2008 |
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28 | Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski, and Matej Orešic. Gender dependent progression of systemic metabolic states in early childhood. Molecular Systems Biology, 4:197, 2008. |
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27 | Janne Nikkilä, Timo Erkkilä, and Harri Lähdesmäki. Decomposing gene expression into regulatory and differential parts with bayesian data fusion. In Proceedings of WCSB 2008, The Fifth International Workshop on Computational Systems Biology, Leipzig, Germany, 11-13 June, 2008. |
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2007 |
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26 | Antti Ajanki, Janne Nikkilä, and Samuel Kaski. Discovering condition-dependent Bayesian networks for gene regulation. In Proceedings of GENSIPS 2007, The Fifth IEEE International Workshop on Genomic Signal Processing and Statistics, Tuusula, Finland, 10-12 June, 2007. |
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2006 |
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25 | Janne Nikkilä, Antti Honkela, and Samuel Kaski. Exploring the independence of gene regulatory modules. In Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors, Proceedings of Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), pages 131–136, Helsinki, Finland, 2006. Poster. |
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2005 |
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24 | Janne Sinkkonen, Samuel Kaski, Janne Nikkilä, and Leo Lahti. Associative clustering (AC): Technical details. Publications in Computer and Information Science A84, Helsinki University of Technology, Espoo, Finland, April 2005. |
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23 | Samuel Kaski and Janne Nikkilä. Dependency exploration in computational systems biology. In Tiina Manninen, Marja-Leena Linne, and Olli Yli-Harja, editors, Proceedings of The 3rd TICSP Workshop on Computational Systems Biology, TICSP Series #29, pages 49–50, Tampere, Finland, 2005. Tampere University of Technology. |
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22 | Samuel Kaski and Janne Nikkilä. Of mice and men and yeast, and dependency exploration. CSCnews, Information Technology for Science in Finland, N/A(4):24–26, 2005. |
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21 | 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, Berlin, 2005. Springer. |
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20 | 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, 2(3):203–216, 2005. |
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19 | Arto Klami, Janne Nikkilä, Christophe Roos, and Samuel Kaski. Extracting yeast stress genes by dependencies between stress treatments, 2005. Abstract in web, http://tinyurl.com/98kcx. |
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18 | Janne Nikkilä, Tapio Rinnet, Antti Ajanki, and Samuel Kaski. Stress in yeast knockout experiments. In ICSB 2005, 6th International Conference on Systems Biology, abstract proceedings, page 249, 2005. Poster abstract. |
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17 | Janne Nikkilä, Christophe Roos, and Samuel Kaski. Integration of transcription factor binding and gene expression by associative clustering. In Catherine Bounsaythip, Jaakko Hollmén, Samuel Kaski, and Matej Orešic, editors, Proc. KRBIO05, Symposium on Knowledge Representation in Bioinformatics, pages 22–29, Espoo, Finland, 2005. Helsinki University of Technology. |
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16 | 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, 15(4):237–246, 2005. |
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2004 |
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15 | 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 IDEAL04, Intelligent Data Engineering and Automated Learning, pages 92–98, Berlin, 2004. Springer-Verlag. |
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14 | Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski. Associative clustering. In Jean-Francois Boulicaut, Floriana Esposito, Fosca Giannotti, and Dino Pedreschi, editors, Machine Learning: ECML'04. Proceedings of the 15th European Conference on Machine Learning, pages 396–405, Berlin, 2004. Springer. |
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2003 |
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13 | Janne Sinkkonen, Janne Nikkilä, Leo Lahti, and Samuel Kaski. Associative clustering by maximizing a Bayes factor. Publications in Computer and Information Science A68, Helsinki University of Technology, Espoo, Finland, June 2003. |
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12 | Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for exploratory cluster analysis. In P. S. Szczepaniak, J. Segovia, J. Kacprzyk, and L. A. Zadeh, editors, Intelligent Exploration of the Web, pages 136–151, Heidelberg, 2003. Physica-Verlag. |
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11 | Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, and Eero Castrén. Trustworthiness and metrics in visualizing similarity of gene expression. BMC Bioinformatics, 4(48), 2003. |
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10 | 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, and Marie-France Sagot, editors, Proceedings of ECCB'2003, European Conference on Computational Biology, pages 433–434, 2003. |
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2002 |
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9 | 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, 15:953–966, 2002. |
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8 | 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. Proceedings of the 10th Finnish Artificial Intelligence Conference, pages 31–40, Oulu, Finland, 2002. Finnish Artificial Intelligence Society. |
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7 | 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, Boston, MA, 2002. Kluwer. |
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6 | Janne Sinkkonen, Samuel Kaski, and Janne Nikkilä. Discriminative clustering: optimal contingency tables by learning metrics. In Tapio Elomaa, Heikki Mannila, and Hannu Toivonen, editors, Machine Learning: ECML 2002, pages 418–430, Berlin, 2002. Springer. |
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2001 |
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5 | 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). |
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4 | 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, Berlin, 2001. Springer. |
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3 | 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, 03.06.2001 - 06.06.2001, Baltimore, Maryland USA, 2001. Proceedings on CD-ROM. |
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2000 |
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2 | Samuel Kaski, Janne Nikkilä, and Teuvo Kohonen. Methods for exploratory cluster analysis. 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). |
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1998 |
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1 | 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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