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
Computational Modeling of the Eukaryotic Heat Shock Response
Academy of Finland, 2008-2010. In cooperation with the Software Construction laboratory of TUCS (Academy Professor Ralph Back) and Turku Centre for Biotechnology (Academy Professor Lea Sistonen and Professor John Eriksson) Cells exposed to elevated temperature or other stress stimuli respond by increased expression of heat shock proteins (HSPs). The heat shock response and the proteins …
Computing at nano-scale
Academy of Finland, 2005-2010 Nanotechnology (manipulating matter at the atomic scale) gets its name from the measurement unit of nanometer (a billionth of a meter), the width of about 4 individual atoms. Being able to manipulate single atoms, one can create in principle new materials with very special properties: smaller, stronger, tougher, lighter, or more …
Logicome
There has been much progress in recent years towards building larger and larger computational models for biochemical networks, driven by advances both in high throughput data techniques, and in computational modelling and simulation. Such models are often given as unstructured lists of species and interactions between them, making it very difficult to understand the logicome …
Molecular Computing Network (MolCoNet)
In cooperation with Professor Tero Harju, University of Turku, and other 14 European groups. European Union IST FWP5, 2002-2004. Molecular computing is a novel, exciting and a genuinely interdisciplinary research area which lies at the boundary of Computer Science and Molecular Biology. An important advantage offered by computations with bio-molecules is the massive parallelism: the …
Network Controllability Project
Networks are all around us. The first example crossing one’s mind might be the World Wide Web, but probably not the only one. Our world is full of social structures, networks, where individuals are connected with each other by different means such as mobile phones or transportation. A network can be represented by nodes and …
Network pharmacology
Network pharmacology: drug re-purposing and discovery of multi-drug therapies by analytical approaches What challenges are we solving? The intrinsic robustness of living systems against perturbations is a key factor that explains why many single-target drugs have been found to provide poor efficacy or lead to significant side effects. Rather than trying to design selective ligands …
Quantitative Model Refinement
Much effort is currently invested in developing larger, more finely-grained computational models in many branches of science, supported by developments in computing infrastructure and by advances in quantitative experimental measuring techniques. This is supported by developments in the computing infrastructure and by advances in quantitative experimental techniques. The main parts of a typical computational biomodeling …
Quantitative strategies for the self-assembly of intermediate filaments
One of the characteristics of eukaryotic cells is the existence of the cytoskeleton – an intricate network of protein filaments that extends throughout the cytoplasm. It enables the cells to adopt a variety of shapes, interact mechanically with the environment, organize the many components in their interior, carry out coordinated and directed movements. It also …
Reaction Systems
Reaction systems were proposed in [3] as a formal framework with underlying rationale adopted from the biochemical reactions. The interaction between individual biochemical reactions takes place through their influence on each other, and this influence happens through the basic mechanisms of facilitation and inhibition. A reaction is modeled as a triplet: a set of reactants, …
Computational Processes in Living Cells (COMPROC)
Academy of Finland, 2004-2007, within the research program for Systems Biology and Bioinformatics. Ciliates are an ancient group of organisms (about 2.5 billion years old), often classified as the most complex unicellular organisms on Earth. This family includes the fastest living form on Earth (Strombidium), as well as some unicellular organisms with digestive systems almost …