Pekka Ruusuvuori

Research positions (current/recent)

• University teacher, Tampere University of Technology, Pori.
• Post-doctoral researcher, University of Tampere, BioMediTech, Tampere, Finland.
• Academy of Finland Postdoctoral Researcher at the Department of Signal Processing, Tampere University of Technology, Tampere, Finland, 2011-2013.
• Post-doctoral researcher in the Department of Biological and Environmental Science, University of Jyväskylä (Jyväskylä, FI), 2010.
• Researcher/post-doctoral researcher, Institute for Systems Biology (Seattle, USA), 2009-2010.

Research interests

• Image and data analysis
• Pattern recognition, machine learning
• Applications in systems biology, biomedicine and industrial processes

Doctoral thesis "Methods for Image Analysis, Object Classification and Validation in Biomedical Microscopy Applications" was examined 05.01.2010. Masters thesis "Tumor Classification using Support Vector Machines", was accepted 06.04.2005.

Publications

1. 

   C. Garmendia-Torres, A. Skupin, SA. Michael, P. Ruusuvuori, NJ. Kuwada, D. Falconnet, GA. Cary, C. Hansen, PA. Wiggins, AM. Dudley

   Unidirectional P-body transport during the yeast cell cycle.

   PLoS ONE 9(6): e99428. doi:10.1371/journal.pone.0099428, 2014.

2. 

   P. Ruusuvuori, L. Paavolainen, K. Rutanen, A. Mäki, H. Huttunen, V. Marjomäki.

   Quantitative analysis of dynamic association in live biological fluorescent samples.

   PLoS One, 9(4): e94245. doi:10.1371/journal.pone.0094245, 2014.

3. 

   P. Ruusuvuori, J. Lin, A.C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, A.M. Dudley.

   Quantitative analysis of colony morphology in yeast.

   BioTechniques, Vol. 56, No. 1, January 2014, pp. 18-27.

4. F. Briggs et al.

   The 9th annual MLSP competition: New methods for acoustic classification of multiple simultaneous bird species in a noisy environment.

   IEEE MLSP, Southampton, UK, Sept. 2013.

5. 

   T. Manninen, H. Huttunen, P. Ruusuvuori, M. Nykter,

   Leukemia Prediction Using Sparse Logistic Regression.

   PLoS One. 2013; 8(8): e72932.

6. 

   M. Farhan, P. Ruusuvuori. M. Emmenlauer, P. Rämö, C. Dehio, O. Yli-Harja,

   Multi-scale Gaussian representation and outline-learning based cell image segmentation.

   BMC Bioinformatics, 14:S6, 2013.

7. 

   N. Aghaeepour, G. Finak, The FlowCAP Consortium, The DREAM Consortium*, H. Hoos, T. Mosmann, R. Brinkman, R. Gottardo and R. Scheuermann,

   Critical assessment of automated flow cytometry data analysis techniques,

   Nature Methods 10, 228-238 (2013).

8. 

   M. Farhan, P. Ruusuvuori, M. Emmenlauer, P. Rämö, O. Yli-Harja, C. Dehio,

   Graph-cut and image intensity-based splitting improves nuclei segmentation in high-content screening.

   Proc. SPIE 8655, February 2013.

9. 

   H. Huttunen, T. Erkkilä, P. Ruusuvuori, T. Manninen,

   The Eight Annual MLSP Competition: Second Place Team,

   2012 IEEE International Workshop on Machine Learning for Signal Processing (MLSP), Santander, Spain, 23-26 Sept. 2012.

10. 

    J-R. Sarkanen, P. Ruusuvuori, H. Kuokkanen, T. Paavonen and T. Ylikomi,

    Bioactive acellular implant induces angiogenesis and adipogenesis and permanent soft tissue restoration in vivo,

    Tissue Engineering Part A, December 2012, 18(23-24): 2568-2580.

11. 

    P. Ruusuvuori, T. Manninen, and H. Huttunen,

    Image Segmentation Using Sparse Logistic Regression with Spatial Prior,

    in Proceedings of the 20th European Signal Processing Conference EUSIPCO 2012, Bucharest, Romania, 27-31 Aug. 2012, pp. 2253 - 2257.

12. 

    H. Huttunen, H. Oinonen, J. Selinummi, P. Ruusuvuori, V. Voipio,

    Polynomial Pulp Fiber Modeling,

    in Proceedings of the 20th European Signal Processing Conference EUSIPCO 2012, Bucharest, Romania, 27-31 Aug. 2012, pp. 2099 - 2103.

13. 

    L. Paavolainen, P. Kankaanpää, P. Ruusuvuori, G. McNerney, M. Karjalainen, V. Marjomäki,

    Application Independent Greedy Particle Tracking Method for 3D Fluorencence Microscopy Image Series,

    2012 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Barcelona, Spain, 2-5 May 2012, pp. 672 - 675.

14. 

    N. Hayrapetyan, P. Ruusuvuori, I. Shmulevich, N. Blake, A. Ozinsky, N. Flann,

    Correcting Cell Tracking Errors Using Adaptive Re-segmentation and Coupled Flow,

    2011 8th International Workshop on Computational Systems Biology, Zürich, Switzerland

15. 

    A. Ozinsky, J. Selinummi, I Shmulevich, P. Ruusuvuori,

    Automated Analysis of Images Using Bright Field Microscopy,

    US Pat. App 13079776 - Filed 4 Apr 2011

Currently I have authored or co-authored 2 patent applications, 17 peer reviewed journal articles, 25 peer reviewed conference articles and edited two conference proceedings. An incomplete publication list can be found by searching from the university library database.

Teaching

Courses in 2011-2013:

• SGN-6106 Computational Systems Biology (Lecture)
• SGN-2500 Johdatus hahmontunnistukseen (Exercises)
• SGN-2506 Introduction to Pattern Recognition (Exercises)
• SGN-1650 Signaalinkäsittelyn työkurssi/SGN-1656 Signal Processing Laboratory
• SGNP-3021 Kuvankäsittelyn menetelmät (Course responsible)
• SGN-9406 Databases in Systems Biology and Bioinformatics (Lecture)

Contact information

pekka.ruusuvuori@tut.fi
Department of Signal Processing
Tampere University of Technology
P.O. Box 553
33101 Tampere, FINLAND

12.04.2014