Research

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

Seminars

Facilities

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

Computational Modeling of the Eukaryotic Heat Shock Response

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 …

View page »

Computational Processes in Living Cells (COMPROC)

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 …

View page »

Computing at nano-scale

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, …

View page »

Gene Assembly in Ciliates

Seminar Series on Gene Assembly in Ciliates We are running seminar series on computational aspects of gene assembly in ciliates. The purpose of our seminars is to bring people from our group and all others interested in together, to make brainstorming sessions, to learn new techniques, to identify open questions in the area, etc. We …

View page »

Guest Lectures

Guest Lectures We are glad to mention here presentations given by the guests of our laboratory   Guests 5th of May Robert Brijder University of Leiden, the Netherlands The talk given: Breakpoint graphs for gene assembly in ciliates 17th of May Professor Adrian Atanasiu University of Bucharest The talk given: Binary amiable words Click here …

View page »

Heat-Shock Response

Seminar Series on Heat-Shock Response We are running seminar series on computational aspects of eukaryotic heat-shock response. We will review the work already done in our group and elsewhere and we will try to identify the challenges posed by this research. All interested in are warmly welcome.   Schedule 5th of October Dr. Ion Petre …

View page »

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 …

View page »

Molecular Computing Network (MolCoNet)

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 …

View page »

Network Controlability 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 …

View page »

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 …

View page »

Quantitative Model Refinement

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 …

View page »

Quantitative strategies for the self-assembly of intermediate filaments

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, …

View page »

An interactive process.

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, …

View page »