J M Ruijter

Summary

Affiliation: Academic Medical Center
Country: The Netherlands

Publications

  1. pmc Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
    Fred van Ruissen
    Department of Neurogenetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
    BMC Genomics 6:91. 2005
  2. doi request reprint Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications
    Jan M Ruijter
    Department of Anatomy, Embryology and Physiology, Academic Medical Center, Meibergdreef 15, 1100AZ Amsterdam, The Netherlands
    Methods 59:32-46. 2013
  3. pmc The human neonatal small intestine has the potential for arginine synthesis; developmental changes in the expression of arginine-synthesizing and -catabolizing enzymes
    Eleonore S Köhler
    Department of Anatomy and Embryology, Maastricht University, Maastricht, The Netherlands
    BMC Dev Biol 8:107. 2008
  4. pmc Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
    J M Ruijter
    Heart Failure Research Center, Academic Medical Center, University of Amsterdam, The Netherlands
    Nucleic Acids Res 37:e45. 2009
  5. pmc Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology
    Jan M Ruijter
    Department of Anatomy and Embryology, Academic Medical Centre, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 3:2. 2006
  6. ncbi request reprint Molecular imaging of the embryonic heart: Fables and facts on 3D imaging of gene expression patterns
    Jan M Ruijter
    Department of Anatomy and Embryology, Experimental and Molecular Cardiology Group, Academic Medical Center, Amsterdam, The Netherlands
    Birth Defects Res C Embryo Today 72:224-40. 2004
  7. ncbi request reprint Statistical evaluation of SAGE libraries: consequences for experimental design
    Jan M Ruijter
    Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
    Physiol Genomics 11:37-44. 2002
  8. pmc A caudal proliferating growth center contributes to both poles of the forming heart tube
    Gert van den Berg
    Heart Failure Research Center, Academic Medical Center, Amsterdam, The Netherlands
    Circ Res 104:179-88. 2009
  9. ncbi request reprint Expression analysis of subtractively enriched libraries (EASEL): a widely applicable approach to the identification of differentially expressed genes
    M Paola Lombardi
    Experimental and Molecular Cardiology Group, Cardiovascular Research Institute Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands
    J Biochem Biophys Methods 57:17-33. 2003
  10. pmc Epicardium and myocardium separate from a common precursor pool by crosstalk between bone morphogenetic protein- and fibroblast growth factor-signaling pathways
    Bram van Wijk
    Academic Medical Center, Department Anatomy and Embryology, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
    Circ Res 105:431-41. 2009

Collaborators

Detail Information

Publications45

  1. pmc Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
    Fred van Ruissen
    Department of Neurogenetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
    BMC Genomics 6:91. 2005
    ..This study evaluates these overall measures and introduces the between-ratio difference as a concordance measure pergene...
  2. doi request reprint Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications
    Jan M Ruijter
    Department of Anatomy, Embryology and Physiology, Academic Medical Center, Meibergdreef 15, 1100AZ Amsterdam, The Netherlands
    Methods 59:32-46. 2013
    ..The data and the analysis results per method are made available to serve as benchmark for further development and evaluation of qPCR curve analysis methods (http://qPCRDataMethods.hfrc.nl)...
  3. pmc The human neonatal small intestine has the potential for arginine synthesis; developmental changes in the expression of arginine-synthesizing and -catabolizing enzymes
    Eleonore S Köhler
    Department of Anatomy and Embryology, Maastricht University, Maastricht, The Netherlands
    BMC Dev Biol 8:107. 2008
    ....
  4. pmc Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
    J M Ruijter
    Heart Failure Research Center, Academic Medical Center, University of Amsterdam, The Netherlands
    Nucleic Acids Res 37:e45. 2009
    ..The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample...
  5. pmc Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology
    Jan M Ruijter
    Department of Anatomy and Embryology, Academic Medical Centre, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Retrovirology 3:2. 2006
    ..Normalisation, however, adds variation because the control value is not without error, while standardisation is biased if the data set is incomplete...
  6. ncbi request reprint Molecular imaging of the embryonic heart: Fables and facts on 3D imaging of gene expression patterns
    Jan M Ruijter
    Department of Anatomy and Embryology, Experimental and Molecular Cardiology Group, Academic Medical Center, Amsterdam, The Netherlands
    Birth Defects Res C Embryo Today 72:224-40. 2004
    ..Other methods can be used very efficiently in rapid evaluation of biological experiments and high-throughput screens of large-scale gene expression profiling efforts when high spatial resolution is not required...
  7. ncbi request reprint Statistical evaluation of SAGE libraries: consequences for experimental design
    Jan M Ruijter
    Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
    Physiol Genomics 11:37-44. 2002
    ..The consequences for the choice of SAGE library sizes are discussed...
  8. pmc A caudal proliferating growth center contributes to both poles of the forming heart tube
    Gert van den Berg
    Heart Failure Research Center, Academic Medical Center, Amsterdam, The Netherlands
    Circ Res 104:179-88. 2009
    ..These data show how a proliferating growth center in the caudal coelomic wall elongates the heart tube at both its venous and arterial pole, providing a morphological mechanism for early heart formation...
  9. ncbi request reprint Expression analysis of subtractively enriched libraries (EASEL): a widely applicable approach to the identification of differentially expressed genes
    M Paola Lombardi
    Experimental and Molecular Cardiology Group, Cardiovascular Research Institute Amsterdam, Academic Medical Centre, Amsterdam, The Netherlands
    J Biochem Biophys Methods 57:17-33. 2003
    ....
  10. pmc Epicardium and myocardium separate from a common precursor pool by crosstalk between bone morphogenetic protein- and fibroblast growth factor-signaling pathways
    Bram van Wijk
    Academic Medical Center, Department Anatomy and Embryology, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
    Circ Res 105:431-41. 2009
    ..Not much is known about the relation between the myocardial and epicardial lineage during development, whereas insights into these embryonic mechanisms could facilitate the design of future regenerative strategies...
  11. ncbi request reprint Development of macronutrient composition of very preterm human milk
    Y G Maas
    Department of Neonatology, University of Amsterdam, Emma Childrens Hospital, The Netherlands
    Br J Nutr 80:35-40. 1998
    ..We conclude that in accordance with current opinion in paediatrics, human milk is the best source of nutrients even for very preterm (< 30 weeks GA) infants...
  12. ncbi request reprint Atrial and ventricular myosin heavy-chain expression in the developing chicken heart: strengths and limitations of non-radioactive in situ hybridization
    Semir Somi
    Academic Medical Center, Department of Anatomy and Embryology, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    J Histochem Cytochem 54:649-64. 2006
    ..This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials...
  13. doi request reprint Msx1 and Msx2 are functional interacting partners of T-box factors in the regulation of Connexin43
    Kees Jan Boogerd
    Department of Anatomy and Embryology, Heart Failure Research Centre, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
    Cardiovasc Res 78:485-93. 2008
    ..Discovering protein partners of Tbx2 and Tbx3 will shed light on the mechanisms by which these factors regulate these gene programs...
  14. ncbi request reprint Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries
    Gerben J Schaaf
    Department of Neurogenetics, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
    FASEB J 19:404-6. 2005
    ....
  15. ncbi request reprint 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
    Alexandre T Soufan
    Experimental and Molecular Cardiology Group, Academic Medical Centre, University of Amsterdam, The Netherlands
    Circ Res 95:1207-15. 2004
    ..All these regions are derived from primary myocardium, providing a molecular basis for the observed nonrandom distribution of focal right atrial tachycardias...
  16. ncbi request reprint Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
    Christian Ramakers
    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
    Neurosci Lett 339:62-6. 2003
    ..A computer program to perform this calculation is available on request (e-mail: bioinfo@amc.uva.nl; subject: LinRegPCR)...
  17. ncbi request reprint Increased cardiac workload by closure of the ductus arteriosus leads to hypertrophy and apoptosis rather than to hyperplasia in the late fetal period
    Maurice J B van den Hoff
    Experimental and Molecular Cardiology Group, Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Naunyn Schmiedebergs Arch Pharmacol 370:193-202. 2004
    ..It is concluded that pressure-overload imposed on the late-fetal heart induces limited proliferative growth complemented by extensive hypertrophic growth...
  18. ncbi request reprint Cardiomyocytes derived from embryonic stem cells resemble cardiomyocytes of the embryonic heart tube
    Arnoud C Fijnvandraat
    Experimental and Molecular Cardiology Group, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Cardiovasc Res 58:399-409. 2003
    ..To assess whether this program is recapitulated in in vitro differentiated embryonic stem cells, we performed qualitative and quantitative analyses of cardiogenesis in vivo and in vitro...
  19. ncbi request reprint Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions
    Ronald H Lekanne Deprez
    Experimental and Molecular Cardiology Group, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    Anal Biochem 307:63-9. 2002
    ..Finally, accurate quantification of mRNAs by real-time PCR using SYBR green I requires verification of the specificity of PCR by both melting curve and gel analysis...
  20. ncbi request reprint TBX5 overexpression stimulates differentiation of chamber myocardium in P19C16 embryonic carcinoma cells
    Arnoud C Fijnvandraat
    Experimental and Molecular Cardiology Group, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    J Muscle Res Cell Motil 24:211-8. 2003
    ..This indicates that Tbx5 enhances cardiac maturation within this system rather than cardiogenesis...
  21. ncbi request reprint Three-dimensional measurement and visualization of morphogenesis applied to cardiac embryology
    A T Soufan
    Heart Failure Research Center, Department of Anatomy and Embryology, Academic Research Center, 1105 AZ, Amsterdam, The Netherlands
    J Microsc 225:269-74. 2007
    ..The resulting 3D quantitative reconstructions revealed novel observations regarding the morphogenesis of the heart...
  22. ncbi request reprint Regionalized sequence of myocardial cell growth and proliferation characterizes early chamber formation
    Alexandre T Soufan
    Molecular and Experimental Cardiology Group, Academic Medical Centre, University of Amsterdam, The Netherlands
    Circ Res 99:545-52. 2006
    ..The significance of these observations is 2-fold. First, they support a model of early cardiac morphogenesis in 2 stages. Second, they demonstrate that regional increase in size of myocytes contributes significantly to chamber formation...
  23. ncbi request reprint Statistical comparison of two or more SAGE libraries: one tag at a time
    Gerben J Schaaf
    Department of Human Genetics, Academic Medical Center, Amsterdam, The Netherlands
    Methods Mol Biol 387:151-68. 2008
    ..The Z-test and the G-test encompass these characteristics and are described for the comparison of two libraries and (two or more) groups of libraries, respectively...
  24. ncbi request reprint Scaling of gene expression data allowing the comparison of different gene expression platforms
    Fred van Ruissen
    Department of Neurogenetics, Academic Medical Center, Amsterdam, The Netherlands
    Methods Mol Biol 387:169-83. 2008
    ..This between-ratio difference is a filtering-independent measure for between-platform concordance. Moreover, the between-ratio difference per gene can be used to identify transcripts with similar regulation on both platforms...
  25. doi request reprint Glutamine synthetase deficiency in murine astrocytes results in neonatal death
    Youji He
    AMC Liver Center and Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Glia 58:741-54. 2010
    ....
  26. pmc More than a decade of developmental gene expression atlases: where are we now?
    Bouke A de Boer
    Heart Failure Research Center, Department of Anatomy and Embryology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
    Nucleic Acids Res 37:7349-59. 2009
    ..e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms...
  27. ncbi request reprint Three-dimensional reconstruction of gene expression patterns during cardiac development
    Alexandre T Soufan
    Experimental and Molecular Cardiology Group, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
    Physiol Genomics 13:187-95. 2003
    ..The use of the protocol is demonstrated on a series of serially sectioned mouse hearts, ranging from embryonic day 8.5 to 14.5. The myocardium of the hearts was identified by ISH using a mixture of specific mRNA probes and reconstructed...
  28. ncbi request reprint USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression
    A H van Kampen
    Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands
    Bioinformatics 16:899-905. 2000
    ..Furthermore, to facilitate data sharing between users, the application should reside on a central server and be accessed via the internet. Since such an application was not available we developed the USAGE package...
  29. ncbi request reprint Glutamine synthetase expression in perinatal spiny mouse liver
    W H Lamers
    Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, The Netherlands
    Eur J Biochem 262:803-9. 1999
    ..The kinetics of GS protein accumulation, in conjunction with GS mRNA content, are consistent with an approximately sixfold increase in its rate of synthesis at birth as the result of a corresponding stimulation of the rate of elongation...
  30. ncbi request reprint Comparison of Schwann cell and sciatic nerve transcriptomes indicates that mouse is a valid model for the human peripheral nervous system
    Anneloor L M A ten Asbroek
    Neurogenetics Laboratory, Academic Medical Center, Amsterdam, The Netherlands
    J Neurosci Res 84:542-52. 2006
    ....
  31. doi request reprint Tubulin polymerization modifies cardiac sodium channel expression and gating
    Simona Casini
    Department of Clinical and Experimental Cardiology, Heart Failure Research Center, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
    Cardiovasc Res 85:691-700. 2010
    ..5) function. Therefore, we investigated whether enhanced tubulin polymerization by TXL affects Na(v)1.5 function and expression and whether these effects are beta1-subunit-mediated...
  32. ncbi request reprint Hepatic response to right ventricular pressure overload
    Roben G Gieling
    AMC Liver Center, Academic Medical Center, University of Amsterdam, The Netherlands
    Gastroenterology 127:1210-21. 2004
    ..Modifying the afferent blood supply to the liver does not change the zonal expression pattern of hepatic enzymes in the rat...
  33. pmc Fever-induced QTc prolongation and ventricular arrhythmias in individuals with type 2 congenital long QT syndrome
    Ahmad S Amin
    Heart Failure Research Center, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
    J Clin Invest 118:2552-61. 2008
    ....
  34. ncbi request reprint Overexpression of arginase I in enterocytes of transgenic mice elicits a selective arginine deficiency and affects skin, muscle, and lymphoid development
    Wouter J de Jonge
    Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Netherlands
    Am J Clin Nutr 76:128-40. 2002
    ..In suckling mammals, arginine is synthesized in the enterocytes of the small intestine, but this capacity is lost after weaning...
  35. ncbi request reprint The 3'-UTR of the glutamine-synthetase gene interacts specifically with upstream regulatory elements, contains mRNA-instability elements and is involved in glutamine sensing
    V S Stanulović
    AMC Liver Center and Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
    Biochimie 88:1255-64. 2006
    ..A stretch of 21 adenines inside this fragment conferred, in conjunction with the upstream enhancer and the 3'-part of the first intron, sensitivity of GS expression to ambient glutamine...
  36. ncbi request reprint Overexpression of arginase alters circulating and tissue amino acids and guanidino compounds and affects neuromotor behavior in mice
    W J de Jonge
    Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
    J Nutr 131:2732-40. 2001
    ..In addition, hypoargininemia was associated with disturbed neuromotor behavior, although brain levels of toxic guanidino compounds and ammonia were normal...
  37. doi request reprint Serial noninvasive assessment of apoptosis during right ventricular disease progression in rats
    Maria E Campian
    Heart Failure Research Center, Academic Medical Center, Amsterdam, The Netherlands
    J Nucl Med 50:1371-7. 2009
    ....
  38. pmc Structural requirements of the glucocorticoid-response unit of the carbamoyl-phosphate synthase gene
    Onard J L M Schoneveld
    AMC Liver Center, Academic Medical Center, University of Amsterdam, Meibergdreef 69 71, 1105 BK, Amsterdam, The Netherlands
    Biochem J 382:463-70. 2004
    ....
  39. ncbi request reprint The RL-ET-14 cell line mediates expression of glutamine synthetase through the upstream enhancer/promoter region
    Marianna Kruithof-de Julio
    AMC Liver Center, Academic Medical Center, Amsterdam, The Netherlands
    J Hepatol 43:126-31. 2005
    ..We exploited these observations to identify the regulatory regions of the GS gene and the responsible signal-transduction pathway that mediates this effect...
  40. doi request reprint Exercise-induced ECG changes in Brugada syndrome
    Ahmad S Amin
    Heart Failure Research Center and Department of Cardiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
    Circ Arrhythm Electrophysiol 2:531-9. 2009
    ..Yet, the effects of exercise on the BrS ECG phenotype have not been studied. We aimed to assess ECG responses to exercise in BrS and determine whether these responses are affected by the presence of an SCN5A mutation...
  41. ncbi request reprint Hepatic HNF4alpha deficiency induces periportal expression of glutamine synthetase and other pericentral enzymes
    Vesna S Stanulovic
    AMC Liver Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Hepatology 45:433-44. 2007
    ..Furthermore, we show that HNF4alpha deficiency induces foci of regenerating hepatocytes...
  42. pmc Glutamine synthetase in muscle is required for glutamine production during fasting and extrahepatic ammonia detoxification
    Youji He
    Academic Medical Center Liver Center and Department of Anatomy and Embryology, Academic Medical Center, University of Amsterdam, Meibergdreef 69 71, 1105 BK Amsterdam
    J Biol Chem 285:9516-24. 2010
    ..Furthermore, muscle GS contributes to ammonia detoxification and urea synthesis. These functions are apparently not vital as long as other organs function normally...
  43. ncbi request reprint Stereological measurement of porto-central gradients in gene expression in mouse liver
    Jan M Ruijter
    Department of Anatomy and Embryology and AMC Liver Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
    Hepatology 39:343-52. 2004
    ..The method can be applied to any tissue component that can be stained quantitatively...
  44. ncbi request reprint Prenatal exposure to thyroid hormone is necessary for normal postnatal development of murine heart and lungs
    Minke van Tuyl
    Department of Pediatric Surgery, Sophia Children s Hospital, Erasmus Medical Center, Rotterdam, The Netherlands
    Dev Biol 272:104-17. 2004
    ..Our study shows that these effects of maternal hypothyroidism become manifest after birth and are aggravated by the concomitant existence of neonatal hypothyroidism...
  45. ncbi request reprint Cellular concentrations of glutamine synthetase in murine organs
    Henny W M van Straaten
    Department of Anatomy and Embryology, University of Maastricht, Netherlands
    Biochem Cell Biol 84:215-31. 2006
    ..GS activity in muscle amounted to only 0.4 micromol.g(-1).min(-1). Our findings confirmed the postulated dichotomy between cellular concentration and GS function...