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).

Highlights 2018

In 2018, our group has devised an entirely new database and online resource dedicated to microbes in their natural environments. This new resource ("microbeatlas.org") 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. Apart from MicrobeAtlas, the group has continued its work on the protein-protein interaction database STRING (updating it to version 11 covering more than 5000 organisms), and has also continued a long-standing project around the molecular diagnosis and management of the disease cystic fibrosis.

Find out more about the Group’s activities

Main publications 2018

  • Tackmann J et al.
    Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.
  • Daga N et al.
    Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition.
    Nucleic Acids Res.
  • Huerta-Cepas J et al.
    eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
    Nucleic Acids Res.
In Brief