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 2015

Our lab’s 2015 highlights include the development and release of:

  1. gespeR, a computational method for deconvoluting off-target-confounded RNA interference screens,
  2. QuasiFit, a Bayesian MCMC sampler for inferring fitness landscapes from dynamic population equilibrium distributions, and
  3. BitPhylogeny, a probabilistic framework for reconstructing intra-tumour phylogenies.

Main publications 2015

  • Schmich F et al. Deconvoluting off-target-confounded RNA interference screens. Genome Biol 2015; 16:220.
  • Seifert D et al. A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory. Genetics 2015;199(1):191-203.
  • Yuan K et al. BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biol 2015;16:36.

Our research topics: