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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

Projects

Facilities

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

People involved in the laboratory:

  • Ralph-Johan Back, Åbo Akademi University, Department of Information Technologies
  • Andrzej Mizera, Åbo Akademi University, Department of Information Technologies
  • Ion Petre, Åbo Akademi University, Department of Information Technologies
  • Vladimir Rogojin, Åbo Akademi University, Department of Information Technologies
  • Ishdorj Tseren-Onolt, Åbo Akademi University, Department of Information Technologies

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Publications

Alhazov, Artiom and Petre, Ion and Rogojin, Vladimir:
The Parallel Complexity of Signed Graphs: Decidability and an Improved Algorithm
Theoretical Computer Science, 2009

Alhazov, Artiom and Li, Chang and Petre, Ion:
Computing the Graph-Based Parallel Complexity of Gene Assembly
Theoretical Computer Science, Volume to appear, 2009

Petre, Ion and Salomaa, Arto:
Algebraic Systems and Pushdown Automata
Springer, 2009

Petre, Ion and Mizera, Andrzej and Hyder, Claire and Mikhailov, Andrey and Eriksson, John and Sistonen, Lea and Back, Ralph-Johan:
A New Mathematical Model for the Heat Shock Response
TUCS General Series, Number 47, 2008

Petre, Ion and Rogojin, Vladimir:
Decision Problems for Shuffled Genes
Information and Computation, Volume 206, Number 11, 2008

Harju, Tero and Petre, Ion and Rogojin, Vladimir and Rozenberg, Grzegorz:
Patterns of Simple Gene Assembly
Discrete applied mathematics, Volume 156, Number 14, 2008

Alhazov, Artiom and Petre, Ion and Rogojin, Vladimir:
Solutions to Computational Problems Through Gene Assembly
Natural computing, Volume 7, Number 3, 2008

Back, Ralph-Johan and Ishdorj, Tseren-Onolt and Petre, Ion:
A Petri-net formalization of the heat shock response model
2008

Chen, Haiming and Ionescu, Mihai and Ishdorj, Tseren-Onolt and Paun, Andrei and Paun, Gheorghe and Pérez-Jiménez, Mario J.:
Spiking Neural P Systems with Extended Rules: Universality and Languages
Natural Computing,, Volume 7, Number 2, 2008

Ishdorj, Tseren-Onolt and Leporati, Alberto:
Uniform Solutions to SAT and 3-SAT by Spiking Neural P Systems with Pre-computed Resources
Natural Computing, Volume 7, Number 4, 2008

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