Home | Company | Services | News | Contacts


 
Company
 
 
 




Publications
 
2005
Samuel Kaski, Janne NikkiläOf mice and men and yeast, and dependency exploration. CSC News 4/2005, pdf
 
Iiris Hovatta, Katja Kimppa, Antti Lehmussola, Tomi Pasanen, Janna Saarela, Ilana Saarikko, Juha Saharinen, Pekka Tiikkainen, Teemu Toivanen, Martti Tolvanen, Mauno Vihinen and Gary Wong. DNA microarray data analysis Edited by Laine MM and Tuimala J: CSC; 2005. ISBN 952-5520-11-0
 
Janne Nikkilä: Exploratory Cluster Analysis of Genomic High-Throughput Data Sets and Their Dependencies. ISBN 951-22-7909-6, Otamedia Oy, Espoo 2005, Available in pdf format at http://lib.tkk.fi/Diss/2005/isbn9512279096/
 
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, no. 3, pages 203-216, July-September  2005.
 
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, Special  Issue on Bioinformatics. To appear in vol 15, no. 4, 2005. 
 
Pajusola, K., Kunnapuu, J.*, Vuorikoski, S.*, Soronen, J.*, Andre, H., Pereira, T., Korpisalo, P., Ylä-Herttuala, S., Poellinger, L. & Alitalo, K. Stabilized HIF-1? is superior to VEGF for angiogenesis in skeletal muscle via adeno-associated virus gene transfer. FASEB Journal. 19:1365-1367. 2005 *equal contribution
 
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. 
 
Janne Nikkilä, Christophe Roos, and Samuel Kaski. Integration of  transcription factor binding and gene expression by associative  clustering. In Proceedings of Symposium of Knowledge Representation  in Bioinformatics. Espoo, Finland, 15.-17. June 2005.
 
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.
 
2004
 
Samuel Kaski, Janne Nikkilä, Eerika Savia, and Christophe Roos: Discriminative Clustering of Yeast Stress Response. Accepted to book 'Bioinformatics using Computational Intelligence', eds. U.Sei_ert et al. 2004.
 
Janne Nikkilä, Samuel Kaski, and Christophe Roos: Exploring Dependencies between Yeast Stress Genes and their Regulators. In: Yang, Everson, Yin (eds.): Intelligent Data Engineering and Automated Learning (Proceedings of 5th International Conference IDEAL04), Lecture Notes in Artificial Intelligence 3177, Springer,Berlin, pages 92-98, 2004.
 
Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski: Associative Clustering. 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.
 
Leo Lahti, Juha Knuuttila, Janne Nikkilä, and Samuel Kaski: Exploring dependencies in the expression of orthologous man-mouse gene pairs. A poster in Bioinformatics 2004, Linköping, Sweden, June 3-6, 2004.
 
Samuel Kaski, Janne Nikkilä, and Christophe Roos: What do data sets have in common? The yeast stress case. Poster abstract in Intelligent Systems in Molecular Biology (ISMB)/European Conference on Computational Biology 2004.
 
2003
 
Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, and Eero Castrén: Computational visualization of gene functional similarity. BMC Bioinformatics 2003, 4:48 (13 October 2003).
 
Tuimala J, Saarikko I and Laine MM. Normalization. In: DNA microarray data analysis Edited by Laine MM and Tuimala J: CSC; 2003.
 
Janne Nikkilä, Christophe Roos, Janne Sinkkonen, and Samuel Kaski. Associative clustering to find dependencies between expression profiles and transcription factor binding. In: Catherine Christophe, Hans-Peter Lenhof, Marie-France Sagot, ECCB2003 (Proceedings of the European Conference on Computational Biology), pages 433-434, 2003.
 
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.
 
2002
 
Janne Nikkilä, Petri Törönen, Samuel Kaski, 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.
 
Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for exploratory cluster analysis. In: Szczepaniak, Piotr S.; Segovia, Javier; Kacprzyk, Janusz; Zadeh, Lotfi A.(Eds.): Intelligent Exploration of the Web, pp. 136-151, Springer, Berlin, 2002.
 
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.
 
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.
 
Janne Sinkkonen, Samuel Kaski, and Janne NikkiläDiscriminative Clustering: Optimal Contingency Tables by Learning Metrics. In: Tapio Elomaa, Heikki Mannila, Hannu Toivonen (eds.) Machine Learning: ECML 2002 (Proceedings of the ECML'02, 13th European Conference on Machine Learning), Lecture Notes in Artificial Intelligence 2430, Springer, Berlin, pp. 418-430, 2002
 
Stark T, Mankowitz L and DePierre JW (2002) Expression of glutathione transferase isoenzymes in the human H295R adrenal cell line and the effect of forskolin. J. Biochem. Molecular Toxicology 16, 169-173
 
Merja Oja, Petri Törönen, Janne Nikkilä, Eero Castrén, and Samuel Kaski. Learning metrics for SOM-based clustering and visualization of yeast gene expression data. A poster in Bioinformatics 2002, Bergen, Norway, April 4-7, 2002.
 
2001
 
Samuel Kaski, Janne Sinkkonen, and Janne NikkiläClustering gene expression data by mutual information with gene function. In Proc. ICANN'01, International Conference on Neural Networks 2001, Wien, August 21.-25., pages 81-86, Springer, Berlin, Germany, 2001.
 
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, IEEEEURASIP Workshop on Nonlinear Signal and Image Processing, 2001.
 
Stark T, Mankowitz L and DePierre JW (2001) Regulation of the GST Mu-1 isoenzyme in Y1 cells by adrenocorticotropic hormone is primarily transcriptional. J. Biochem. Molecular Toxicology 15, 128-132
 
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. A poster.
 
1999
 
Janne Nikkilä. MSc (Tech.) Thesis: Methods for Interpreting the Mapping Formed by Self-Organizing Map in Data Analysis, Helsinki University of Technology, 1999.
 
1998
 
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.
 
Eliasson M, Stark T and DePierre JW (1998) Expression of glutathione transferase isoenzymes in the porcine ovary in relationship to follicular maturation and luteinization. Chemico-Biological Interactions 117/1, 35-48