BioMediTech Research Groups

Computational Systems Biology

Group Leader: Professor Olli Yli-Harja

olli.yli-harja(at)tut.fi

About Us

The research of the Computational Systems Biology (CSB) group is aimed at gaining system level understanding of biological processes. This is achieved by applying systematic computational modeling approaches of biological processes and experimental techniques, as well as developing computational methods for analysis, interpretation, and integration of biological data.

Prof. Yli-Harja holds an Affiliate Professorship in the Institute for Systems Biology (ISB), Seattle. https://www.systemsbiology.org/bio/olli-yli-harja/

Research interests and expertise

Our method development is based on deep understanding of the role of mathematical models in theoretical biology, rooted in complex systems theory. Our research is based on a close daily interaction within our multidisciplinary research team. All faces of the research work: wet lab work, image processing, statistical analysis, and mathematical modeling are tightly coupled together.

While the models provide quantitative prediction of the experiments, they also serve the purpose of providing a shared context that systematically supports communication between members of the research group, who represent different disciplines. The development and deployment of computational tools, aimed at seamlessly integrating expert knowledge into the models, is followed by keen observation of their reception and evaluation of their impact to the research.

Achievements

One of our biggest achievements in this field is experimental verification of the self-organized criticality in the regulatory systems of yeast and mammalian cells (1). Improved understanding of the biological processes has led to many remarkable achievements within the CSB group: We have developed computational methods and resources for stem cell research for the ESTOOL research consortium (2), developed tools for observing genomic alterations in stem cells (3), developed computational methods for large scale data analysis for glioblastoma (4), and developed new computational methods for microscopy, for validation purposes (5)

Infrastructure

The Computational Systems Biology research group has 10 members with a variety of backgrounds: signal processing, molecular biology, biotechnology, computer science, etc. The group has produced 30 doctoral theses. Key member of the group is Research Fellow Dr. Meenakshisundaram Kandhavely, with expertise on molecular biology and high-throughput single cell imaging.

Collaboration offer and requests

We are interested in collaborating with groups from medicine, biology, social sciences and data science.

Major Publications

  1. Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood L, Yli- Harja O, Shmulevich I. Gene expression dynamics in the macrophage exhibit criticality. Proceedings of the National Academy of Sciences USA, 105(6):1897–1900, 2008.
  2. Kong L, Aho K-L, Granberg K, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Närvä E, Yli-Harja O, Andrews PW, Nykter M, Lahesmaa R, Roos C, Autio R. ESTOOLS Data@Hand: human stem cell gene expression resource. Nature Methods vol. 10(9), 814-815, 2013.
  3. Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R. High resolution DNA analysis reveals loss of heterozygosity and copy number variation changes associated with culture and affecting gene expression in human embryonic stem cell lines. Nature Biotechnology, 28(4):371–377, 2010.
  4. Turner K, Sun Y, Ji P, Granberg K, Bernard B, Hu L, Cogdell D, Zhou X, Yli- Harja O, Nykter M, Shmulevich I, Yungd W, Fuller G, Zhang W. Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression, Proceedings of the National Academy of Sciences USA, vol. 112 no. 11, 2015.
  5. Lehmussola A, Ruusuvuori P, Selinummi J, Rajala T, Yli-Harja O. Synthetic images of high-throughput microscopy for validation of image analysis methods. The Proceedings of the IEEE, 96(8):1348–1360, Aug 2008.
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