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Research interests

I am interested in computational modelling and analysis of complex systems, with a special focus on systems biomedicine. My research methods are based on network modelling, systems biology, bioinformatics, and data science.

My research group

The Computational Biomodeling Laboratory

Recent projects

  • (2016-2018) Finnish Agency for Innovation for “Network Pharmacology” (co-PI)
  • (2013-2017) Academy of Finland grant for “Quantitative model refinement”
  • (2013-2017) Academy of Finland grant for “Synthetic controllability of biological networks through understanding and engineering of their control elements” – funded in the “Synthetic Biology (FinSynBio) research program of the Academy of Finland

Active projects

  • Disease network analysis for precision cancer medicine (multiple myeloma)
  • Machine learning for personalised cancer medicine (multiple myeloma and glioblastoma)

Software and models

Network controllability for biomedicine

We develop a novel bioinformatics data analysis pipeline called NetControl4BioMedbased on the concept of target structural control of linear networks. Our pipeline generates novel molecular interaction networks by combining pathway data from various public databases starting from the user’s query. The pipeline then identifies a set of nodes that is enough to control a given, user-defined set of disease-specific essential proteins in the network, i.e., it is able to induce a change in their configuration from any initial state to any final state. The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.

The article is available here.


Bionetgen Implementation of the Heat Shock Response Bogdan Iancu has implemented the Bionetgen source code of the Heat Shock Response. It can also be downloaded as a zip-file.

Gene Assembly Simulator

Download: GeneAssemblySimulator.jar_.tar.gz


User: demo, password: demo

Tutorial: Creating a new drawing area

To be able to draw a new graph you have to create a new drawing area. By clicking on the icon �in the toolbar or choosing �New Graph� in file menu, a new internal window will popup where it is.

Heat Shock Response – Petri Net

Petri Net Implementation of the Heat Shock Response Diana-Elena Gratie has built several Petri net models of the heat shock response. The latest standard and coloured Petri net models are available for download.

Heat Shock Response – PRISM

PRISM Implementation of the Heat Shock Response implemented by Sepinoud Azimi.

Heat Shock Response Simulator

Kristian Nylund has developed the Heat Shock Simulator. An in-browser demo can be accessed from the link above.

User/password: demo/demo

WEBRSIM – Reaction System Simulator

This page provides a Web interface to the brsim reaction system simulator.