Computational Systems Biology

Systems Biology is based on an integrative approach and applies various computational strategies to integrate heterogeneous data to model and discover properties of biological systems. A main goal of the laboratory of Systems and Synthetic Biology is to gain a systems understanding of societal relevant microorganisms and microbial ecosystems and to translate this knowledge into applications of biotechnological, medical and environmental interest.

Research

Our research focus is on deriving a deeper understanding of microbial systems by uncovering biological meaning from genome scale data and through multiscale data integration. Specifically we are interested in (i) how genome information leads to function, (ii) how microbial metabolic processes are regulated and adapt in extant species, (iii) how microbial organisms and ecosystems respond to (a)biotic environmental cues and (iv) how they can be manipulated to enhance the yield of desired products or to diminish their pathogenicity.

To address these questions we build Systems Biology frameworks encompassing different levels of granularity within the fields of Semantics, Metabolic Engineering and Synthetic Biology and apply them in the fields of Host-Pathogen interactions, Systems Medicine and Biotechnology to describe biological phenomena with the specific aim of extracting emergent system properties, biological concepts and knowledge.

Projects

For details see projects-page.

Recent Publications

van Dam, Jesse CJ; Koehorst, Jasper J; Schaap, Peter J; dos Santos, Vitor AP Martins; Suarez-Diez, Maria ( 2015) RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. Journal of biomedical semantics 6,1,1-12,

Fiebig, Anne; Loof, Torsten G; Babbar, Anshu; Itzek, Andreas; Koehorst, Jasper J; Schaap, Peter J; Nitsche-Schmitz, D Patric (2015) Comparative Genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice. International Journal of Medical Microbiology 305,6,532-543

Saccenti, Edoardo; Nieuwenhuijse, David; Koehorst, Jasper J; dos Santos, Vitor AP Martins; Schaap, Peter J (2015) Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PloS one 10,9,e0137908

van Dam, Jesse CJ; Koehorst, Jasper J; Schaap, Peter J; dos Santos, Vitor AP Martins; Suarez-Diez, Maria ( 2015) RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource Journal of biomedical semantics 6,1,1-12,

Reijnders, Maarten JMF; van Heck, Ruben GA; Lam, Carolyn MC; Scaife, Mark A; dos Santos, Vitor AP Martins; Smith, Alison G; Schaap, Peter J (2014) Green genes: bioinformatics and systems-biology innovations drive algal biotechnology Trends in biotechnology 32,12,617-626

Rienksma, R.A. ; Suarez Diez, M. ; Spina, L. ; Schaap, P.J. ; Martins dos Santos, V.A.P. (2014) Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets Seminars in Immunology 26,6,610 - 622.

A full list of recent publications by can be found here.