Research

The Malmström group is a computational research group taking a systems biology approach to gain deep insight into the spatial and temporal organization of Streptococcus pyogenes, an important human pathogen that infects 700 million people and kills over 500,000 yearly. We rely on strong partners to provide a wealth of mass spectrometry (MS) and genome sequencing data in addition to the growing amounts of data available online. This data is the basis for two main research activities. First, we develop technologies to extract more and more accurate information from the raw data and second, we are using various modeling techniques to interpret this information from a biological perspective.

We are primarily working with protein-based shotgun (SG), Selected Reaction Monitoring (SRM) and SWATH MS and have developed several algorithms and information technologies to extract signals (both identities and quantitative) and information from the various data types these instruments generate. An underlying theme is that we utilize high-throughput computational approaches allowing us to apply our tools to large datasets and also to optimize input parameters. Several auxiliary algorithms allow us to estimate absolute abundances of proteins in complex mixtures.

These technologies are applied in large S. pyogenes cohorts that are perturbed chemically or genetically. The resulting data sets are then used to infer regulatory networks and co-regulated proteins. Co-regulation is often observed in functionally related proteins and it is therefore possible to learn the role of un-characterized proteins with enough perturbation experiments provided that the perturbations are designed intelligently.

We use crosslink MS (XLMS) to generate distance constraints between members of protein complexes. These distance constraints can then be used to create high-resolution protein structure models of the complexes using the Rosetta software suit. We use de novo and homology modeling approaches to make high-resolution models of proteins for which there is no experimentally determined structure.

The group participates in the following projects that provide additional funding to work on infrastructure topics:
- SystemsX.ch/SyBIT sybit.net
- SCI-BUS sci-bus.eu
- SHIWA shiwa
- proteomeXchange proteomeXchange
- CTI together with biognosys: KTI