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Research

Research mission
The IBIVU integrates the VU Bioinformatics activities at three levels:
  • It integrates information from all layers of genomics: from DNA sequence data via molecules and cells to patients and ecosystems.
  • It integrates computer science, mathematics and visualisation techniques required for optimal analysis of genomics and other life science data.
  • It ties medical, ecological and social genomics with bioinformatics to optimise both experimental design and computational analysis.

Approach
To drive these integrative initiatives, the IBIVU has a core Bioinformatics unit which develops bioinformatics methods to analyse sequence data and predict protein structure and function. In collaboration with the Institute of Molecular Cell Physiology at the Vrije Universiteit we are also integrating various genomic data sets and methods to increase our understanding of ‘vertical’ genomics; i.e. the coding and regulation through all genomic levels from DNA sequence to cell functioning: from genotype to phenotype.

Current focusses
Projects currently focussed on include:
  • Bioinformatics methods and data integration
  • Genome analysis
    • Applying the transitivity concept to phylogenetic footprinting and shadowing
  • Systems Biology
  • Protein structure prediction
    • Domain boundary prediction
    • Secondary structure prediction
    • Tertiary structure prediction
  • Sequence database searching
  • Multiple sequence alignment
    • Multiple sequence alignment and (predicted) secondary or tertiary structure information
    • Multiple sequence alignment and profile analysis using local weighting schemes
    • Multiple sequence alignment parameter optimalisation using genetic algorithms
    • Multiple sequence alignment quality control and iterative optimisation
    • Repeats-aware multiple alignment
  • Genomic and internal protein repeats detection
  • Microarray (gene expression) analysis in the context of Ecogenomics
  • Algorithms and tools for data analysis of large-scale nanoLC-FT mass spectrometry data


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