319-344, ISBN 9780470843932
  • Ruijter J. M., Verhoeven J. W., van der Linden J. A. M., Cune M. S., Terlou M. Image processing and analysis program for measurement of bone density changes in reference and follow-up standardized extraoral oblique lateral cephalometric radiographs of the mandible Dento maxillo facial radiology 2003;32 (6):379-384 [PubMed]
  • van Tuyl Minke, Blommaart Piet jan E., Keijzer Richard, Wert Susan E., Ruijter Jan M., Lamers Wouter H., Tibboel Dick Pulmonary surfactant protein A, B, and C mRNA and protein expression in the nitrofen-induced congenital diaphragmatic hernia rat model Pediatric research 2003;54 (5):641-652 [PubMed]
  • Ramakers C., Timmer D. C., Bakker O., Lekanne dit Deprez R. H., Ruijter J. M., Moorman A. F. M. Quantification of mRNA using linear regression of log-linear pcr data-points as an alternative for the standard curve approachin: C. Wittwer, M. Hahn, K. Kaul, editors. Rapid Cycle real-time PCR - Methods and applications. S.l.: Springer; 2003. p. 21-29, ISBN 9783540206293
  • Fijnvandraat Arnoud C., Lekanne Deprez Ronald H., Christoffels Vincent M., Ruijter Jan M., Moorman Antoon F. M. TBX5 overexpression stimulates differentiation of chamber myocardium in P19C16 embryonic carcinoma cells Journal of muscle research and cell motility 2003;24 (2-3):211-218 [PubMed]
  • Soufan Alexandre T., Ruijter Jan M., van den Hoff Maurice J. B., de Boer Piet A. J., Hagoort Jaco, Moorman Antoon F. M. Three-dimensional reconstruction of gene expression patterns during cardiac development Physiological genomics 2003;13 (3):187-195 [PubMed]
  • Garcia de Veas Lovillo Rocio M., Ruijter Jan M., Labruyère Wil T., Hakvoort Theodorus B. M., Lamers Wouter H. Upstream and intronic regulatory sequences interact in the activation of the glutamine synthetase promoter European Journal of Biochemistry / FEBS 2003;270 (2):206-212 [PubMed]

2002

  • de Jonge Wouter J., Kwikkers Karin L., te Velde Anje A., van Deventer Sander J. H., Nolte Martijn A., Mebius Reina E., Ruijter Jan M., Lamers Marinus C., Lamers Wouter H. Arginine deficiency affects early B cell maturation and lymphoid organ development in transgenic mice Journal of clinical investigation 2002;110 (10):1539-1548 [PubMed]
  • Verhoeven J. W., Ruijter J. M., Cune M. S., Terlou M., Zoon M. A. O. W., Koole R. Botopbouwen in combinatie met implantaten bij sterke atrofie van de onderkaak. Een prospectief röntgenologisch onderzoek Nederlands tijdschrift voor tandheelkunde 2002;109 (1):8-14 [PubMed]
  • de Jonge Wouter J., Hallemeesch Marcella M., Kwikkers Karin L., Ruijter Jan M., de Gier-de Vries Corrie, van Roon Marian A., Meijer Alfred J., Marescau Bart, de Deyn Peter P., Deutz Nicolaas E. P., Lamers Wouter H. Overexpression of arginase I in enterocytes of transgenic mice elicits a selective arginine deficiency and affects skin, muscle, and lymphoid development American journal of clinical nutrition 2002;76 (1):128-140 [PubMed]
  • Lekanne Deprez Ronald H., Fijnvandraat Arnoud C., Ruijter Jan M., Moorman Antoon F. M. Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions Analytical biochemistry 2002;307 (1):63-69 [PubMed]
  • Ruijter Jan M., van Kampen Antoine H. C., Baas Frank Statistical evaluation of SAGE libraries: consequences for experimental design Physiological genomics 2002;11 (2):37-44 [PubMed]

2001

  • Bliek J., maas S. M., Ruijter J. M., Hennekam R. C., Alders M., Westerveld A., Mannens M. M. Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS Human molecular genetics 2001;10 (5):467-476 [PubMed]
  • van den Top M., Buijs R. M., Ruijter J. M., Delagrange P., Spanswick D., Hermes M. L. Melatonin generates an outward potassium current in rat suprachiasmatic nucleus neurones in vitro independent of their circadian rhythm Neuroscience 2001;107 (1):99-108 [PubMed]
  • de Jonge W. J., Marescau B., D'Hooge R., de Deyn P. P., Hallemeesch M. M., Deutz N. E., Ruijter J. M., Lamers W. H. Overexpression of arginase alters circulating and tissue amino acids and guanidino compounds and affects neuromotor behavior in mice Journal of nutrition 2001;131 (10):2732-2740 [PubMed]
  • Simonsz H. J., van Els J., Ruijter J. M., Bakker D., Spekreijse H. Preliminary report: prescription of prism-glasses by the Measurement and Correction Method of H.-J. Haase or by conventional orthoptic examination: a multicenter, randomized, double-blind, cross-over study Strabismus 2001;9 (1):17-27 [PubMed]

2000

  • van Gelderen B. E., van der Lelij A., Peek R., Broersma L., Treffers W. F., Ruijter J. M., van der Gaag R. Cytokines in aqueous humour and serum before and after corneal transplantation and during rejection Ophthalmic research 2000;32 (4):157-164 [PubMed]
  • Moorman A. F., de Boer P. A., Ruijter J. M., Hagoort J., Franco D., Lamers W. H. Radio-isotopic in situ hybridization on tissue sections. Practical aspects and quantification Methods in molecular biology (Clifton, N.J.) 2000;137:97-115 [PubMed]
  • van Kampen A. H., van Schaik B. D., Pauws E., Michiels E. M., Ruijter J. M., Caron H. N., Versteeg R., Heisterkamp S. H., Leunissen J. A., Baas F., van der Mee M. USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression Bioinformatics (Oxford, England) 2000;16 (10):899-905 [PubMed]
  • Hermes M. L., Ruijter J. M., Klop A., Buijs R. M., Renaud L. P. Vasopressin increases GABAergic inhibition of rat hypothalamic paraventricular nucleus neurons in vitro Journal of neurophysiology 2000;83 (2):705-711 [PubMed]

1999

  • Christoffels V. M., Sassi H., Ruijter J. M., Moorman A. F., Grange T., Lamers W. H. A mechanistic model for the development and maintenance of portocentral gradients in gene expression in the liver Hepatology (Baltimore, Md.) 1999;29 (4):1180-1192 [PubMed]
  • Kal A. J., van Zonneveld A. J., Benes V., van den Berg M., Koerkamp M. G., Albermann K., Strack N., Ruijter J. M., Richter A., Dujon B., Ansorge W., Tabak H. F. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources Molecular biology of the cell 1999;10 (6):1859-1872 [PubMed]
  • Lamers W. H., Boon L., van Hemert F. J., Labruyère W. T., de Jong P., Ruijter J. M., Moorman A. F. Glutamine synthetase expression in perinatal spiny mouse liver European Journal of Biochemistry / FEBS 1999;262 (3):803-809 [PubMed]
  • van den Hoff M. J., Moorman A. F., Ruijter J. M., Lamers W. H., Bennington R. W., Markwald R. R., Wessels A. Myocardialization of the cardiac outflow tract Developmental biology 1999;212 (2):477-490 [PubMed]
  • Habets P. E., Franco D., Ruijter J. M., Sargeant A. J., Pereira J. A., Moorman A. F. RNA content differs in slow and fast muscle fibers: implications for interpretation of changes in muscle gene expression journal of histochemistry and cytochemistry 1999;47 (8):995-1004 [PubMed]

1998

  • Verhoeven J. W., Ruijter J. M., Cune M. S., de Putter C. Densitometric measurements of the mandible: accuracy and validity of intraoral versus extraoral radiographical techniques in an in vitro study Clinical oral implants research 1998;9 (5):333-342 [PubMed]
  • Maas Y. G., Gerritsen J., Hart A. A., Hadders-Algra M., Ruijter J. M., Tamminga P., Mirmiran M., Spekreijse H. Development of macronutrient composition of very preterm human milk British journal of nutrition 1998;80 (1):35-40 [PubMed]
  • Hollants-Gilhuijs M. A., Ruijter J. M., Spekreijse H. Visual half-field development in children: detection of colour-contrast-defined forms Vision research 1998;38 (5):645-649 [PubMed]
  • Hollants-Gilhuijs M. A., Ruijter J. M., Spekreijse H. Visual half-field development in children: detection of motion-defined forms Vision research 1998;38 (5):651-657 [PubMed]

1996

  • Vandenbranden C. A., Verweij J., Kamermans M., Müller L. J., Ruijter J. M., Vrensen G. F., Spekreijse H. Clearance of neurotransmitter from the cone synaptic cleft in goldfish retina Vision research 1996;36 (24):3859-3874 [PubMed]
  • Dijkstra B. G., Ruijter J. M., Hoyng P. F. Outflow characteristics of isolated anterior segments of human eyes Investigative ophthalmology & visual science 1996;37 (10):2015-2021 [PubMed]
  • Hoppenreijs V. P., Pels E., Felten P. C., Ruijter J. M., Vrensen G. F., Treffers W. F. Synergistic action of heparin and serum on basic fibroblast growth factor-modulated DNA synthesis and mitochondrial activity of cultured bovine corneal endothelial cells Cornea 1996;15 (4):386-396 [PubMed]

1995

  • Meijer F., Ruijter J. M., van Delft J. L., van Haeringen N. J. Nitric oxide induces vascular permeability changes in the guinea pig conjunctiva European journal of pharmacology 1995;284 (1-2):61-67 [PubMed]
  • van Muiswinkel F. L., Bol J. G., Ruijter J. M., Stoof J. C., Drukarch B., Steinbusch H. W. Repeated administration of a selective dopamine D2 receptor agonist to 6-OHDA-lesioned rats does not affect the survival and outgrowth of intrastriatal fetal mesencephalic grafts Experimental brain research. Experimentelle Hirnforschung. Experimentation cerebrale 1995;107 (1):52-58 [PubMed]

1992

  • Baker R. E., Ruijter J. M., Corner M. A., Mud M. T. Effects of spontaneous bioelectric activity and gangliosides on cell survival in vitro Brain research bulletin 1992;28 (6):975-978 [PubMed]

1991

  • Ruijter J. M., Baker R. E., de Jong B. M., Romijn H. J. Chronic blockade of bioelectric activity in neonatal rat cortex grown in vitro: morphological effects International journal of developmental neuroscience 1991;9 (4):331-338 [PubMed]
  • Baker R. E., Ruijter J. M. Chronic blockade of bioelectric activity in neonatal rat neocortex in vitro: physiological effects International journal of developmental neuroscience 1991;9 (4):321-329 [PubMed]
  • Baker R. E., Ruijter J. M., Bingmann D. Effect of chronic exposure to high magnesium on neuron survival in long-term neocortical explants of neonatal rats in vitro International journal of developmental neuroscience 1991;9 (6):597-606 [PubMed]
  • Baker R. E., Ruijter J. M., Bingmann D. Elevated potassium prevents neuronal death but inhibits network formation in neocortical cultures International journal of developmental neuroscience 1991;9 (4):339-345 [PubMed]
  • Baker R. E., Ruijter J. M., Walden J., Bingmann D., Straub H., Speckmann E. J. Reduction in bioelectric GABA and NMDA responses in organotypic neocortical explants by chronic elevation of potassium Neuroscience letters 1991;131 (1):61-65 [PubMed]
  • Ruijter J. M. The mass media alone are not effective change agents Africa media review 1991;5 (1):37-48 [PubMed]

1990

  • Ruijter J. M., Baker R. E. The effects of potassium-induced depolarization, glutamate receptor antagonists and N-methyl-D-aspartate on neuronal survival in cultured neocortex explants International journal of developmental neuroscience 1990;8 (4):361-370 [PubMed]

1989

  • Ruijter J. M. Calculation of survival curves and statistical comparison of two censored populations: a computer program in BASIC Computers and biomedical research, an international journal 1989;22 (1):11-17 [PubMed]
  • de Jong B. M., Ruijter J. M. Cell number, tissue thickness and protein content as measures for development and variability in cultured neocortex explants International journal of developmental neuroscience 1989;7 (6):575-579 [PubMed]
  • Baker R. E., Ruijter J. M., Bingmann D. Effects of elevated potassium on neuronal death and network formation in neocortical cultures Pflugers Archiv 1989;414 (Suppl. 1):S126 [PubMed]
  • Baker R. E., Bingmann D., Ruijter J. M. Electrophysiological properties of neurons in neonatal rat occipital cortex slices grown in a serum-free medium Neuroscience letters 1989;97 (3):310-315 [PubMed]
  • de Jong B. M., Ruijter J. M., Buijs R. M. Immunocytochemical indications for neuronal co-localization of GABA and aspartate in cultured neocortex explants Neuroscience letters 1989;100 (1-3):1-5 [PubMed]
  • de Jong B. M., Ruijter J. M., van der Woude T. P., Mirmiran M., van Royen E. A. Serotonergic denervation does not reduce brain uptake of n-isopropyl-p-[123I]iodoamphetamine in vivo International journal of radiation applications and instrumentation. Part B, Nuclear medicine and biology 1989;16 (8):753-757 [PubMed]
  • de Jong B. M., Feenstra M. G., Ruijter J. M., van Royen E. A. Serotonin uptake in cerebral cortex cultures: imipramine-like inhibition by N-isopropyl-p-iodoamphetamine Experimental neurology 1989;103 (3):297-299 [PubMed]

1988

  • Romijn H. J., de Jong B. M., Ruijter J. M. A procedure for culturing rat neocortex explants in a serum-free nutrient medium Journal of neuroscience methods 1988;23 (1):75-83 [PubMed]
  • de Jong B. M., Ruijter J. M., Romijn H. J. Cytoarchitecture in cultured rat neocortex explants International journal of developmental neuroscience 1988;6 (4):327-339 [PubMed]
  • Romijn H. J., Ruijter J. M., Wolters P. S. Hypoxia preferentially destroys GABAergic neurons in developing rat neocortex explants in culture Experimental neurology 1988;100 (2):332-340 [PubMed]
  • Ruijter J. M., Creuwels L. A. The ultrastructure of prolactin cells in the annual cyprinodont Cynolebias whitei during its life cycle. A morphometric study in freshwater- and saltwater-reared fish Cell and tissue research 1988;253 (2):477-483 [PubMed]

1987

  • Ruijter J. M., Wendelaar Bonga S. E. Allometric relations of total volumes of prolactin cells and corticotropic cells to body length in the annual cyprinodont Cynolebias whitei: effects of environmental salinity, stress and ageing Cell and tissue research 1987;249 (3):691-699 [PubMed]
  • Ruijter J. M. Development and aging of the teleost pituitary: qualitative and quantitative observations in the annual cyprinodont Cynolebias whitei Anatomy and embryology 1987;175 (3):379-386 [PubMed]
  • Ruijter J. M., Peute J., Levels P. J. The relation between pituitary gland and thyroid growth during the lifespan of the annual fish Cynolebias whitei and Nothobranchius korthausae: gonadotropic and thyrotropic cells Cell and tissue research 1987;248 (3):689-697 [PubMed]

1984

  • Ruijter J. M., van Kemenade J. A., Wendelaar Bonga S. E. Environmental influences on prolactin cell development in the cyprinodont fish, Cynolebias whitei Cell and tissue research 1984;238 (3):595-600 [PubMed]

1983

  • Schoots A. F., Ruijter J. M., van Kemenade J. A., Denucé J. M. Immunoreactive prolactin in the pituitary gland of cyprinodont fish at the time of hatching Cell and tissue research 1983;233 (3):611-618 [PubMed]
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