Laboratory of Computer and Information Science / Neural Networks Research Centre CIS Lab Helsinki University of Technology

Publications of Janne Nikkilä

  1. Janne Nikkilä, Antti Honkela, and Samuel Kaski. Exploring the independence of gene regulatory modules In Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors, Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), workshop proceedings, pages131-136, Helsinki University Printing House, 2006. (pdf)
  2. Janne Nikkilä Exploratory cluster analysis of genomic high-throughput data sets and their dependencies. PhD Thesis, Helsinki University of Technology, Dissertations in Computer and Information Science, Report D11. (pdf)
  3. Janne Nikkilä, Christophe Roos, Eerika Savia, and Samuel Kaski. Explorative modeling of yeast stress response and its regulation with gCCA and associative clustering. International Journal of Neural Systems, vol.15, nr.4, pages 237-246, 2005.
  4. Samuel Kaski, Janne Nikkilä, Janne Sinkkonen, Leo Lahti, Juha Knuuttila, and Christophe Roos. Associative clustering for exploring dependencies between functional genomics data sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Special Issue on Machine Learning for Bioinformatics -- Part 2, vol. 2, nr. 3, pages 203-216, 2005 (preprint pdf, ps, gzipped ps)
  5. Janne Sinkkonen, Samuel Kaski Janne Nikkilä, and Leo Lahti. Associative Clustering (AC): Technical Details. Technical Report A84, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, April 2005. (ps, pdf; accompanying report including only additional technical details and derivations of the method.)
  6. Janne Nikkilä, Christophe Roos, and Samuel Kaski. Integration of transcription factor binding and gene expression by associative clustering. In Bounsaythhip, Hollmén, Kaski, Oresic (eds.): KRBIO05, Proceedings of Symposium of Knowledge Representation in Bioinformatics, pages 22--29, Espoo, Finland, 15.-17. June 2005, Otamedia Ltd.
  7. Samuel Kaski, Janne Nikkilä, Eerika Savia, and Christophe Roos. Discriminative clustering of yeast stress response. In Udo Seiffert, Lakhmi Jain, and Patric Schweizer, editors, Bioinformatics using Computational Intelligence Paradigms, pages 75-92. Springer, Berlin, 2005. (preprint pdf; originally submitted in 2003)
  8. Samuel Kaski, Janne Nikkilä, and Christophe Roos What do data sets have in common? The yeast stress case. Poster in ISMB/ECCB 2004. (abstract, postscript (A4 size), gzipped postscript, pdf)
  9. Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski. Associative Clustering. ECML 2004, Pisa, Italy. In: Boulicaut, Esposito, Giannotti,Pedreschi (eds.): Machine Learning: ECML2004 ( Proceedings of 15th European Conference on Machine Learning), Lecture Notes in Computer Science 3201, pages 396-406, 2004. (pdf)
  10. Janne Nikkilä, Christophe Roos, and Samuel Kaski. Exploring dependencies between yeast stress genes and their regulators. In: Zheng Rong Yang, Richard Everson, and Hujun Yin, editors, Proceedings of International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2004), pp.92-98, Springer, 2004. (postscript , gzipped postscript)
  11. Leo Lahti, Juha Knuuttila, Janne Nikkilä and Samuel Kaski Exploring dependencies in the expression of orthologous man-mouse gene pairs In Bioinformatics 2004, Linköping, Sweden, June 3-6, 2004. A poster. (postscript (A4 size), gzipped postscript (A4 size))
  12. Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, and Eero Castren. Trustworthiness and metrics in visualizing similarity of gene expression. BMC Bioinformatics, 4:48, 2003.
  13. Janne Nikkilä, Christophe Roos, Janne Sinkkonen, and Samuel Kaski. Associative clustering to find dependencies between expression profiles and transcription factor binding. In Proceedings of ECCB2003, European Conference on Computational Biology, Paris, France, September 27-30, 2003, pages 433-434. A poster. (abstract)
  14. Janne Sinkkonen, Janne Nikkilä, Leo Lahti and Samuel Kaski. Associative Clustering by Maximizing a Bayes Factor. Technical Report A68, Helsinki University of Technology, Publications in Computer and Information Science, Espoo, Finland, June 2003. (postscript, gzipped postscript)
  15. Merja Oja, Janne Nikkilä, Petri Törönen, Eero Castrén, and Samuel Kaski. Learning metrics for visualizing gene functional similarities. In Pekka Ala-Siuru and Samuel Kaski, editors, STeP 2002 - Intelligence, The Art of Natural and Artificial. The 10th Finnish Artificial Intelligence Conference, Oulu, Finland 15-17 Dec. 2002, pages 31-40, 2002. (postscript, gzipped postscript)
  16. Janne Nikkilä, Petri Törönen, Samuel Kaski, Jarkko Venna, Eero Castrén, and Garry Wong Analysis and visualization of gene expression data using Self-Organizing Maps Neural Networks, Special issue on New Developments on Self-Organizing Maps, 2002. vol. 15, issue 8-9, pages 953-966. (postscript (preprint), gzipped postscript (preprint) )
  17. Merja Oja, Petri Törönen, Janne Nikkilä, Eero Castrén, and Samuel Kaski. Learning metrics for SOM-based clustering and visualization of yeast gene expression data. In Bioinformatics 2002, Bergen, Norway, April 4-7, 2002. A poster. (postscript (A4 size), gzipped postscript (A4 size))
  18. Merja Oja, Janne Nikkilä, Petri Törönen, Garry Wong, Eero Castrén, and Samuel Kaski. Exploratory clustering of gene expression profiles of mutated yeast strains. In Wei Zhang and Ilya Shmulevich, editors, Computational And Statistical Approaches To Genomics, pages 65-78. Kluwer Acadmic Publishers, 2002. (postscript, gzipped postscript)
  19. Samuel Kaski, Janne Nikkilä, Petri Törönen, Eero Castren, and Garry Wong. Analysis and visualization of gene expression data using self-organizing maps. In Proceedings of NSIP-01, IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing, 2001. Proceedings on CD-ROM. (postscript, gzipped postscript)
  20. Samuel Kaski, Janne Sinkkonen, and Janne Nikkilä. Clustering gene expression data by mutual information with gene function. In Georg Dorffner, Horst Bischof, and Kurt Hornik, editors, Artificial Neural Networks - ICANN 2001, pages 81-86. Springer, Berlin, 2001. (postscript, gzipped postscript)
  21. Janne Nikkilä, Petri Törönen, Janne Sinkkonen, and Samuel Kaski. Analysis of gene expression data using semi-supervised clustering. In Proceedings of Bioinformatics 2001, Skövde, Sweden, March 29-April 1, pages 2-3. 2001. (abstract).
  22. Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for exploratory cluster analysis. In Intelligent Exploration of the Web, editors: P. S. Szczepaniak and J. Segovia and J. Kacprzyk and L. A. Zadeh, pp. 136-151, Physica-Verlag,Heidelberg, 2003. (Originally published in Proceedings of SSGRR 2000, International Conference on Advances in Infrastructure for Electronic Business, Science, and Education on the Internet, L'Aquila, July 31--August 6. Scuola Superiore G. Reiss Romoli, 2000. (Proceedings on CD-ROM, ISBN 88-85280-52-8.)( postscript (preprint), gzipped postscript (preprint))
  23. Janne Nikkilä. MSc (Tech.) Thesis: Methods for Interpreting the Mapping Formed by Self-Organizing Map in Data Analysis , Helsinki University of Technology.
  24. Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for interpreting a self-organized map in data analysis. In Michel Verleysen, editor, Proceedings of ESANN'98, 6th European Symposium on Artificial Neural Networks, Bruges, April 22-24, pages 185-190. D-Facto, Brussels, Belgium, 1998.

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