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Niko Beerenwinkel
Computational Biology Group
ETH Zurich, D-BSSE, Basel
Group Webpage

What do we do?

The Computational Biology Group is located in Basel and part of the Department of Biosystems Science and Engineering (D-BSSE) of the ETH Zurich. Our research and teaching activities are in the areas of computational biology, biostatistics, and systems biology. Our activities include the development of mathematical and statistical models, their implementation in computer programs, and application to biomedical problems. We are conducting active research projects on HIV drug resistance, the somatic evolution of cancer, haplotype inference from ultra-deep sequencing data, and reconstruction of signalling pathways from RNAi screens.

Highlights 2016

Our 2016 highlights include the development and release of (i) TiMEx and pathTiMEx, waiting time models for pathways of mutually exclusive cancer alterations and their progression dynamics, (ii) SCITE, a method for full Bayesian phylogenetic tree inference from single-cell data, and (iii) novel algorithms for efficient learning of large-scale mutational networks.

Main publications 2016

  • Cristea S, Kuipers J, Beerenwinkel N. pathTiMEx: Joint inference of mutually exclusive cancer pathways and their progression dynamics. Journal of Computational Biology 2017; in press. (RECOMB 2016)
  • Jahn K, Kuipers J, Beerenwinkel N. Tree inference for single-cell data. Genome Biology 2016;17:86.
  • Montazeri H, Kuipers J, Kouyos R, Böni J, Yerly S, Klimkait T, Aubert V, Günthard H, Beerenwinkel N. Large-scale inference of Conjunctive Bayesian Networks. Bioinformatics 2016;32(17):i727-i735.

Our research topics: