Structural Variant Discovery, Phasing: Fast, statistical and haplotype-oriented discovery of genetic variants. Specialties: "NGS twilight zone indels" (soon also somatic), viral quasispecies assembly and haplotype assembly for future-generation sequencing reads.
Software: CLEVER, HaploClique

Cancer Systems Biology: Together with NKI we have computed cross-platform-stable subtype markers. See ABC Suite and Marker Computation Software.

Statistical Modeling: A special focus is on latent variable models, which are often Markovian and/or of mixture type. On the theoretical end, the emphasis sometimes is on algebraic aspects.


  • The Genome of the Netherlands main paper has been published at Nature Genetics. Our team has made decisive contributions to discovering "twilight zone indels".
  • Alex has got tenure, one year earlier than scheduled.
  • Alex has received a Vidi grant (the most prestigious individual Dutch grant 3-8 y past PhD) for research on the Genome of the Netherland!

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Whole-genome Sequence Variation, Population Structure and Demographic History of the Netherlands
The Genome of the Netherlands Consortium. Nature Genetics, 2014.

Viral Quasispecies Assembly via Maximal Clique Enumeration.
A. Töpfer et al., PLoS Computational Biology, RECOMB 2014)

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
M. Patterson et al., RECOMB 2014.

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  • HaploClique - Viral quasispecies assembly using max-clique enumeration.
  • CLEVER - Fast, reliable and user-friendly prediction of structural variants in next-gen-sequenced genomes.
  • DCSSE - Discovery of motifs that induce next-generation sequencing errors.

... more software



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!