What we do

In the Bioinformatics / Systems Biology Group, we study the dynamics of entire biological systems, both at evolutionary time-scales and at shorter time-scales – down to a few minutes. We often work in close collaboration with laboratory scientists, focusing on the computational aspects of studying such systems, in fields ranging from genetics to genomics and proteomics. In addition, we produce and maintain several online resources for the life science community, including STRING-db (protein networks), EGGNOG-db (gene orthology relations), and PAX-db (protein abundances).

Find out about the Group’s activities

Highlights 2020

In 2020, our group has prepared the release of our new online resource dedicated to microbes in their natural environments. This new resource, microbeAtlas, is based on integrated DNA-based microbial survey data from a large variety of published datasets. We re-process all sequences by means of a standardised pipeline and against a common collection of reference sequences. This yields one of most comprehensive publicly available set of microbial species definitions ("operational taxonomic units"), mapped to the globe and annotated to broadly defined environment categories. We have already used this data to study higher-order structure in the ecological interaction network (Tackmann et al). Apart from MicrobeAtlas, the group has continued its work on the protein-protein interaction database STRING (preparing the upcoming up to version 12 with more than 14'000 genomes covered).

Main publications 2020

  • Szklarczyk D et al.
    The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
    Nucleic Acids Research, 10.1093/nar/gkaa1074
  • Rheinbay E et al.
    Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
    Nature, 10.1038/s41586-020-1965-x
  • Villaseñor R et al.
    ChromID identifies the protein interactome at chromatin marks
    Nature Biotechnology, 10.1038/s41587-020-0434-2
In Brief

Members

University zurich

Christian von Mering
Bioinformatics / Systems Biology
University of Zurich
Group Webpage

Domain(s) of activity:

  • Proteins and proteomes
  • Benchmarking
  • Comparative genomics
  • Database curation
  • Data visualisation
  • Deep sequencing data
  • Metagenomics
  • Protein interactions

Domain(s) of application:

  • Basic research

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