What we do

In the Computational Biochemistry Research Group, we are interested in the modelling and analysis of biological problems at the molecular level. In particular, our expertise lies in searching algorithms, optimizing algorithms, mathematical modelling, and computational systems. Most of our research efforts are concentrated on the Orthologous MAtrix (OMA) project. This particular project aims to produce, automatically, reliable orthologous groups of proteins that are derived from entire genomes.

Highlights 2018

This year we published an update paper on the OMA Browser in the NAR database issue that highlights various new features and improvements to the database. During the year we released two more version of the OMA database and published iHAM and pyHAM, two open source tools that enable scientist to mine hierarchical orthologous groups (HOGs) more easily.
We are also involved in a metagenomic project in which we try to understand the role of environment waters as vehicle for transmission of clinically relevant bacteria that colonizes urban environments.

Find out more about the Group’s activities

Main publications 2018

  • Altenhoff A M et al.
    The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
    Nucleic Acids Res, doi: 10.1093/nar/gkx1019
  • Train C M et al.
    iHam & pyHAM: visualizing and processing hierarchical orthologous groups.
    Bioinformatics, doi: 10.1093/bioinformatics/bty994
  • Antelo V et al.
    First release of the bacterial biobank of the urban environment (BBUE).
    Microbiol Res Announc, doi: 10.1128/MRA.01201-18


eth zurich

Gaston Gonnet
Computational Biochemistry Research Group
ETH Zurich
Group Webpage


Domain(s) of activity:

  • Evolution and phylogeny
  • APIs
  • Benchmarking
  • Comparative genomics
  • Machine learning
  • Mathematical modelling
  • Phylogeny
  • Semantic web format
  • Software engineering

Domain(s) of application:

  • Agriculture
  • Basic research
  • Medicine and health