Juuso Parkkinen

Researcher, doctoral student, M.Sc. (Tech.)

Office:

Room A341 in Computer Science Building,
Konemiehentie 2, Otaniemi campus area, Espoo

Postal Address:

Aalto University School of Science,
Department of Information and Computer Science,
P.O. Box 15400, FI-00076 Aalto, Finland

Telephone:

+358 50 356 3916

Email:

firstname.lastname@aalto.fi

Personal web page:

http://ouzor.github.io/

About Me

I am a doctoral student in the Statistical Machine Learning and Bioinformatics Group (MI) focusing on learning from multiple sources, and model-driven information visualization and retrieval. The group also belongs to the Helsinki Institute for Information Technology. I am a member of the HECSE graduate school. I received my M.Sc. degree in 2009 from the degree programme of bioinformation technology of Helsinki University of Technology with major subject in bioinformatics.

Publications

See my Google Scholar Citations here

• Cross-organism toxicogenomics with group factor analysis
  Tommi Suvitaival, Juuso A. Parkkinen, Seppo Virtanen, and Samuel Kaski
  Systems Biomedicine 2014; 2:e29291
  (html, implementation)
• Probabilistic drug connectivity mapping
  Juuso Parkkinen and Samuel Kaski
  BMC Bioinformatics 2014, 15:113
  (html, R code)
2013
• Cross-organism prediction of drug hepatotoxicity by sparse group factor analysis
  Tommi Suvitaival, Juuso A. Parkkinen, Seppo Virtanen, Samuel Kaski
  In 12th Annual International Conference on Critical Assesment of Massive Data Analysis - CAMDA, 2013. Extended abstract.
  (PDF, conference page)
2012
• Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs.
  Suleiman A Khan, Ali Faisal, John P Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg and Samuel Kaski.
  BMC Bioinformatics 2012, 13:112.
  (html)
2011
• Parkkinen, Juuso et al. (2011) Service Innovation Based on Maslow's Hierarhcy of Needs in Bit Bang 3. Entrepreneurship and Services. Yrjö Neuvo & Sami Ylönen (eds.). Espoo: Aalto University. This chapter was written as part of the Bit Bang 3 post-graduate course.
• Parkkinen, Juuso et al. (2011) Infopreneur - From Nomads to Knowmads in Bit Bang 3. Entrepreneurship and Services. Yrjö Neuvo & Sami Ylönen (eds.). Espoo: Aalto University. This chapter was written as part of the Bit Bang 3 post-graduate course.
2010
• Graph Visualization With Latent Variable Models.
  Juuso Parkkinen, Kristian Nybo, Jaakko Peltonen and Samuel Kaski.
  In MLG '10: Proceedings of the Eighth Workshop on Mining and Learning with Graphs. Washington, D.C. 2010.
  (html)
• Searching for functional gene modules with interaction component models.
  Juuso Parkkinen and Samuel Kaski.
  BMC Systems Biology 2010, 4:4.
  (html, R code)
2009
• Juuso Parkkinen, Adam Gyenge, Janne Sinkkonen and Samuel Kaski. A block model suitable for sparse graphs. In H. Blockeel, K. Borgwardt, X. Yan, editors, Proceedings of the 7th International Workshop on Mining and Learning with Graphs (MLG 2009), Leuven, Belgium, July 2-4 2009. Extended Abstract. (Abstract, PDF extended abstract)
• Juuso Parkkinen and Samuel Kaski. Searching for functional gene modules with interaction component models. Poster presentation in ISMB/ECCB 2009, Stockholm, Sweden, June 27 - July 2 2009.
2008
• Janne Sinkkonen, Juuso Parkkinen, Janne Aukia and Samuel Kaski. A simple infinite topic mixture for rich graphs and relational data. In Proceedings of the NIPS 2008 Workshop on Analyzing Graphs: Theory and Applications, Whistler, BC, Canada, December 12 2009. Extended Abstract. (Abstract, PDF extended abstract)
2007
• Juuso Parkkinen and Samuel Kaski. Searching for functional gene modules with interaction component models. In Proceedings of the NIPS 2007 workshop on Machine Learning in Computational Biology, Whistler, BC, Canada, December 7 2007. Extended Abstract. (Abstract, PDF extended abstract)

Thesis

Juuso Parkkinen. Generative probabilistic models of biological and social network data. Master's thesis, Helsinki University of Technology, Department of Information and Computer Science, September 2009. (PDF)

Software

NetResponse - probabilistic algorithms for functional network analysis. NetResponse includes implementation of the Interaction Component Model (ICMg) for inferring functional gene modules from combinations of protein interaction networks and gene expression data (paper html, earlier package page).