What do we do?
At 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 collaborations with laboratory scientists, focusing on the computational aspects of studying such systems, in fields ranging from genetics to genomics to 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).
In 2015, our group released a major update of our protein-protein interaction database: STRING. This big update brings the coverage of STRING to over 2,000 model organisms, and more than 900 million interactions are now available. The greatest conceptual advance in this update concerned the scaling of the database – in past versions it was necessary to conduct all-against-all homology searches over the involved proteins in order to execute some of the interaction prediction algorithms in STRING. With the current update the group made to version 10, these homology searches have been replaced by group-orthology data that scales much better and allows the STRING pipeline to transfer interaction knowledge from one model organism to the other. This and other improvements have been very well received by the users, with more than 3,000 distinct users now working with the database on a daily basis.
Main publications 2015
- Huerta-Cepas J et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2015;44(D1):D286-93.
- Szklarczyk D et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015;43:D447-52.
- Wang MC et al. Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues and cell-lines. Proteomics 2015;15(18):3163-8.