J.M. Ruijter PhD

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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
Key publications
  • 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]
  • 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]
  • 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]
  • 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]
All Publications
Curriculum Vitae

Jan M Ruijter trained as a medical biologist and worked in endocrinology, neurobiology, ophthalmology, biostatistics and embryology. He is currently appointed in the department of Anatomy, Embryology & Physiology (Academic Medical Centre, Amsterdam, the Netherlands) where he is heading a research group studying the relation between gene expression and the development of the heart with molecular, image analysis and 3D reconstruction techniques. The statistical analysis of research data resulted in the development of the LinRegPCR program for the analysis quantitative PCR data based on PCR efficiency values derived from amplification curves (http://LinRegPCR.nl).
 

Research programmes

PhD J.M. Ruijter (Cardiac Morphogenesis / Quantitative PCR)

The overall aim of my future research is to uncover mechanisms and identify factors that contribute to prenatal development, to postnatal growth and remodelling and to establishment of homeostasis in normal and abnormal cardiac development. During the embryonic and foetal period cardiac structures are formed. Errors in this developmental period result in congenital heart defects. Different cardiac components originate from different populations (fields) of progenitor cells that diverge considerably in their phenotype and sensitivity to developmental defects. After birth, the heart increases in volume and remodels. These processes are influenced by hemodynamic and mechanical forces, although the underlying mechanisms are not known. Furthermore, it is unknown why the regenerative capacity of the heart decreases shortly after birth. Interactions within regulatory networks that control heart development, growth, function and homeostatis will differ in normal and abnormal development, and will be influenced by genetic variation. Current and new methods to quantify gene expression, sequencing and morphogenetic data will serve to study the multivariate associations between morphogenetic, transcriptional and genomic networks that lead to the different homeostatic states in mouse models with morphological, contraction or conduction defects. My research aims at unravelling the involvement of these networks in cardiac health and disease.
 

Postdocs
MSc PhD B. Jensen

Others
BEng J. Hagoort
Prof. PhD A.F.M. Moorman

Current PhD Candidates