Computational Systems Biology

The group’s research aims to understand the function and dysfunctions of biological systems on a molecular level, taking into account the complexity arising from the interplay of biomolecules in large regulatory networks. This work is enabled by the availability of big biological datasets that are generated by high-throughput, biochemical profiling methods. Relevant data include transcriptomics, proteomics, or epigenomics, which are often assayed in combination (“multi-omics”) and at cellular resolution (“single-cell”). The computational methods we use mirror this biological complexity, spanning advanced statistics, machine learning, and network science.

KPNNs


Key contributions

  • Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data.
    Fortelny, N., & Bock, C. (2020). Genome Biology, 21(1), 190.
    DOI:  10.1186/s13059-020-02100-5
  • Structural cells are key regulators of organ-specific immune responses. Krausgruber, T.*,
    Fortelny, N.*, Fife-Gernedl, V., Senekowitsch, M., Schuster, L. C., Lercher, A., Nemc, A., Schmidl, C., Rendeiro, A. F., Bergthaler, A., & Bock, C. (2020). Nature, 583(7815), 296–302.
    DOI:
     10.1038/s41586-020-2424-4
  • Can we predict protein from mRNA levels?
    Fortelny, N., Overall, C. M., Pavlidis, P., & Freue, G. V. C. (2017). Nature, 547(7664), E19–E20.
    DOI:
     10.1038/nature22293
  • Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web.
    Fortelny, N., Cox, J. H., Kappelhoff, R., Starr, A. E., Lange, P. F., Pavlidis, P., & Overall, C. M. (2014). PLoS Biology, 12(5), e1001869.
    DOI:
     10.1371/journal.pbio.1001869