Computational Pangenomics: We develop methods and tools to work with tens of thousands of genomes and analyze and integrate the corresponding data. See here for our Survey. Particular research highlights:

  • Twilight zone indels (Software)
  • The Genome of the Netherlands
  • Associating Disease Traits with genotypes, in particular complex, large and difficult-to-discover ones
  • Cancer genome variants (Software)
  • Read-Based Phasing (Software)

  • Genome Data Mining: We have developed various tools for mining relevant patterns in (huge) genomes and networks. Research highlights:

  • Maximal cliques in overlap graphs (Software)
  • Reconstruction of viral quasispecies (a particular highlight of ours, see here for Software)
  • Cancer subnetwork markers (Software).


    • SAVAGE - De Novo Viral Quasispecies Assembly.
    • PROSIC - Enhancing sensitivity in somatic insertion and deletion discovery and discovering particularly hard-to-discover ones.
    • WhatsHap - Phasing directly from (in particular third-generation) sequencing reads.

    ... more software

  • Publications

    De Novo Viral Quasispecies Assembly using Overlap Graphs
    Baaijens et al., Genome Research, 2017.

    A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population, Hehir-Kwa et al.,
    Nature Communications, 2016.

    Computational Pan-Genomics: Status, Promises and Challenges
    Marschall et al.,
    Briefings in Bioinformatics, 2016.

    ... more publications


    ... more events



    Prof. Dr. Alexander Schönhuth
    Centrum Wisk. & Informatica
    Science Park 123
    1098 XG Amsterdam
    The Netherlands
    p: +31 (0) 20 592 4113
    f: +31 (0) 20 592 4199

    See this link for information on location and directions.
    Interested in Master's Thesis work? Feel free to write us an email!