Computational Biomodelling Laboratory

Leader Dr. Ion Petre

Research description

The research of the laboratory centers on the computational modelling of biochemical systems. The approach is to understand as computations the myriad of biochemical processes that evolve in parallel, influence each other, propagate signals, or cooperate on various tasks. Our goal is to increase the understanding of how entire cells adapt, communicate, and survive in dynamic environments, all in terms of computations. Having sound computational models for a biochemical system allows one to employ formal reasoning about its pathways or regulatory networks, formulating predictions and/or running simulations. Such models are also useful for designing novel sorts of computations based on the principles that underline the functioning of bio-systems. Our group is leading research on computational bio-processes, including computational processes in living cells, as well as nature-inspired human-designed computations. The general interest of the laboratory is gaining an understanding of fundamental structures behind the functioning of all kinds of bio-systems. We have considerable expertise in building discrete models, based on combinatorics, graph theory, stochastic processes, etc.

Research topics

- Computational modelling methodologies for systems biology
- Computational models for cellular processes
- Applications of formal methods in biology
- Quantitative models for molecular self-assembly
- Control motifs in regulatory networks
- Computational models for signaling pathways
- Computer-based simulations for bio-systems
- Nature-inspired computational paradigms

Projects

**Quantitative strategies for the self-assembly of intermediate filaments****Quantitative model refinement****Network controllability****Computing at nano-scale****Computational processes in living cells (COMPROC)****Molecular Computing Network (MolCoNet)****Computational modeling of the eukaryotic heat shock response**

Seminars

Facilities

You can find us in ICT-building, Joukahaisenkatu 3-5 A, 5th floor, FIN-20520 Turku, Finland