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Researcher

Peter De Rijk

  • Research Expertise:In a previous position I set up a database of ribosomal RNA sequences and their structure, and wrote software for the management of this database and for predicting and visualizing the structure of RNA. I also used this database for phylogenetic analysis. My current work is focused on the design, development and implementation of work-flows and software tools to enhance the research of complex diseases. An iomportant part of this is the in-house LIMS (Laboratory Information Management System) managing the entire data-flow in the center from sample management and clinical data to experimental results. Over the years, I developed software covering the setup and analysis of a very diverse set of genotyping technologies, ranging from STR analysis and Sanger sequencing to next generation sequencing, and now also long-read sequencing. During the analysis of some of early complete genomes, I developed software for comparing, annotating, filtering and validating complete genome data (Genomecomb); which is now also used to integrate the in-house analysis of gene panel and exome sequencing using state of the art publicly available tools and local enhancements. We are further exploring new ways to extract meaning from the variants, by e.g. adding novel annotations/targets. For example we developed software for the discovery of novel miRNAs and for predicting the effect of genomic variants on their structure and biogenesis.
  • Keywords:RNA SECUNDARY STRUCTURE, SEQUENCING, SEQUENCE ANALYSIS, BIOINFORMATICS, GENOMICS, GENETICS, Chemistry (incl. biochemistry)
  • Disciplines:Analysis of next-generation sequence data, Bioinformatics of disease, Computational evolutionary biology, comparative genomics and population genomics, Development of bioinformatics software, tools and databases
  • Research techniques:Bioinformatics, both application and development of new tools Genomics and sequencing: analysis of different generations of sequencing (Sanger, ngs, 3d gen), alignment, variant calling, structural variants, annotation, comparison, effect of variants Genetics: pedigrees, linkage, association analysis, homozygosity mapping RNA structure: ribosmal RNA, (precursor) miRNA Databases: technical (relational as well as nosql databases), sequence databases, structure, lims (laboratory information managment system) Molecular Evolution, phylogenetic tree construction High performance computing, workflow design
  • Users of research expertise:Scientists, geneticists, bioinformaticians, biomedical researchers