Structural Variant Discovery: Fast, statistical "next-generation methods" for discovery of genetic variants in next-generation sequenced human genomes.
Software: CLEVER & (soon) LASER

Cancer Systems Biology: Together with NKI and UvA we study genome organization in breast cancer and compute cross-platform-stable subtype markers.
See ABC Suite and Marker Computation Software.

Statistical Modeling: A special focus is on Markovian and latent variable, such as hidden Markov and mixture models. On the theoretical end, the emphasis sometimes is on algebraic aspects.


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Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels. T. Marschall et al. ISMB-HitSeq 2013.

Discovering motifs that induce sequencing errors. M. Allhoff et al., BMC Bioinformatics (Recomb-Seq 2013).
Publisher Link]

CLEVER: Clique-enumerating variant finder. T. Marschall et al., Recomb-Seq, ISMB-HitSeq and Bioinformatics, 2012.
Publisher Link ]

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  • 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.
  • wDCB - Inference of subnetwork cancer markers using density-constrained biclustering.
  • MirrorTreeTop - Efficient, score-optimal alignment of co-evolving gene trees in the presence of paralogs.

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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!