Olli Yli-Harja

Affiliate Faculty

Professor, Tampere University of Technology Department of Signal Processing

OlliYliHarja

During the years 1988-1992 Olli Yli-Harja was a research scientist at the Technical Research Centre of Finland, in 1993-1996 he was a lecturer in computer science in Helsinki University of Technology, and in 1997-1998 an Assistant Professor in University of Helsinki. In 1998 he was a research fellow at East Anglia University, Norwich, UK. In 1998-2001 he was a Senior researcher at the Institute of Signal Processing in Tampere University of Technology. In 2005, he was a visiting scientist in the University of Texas M. D. Anderson Cancer Center, Houston. Currently he is a Professor in the Department of Signal Processing in Tampere University of Technology, Finland and leads the Computational Systems Biology research group.

Dr. Yli-Harja’s research interests focus on three areas in computational systems biology:

  1. Development of computational tools and software for systems biology utilizing advanced methods of signal processing and statistics
    Development and validation of software tools for systems biology with focus on image and data analysis, quantitative simulation of modern biological measurement techniques. We also develop methods for statistical inference, large scale data integration, visualization, and data mining to help interpretation of biological data. This work facilitates the use of large scale data in applied and basic research in biosciences.
  2. Development of computational tools and software for systems biology utilizing advanced methods of signal processing and statistics
    Cross-disciplinary applied research together with several partners in biosciences. We have a range of applications in cancer research, stem cell research, microbe-based biotechnology, yeast metabolics, transcriptional regulation, and signaling networks as well as electro-physiological modeling within mammalian cells. We aim at clinical applications related to, for example, understanding the cellular level signaling in Alzheimer’s disease, and utilization clinical information using natural language processing. We also develop experimental facilities for electro-physiological measurements of mammalian neural networks, and cell image processing in an integrated microfluidic platform.
  3. Cross-disciplinary applied research together with several partners in biosciences
    Basic research in theoretical biology. This includes mathematical modeling of emergent properties of complex biological systems and investigation of information processing and structure-dynamics-relationship within them. We also develop quantitative simulation methods of biological processes using advanced mathematical models.

Detailed information in CSB-group research pages

We are building software tools for systems biology and aim at developing systematic methodology for their validation with regard not only to programming errors, but also usability and accuracy in the intended biological context. We have developed several useful tools that help solving problems in interpretation of biological measurements, image processing, and network modeling. These tools are freely available on our web-pages.

Detailed information in CSB-group software tools pages

Shmulevich Lab – Software tools for systems biology, network models for theoretical biology

Aitchison Lab – Quantitative proteomic characterization of transcriptional regulatory complexes that control peroxisomal gene expression, image analysis for genome-wide analysis of signaling networks regulating peroxisome biogenesis in yeast

Dudley Lab – Image analysis for studies of p-body formation in budding yeast

Computational Systems Biology

PhD, Computer science and applied mathematics, Lappeenranta University of Technology, Finland, 1989