Variable Independiente Participación de los diferentes actores de la sociedad en el proceso de

pening by grouping and

collaborative filtering. In: Koivisto, P. (ed.). Di- gest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 95-99.

67 PUBLICATIONS

Dai, X. 2008. Application of model based me- thods in clustering genes from multiple data sources. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 60-65.

Dai, X. & Lähdesmäki, H. 2008. Inferringtran- scription factor targets from multiple heterogene- ous data sources. Abstracts of papers, posters and talks presented at the 2008 Joint RECOMB Satellite Conference on Regulatory Genomics - Systems Biology - Dream3, Boston, USA, 29 October - 2 November 2008 p. 153.

Gotchev, A. 2008. Research on 3D media: a Finnish and European perspective. The Realistic Media Applications Workshop and Exhibition 2008, Seoul, Republic of Korea, 23 September 2008 pp. 47-80.

Gotchev, A., Jumisko-Pyykkö, S., Boev, A. & Strohmeier, D. 2008. Mobile 3DTV system: quali- ty and user perspective. 4th International Mobile Multimedia Communications Conference Mobi- Media 2008, 7-9th of July 2008, Oulu, Finland 5 p.

Heittola, T. 2008. Musical instrument recognition in polyphonic music. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 48-50.

Intosalmi, J. 2008. Computationally efficient stochastic models for biochemical systems. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 71-75. Intosalmi, J., Manninen, T., Ruohonen, K. & Linne, M-L. 2008. Stochastic modeling of neu- ronal signalling. Abstract book of the 1st INCF Congress of Neuroinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 42.

Kauppi, J.-P. 2008. Pulse repetition interval modulation recognition using multilayer neural networks. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 57-59.

Laurila, K. 2008. Effects of mutations on tran- scription factor binding and binding models. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 66-70. Liski, A. 2008. Selecting knots for penalized splines with MDL. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 40-43.

Lukin, V., Zriakhov, M., Zelensky, A. A., Egiaza- rian, K. & Värri, A. 2008. Lossy compression of multichannel ECG based on 2-D DCT and pre- processing. Proceedings of the International Conference TCSET'2008, Modern Problems of Radio Engineering, Telecommunications and Computer Science, Lviv-Slavsko, Ukraine, 19-23 February 2008 pp. 159-162.

Mäkiraatikka, E., Manninen, T., Nahata, A. K., Jalonen, T. O. & Linne, M-L. 2008. Computation- al model for astroglial cell function in Alzheimer's disease. Abstract book of the 1st INCF Congress of Neuroinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 124.

Manninen, T., Hituri, K. & Linne, M-L. 2008. Modeling long-term potentiation: deterministic and stochastic approaches. Abstract book of the 1st INCF Congress of Neuroinformatics Databas- ing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 121.

Pepe, A., Zhao, L., Koikkalainen, J., Tohka, J., Hietala, J. & Ruotsalainen, U. 2008. Automatic analysis of cerebral shape asymmetry in 3D MRI. Abstract book of the 1st INCF Congress of Neu- roinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 Pettinen, A., Mäkiraatikka, E., Manninen, T., Smolander, O-P., Ylipää, A., Hituri, K. & Linne, M-L. 2008. Evaluation of deterministic and sto- chastic simulation tools for cellular sgnaling. Abstract book of the 1st INCF Congress of Neu- roinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 59.

Popa, V. 2008. Voice conversion. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 51-56. Ryynänen, M. 2008. Applications based on automatic melody transcription. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 44-47.

Ryynänen, M. 2008. Applications based on au- tomatic melody transcription. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 44-47.

Saarinen, A. 2008. Sequential Monte Carlo based estimation technique for neuronal models. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 76- 81.

Saarinen, A., Ylipää, A., Yli-Harja, O. & Linne, M-L. 2008. Computational methods for stochastic modeling and parameter fitting of models based on Hodgkin-Huxley formalism. Abstract book of the 1st INCF Congress of Neuroinformatics Da- tabasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 135.

Teppola, H., Selinummi, J., Sarkanen, J-R., Pettinen, A., Jalonen, T. O., Yli-Harja, O. & Lin- ne, M-L. 2008. Automated image analysis of neuroblastoma cell networks cultured on micro- electrode array plates. Abstract book of the 1st INCF Congress of Neuroinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008

Uzunov, V. 2008. Non-uniform sampling of the diffraction field. In: Koivisto, P. (ed.). Digest of TISE Seminar 2008, Kangasala, Finland, 5 June 2008 7 pp. 100-105.

Zhao, L., Ruotsalainen, U., Hirvonen, J., Hietala, J. & Tohka, J. 2008. Study of cerebral asymme- try in schizophrenia based on an novel automatic cerebral hemisphere segmentation method for MRI. Abstract book of the 1st INCF Congress of Neuroinformatics Databasing and Modeling the Brain, Stockholm, Sweden, 7-9 September 2008 p. 74.

Aho, T., Almusa, H., Matilainen, J., Larjo, A., Ruusuvuori, P., Aho, K-L., Wilhelm, T., Lähdes- mäki, H., Beyer, A., Harju, M., Chowdhury, S., Leinonen, K., Roos, C. & Yli-Harja, O. 2009. Reconstruction and validation of RefRec: a glo- bal model for the yeast molecular interaction network. Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 266.

Äijö, T. 2009. Learning gene regulatory net- works from gene expression measurements using non-parametric molecular kinetics. Pro- ceedings of the 17th Annual International Confe- rence on Intellicent Systems for Molecular Biolo- gy (ISMB) & 8th European Conference on Com- putational Biology (ECCB), Stockholm, Sweden, June 27 - July 2, 2009 1 p.

Äijö, T. & Lähdesmäki, H. 2009. Learning gene regulatory networks with delayed ODEs and continuous-time expression representation. Abst- racts of the 2009 Joint RECOMB Satellite Confe- rence on Regulatory Genomics - Systems Biolo- gy - Dream4, Boston, USA, 2-6 December 2009 p. 146.

Dabov, K. 2009. Image deblurring via regulariza- tion with nonlocal transform-based filtering. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 1-6.

Dai, X. 2009. Determining the noisy attractors of delayed stochastic gene networks from multiple data sources. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 151-156.

Danielyan, A. 2009. Super-resolution via spatial- ly adaptive block-matching filtering. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangas- ala, 4 June 2009 8, pp. 7-13.

Erkkilä, T., Ruusuvuori, P., Shmulevich, I. & Lähdesmäki, H. 2009. Incorporating spatial in- formation of heterogeneous cell populations into Bayesian mRNA- and miRNAexpression ana- lysis. Abstracts of the 2009 Joint RECOMB Sa- tellite Conference on Regulatory Genomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 251.

Heittola, T. 2009. Azimuth estimation in po- lyphonic music. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 14-16.

Hituri, K., Wils, S., Linne, M-L. & De Schutter, E. 2008. Validating models of the IP3 receptor: reproduction of experimental data with stochastic simulations. Abstracts of Neuroinformatics 2008, Stockholm, Sweden, 7-9 September 2008 2 p. Intosalmi, J. 2009. Simulation of biochemical reaction networks: a case study with protein ki- nase C signaling pathway. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 17-20.

Jääskeläinen, I.P., Kauppi, J-P., Koskentalo, K., Saramäki, J., Tohka, J. & Sams, M. 2009. Use of naturalistic stimuli in disclosing brain dynamics. Abstracts of Tuning the Brain for Music Workshop, Helsinki, Finland, 5-6 February 2009 1 p.

Kauppi, J-P. 2009. Inter-subject synchronization of brain hemodynamic responses during wat- ching a movie: localization in space, time, and frequency. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 21-24.

69 PUBLICATIONS

Kauppi, J-P., Jääskeläinen, I. P., Sams, M. & Tohka, J. 2009. Low-frequency specific inter- subject hemodynamic synchronization in frontal cortex during natural vision. Supplement of Neu- roImage, OHBM 15th Annual Meeting, San Francisco, California, USA, 18-23 June 2009 47 supplement 1, 2 p.

Kivinen, V., Nykter, M., Martin, D., Yli-Harja, O. & Shmulevich, I. 2009. Selection of an optimal set of blood biomarker proteins. Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 254.

Kong, L., Yli-Harja, O. & Autio, R. 2009. A com- parison of Affymetrix exon expression values when preprocessed with different library files. Proceedings of the 17th Annual International Conference on Intellicent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden, June 27 - July 2, 2009 1 p .

Larjo, A., Harel, D., Yli-Harja, O. & Kugler, H. 2009. Simulating combined chemotactic and metabolic response using a visual formalism. Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 65.

Laurila, K. & Lähdesmäki, H. 2009. A probabilis- tic model for competitive binding of transcription factors. Proceedings of the 17th Annual Interna- tional Conference on Intellicent Systems for Mo- lecular Biology (ISMB) & 8th European Confe- rence on Computational Biology (ECCB), Stock- holm, Sweden, June 27 - July 2, 2009 1 p. Laurila, K., Pukkila, H., Yli-Harja, O. & Lähdes- mäki, H. 2009. Protein-protein interactions im- prove multiple transcription factor binding site prediction. Abstracts of the 2009 Joint RECOMB Satellite Conference on Regulatory Genomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 131.

Lindroos, B., Aho, K-L., Kuokkanen, H., Räty, S., Huhtala, H., Lemponen, R., Yli-Harja, O., Suuronen, R. & Miettinen, S. 2009. Gene ex- pression profile of human adipose stem cells cultured in allogeneic human serum and fetal bovine serum. Abstracts of the 2009 Joint RE- COMB Satellite Conference on Regulatory Ge- nomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 246.

Liski, A. 2009. NML variable selection for regis- ter data. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 25-27.

Mäkiraatikka, E., Manninen, T., Nahata, A., Ja- lonen, T.O. & Linne, M-L. 2008. Modeling amy- loid-β and serotonin induced calcium oscillations in astrocytes. Abstracts of Neuroscience 2008, Washington D. C., 15-19 November 2008 2 p. Migukin, A. 2009. Inverse digital holographic imaging: toward perfect reconstruction of 2D wavefield distributions based on two-matrix pro- pagation modeling. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 28-34.

Myllyntausta, S., Kivinen, V., Larjo, A., Aho, T., Karp, M. & Santala, V. 2009. Acinetobacter baylyi ADP1 as a cellular framework for synthetic biology. Abstracts of IET BioSysBio Conference 2009, Cambridge, UK, 23-25 March 2009 2 p. Pepe, A., Zhao, L., Tohka, J., Koikkalainen, J., Hietala, J. & Ruotsalainen, U. 2009. Automatic statistical shape analysis of human cerebral asymmetry in 3D MRI. Supplement of NeuroI- mage, OHBM 15th Annual Meeting, San Fran- cisco, California, USA, 18-23 June 2009 47 Supplement 1, 2 p.

Popa, V. 2009. Voice conversion. In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 35-39.

Rautajoki, K., Kong, L., Leinonen, K., Lund, R., Gokhale, P., Seppälä, J., Pukkila, H., Mäkelä, J., Tuomisto, L., Järvenpää, L., Hahne, L., Yli-Harja, O. & Autio, R. 2009. ESTOOLSDB - a compre- hensive database for stem cell research. Abst- racts of the 2009 Joint RECOMB Satellite Confe- rence on Regulatory Genomics - Systems Biolo- gy - Dream4, Boston, USA, 2-6 December 2009 p. 164.

Tauren, T., Vainio, O. & Lehto, R. 2009. Recur- sive FIR filter structures on FPGA. Proceedings of the Nordic Microelectronics Event NORCHIP 2009, 16-17 November 2009, Trondheim, Nor- way 6 p.

Teppola, H., Ruusuvuori, P., Sarkanen, J-R., Selinummi, J., Jalonen, T.O. & Linne, M-L. 2009. Automated imge analyisi of differentiated human SH-SY5Y neuroblastoma cell growth on polyet- hyleneimine coated surfaces. Abstracts of Neu- roscience 2009, Chicago, USA, 17-21 October 2009 2 p.

Uzunov, V. 2009. Light field synthesis from irre- gularly distributed samples . In: Koivisto, P. (ed.), Digest of TISE Seminar 2009, Kangasala, 4 June 2009 8, pp. 40-45.

Ylipää, A., Nykter, M., Yli-Harja, O., Zhang, W. & Shmulevich, I. 2009. Association of genetic fea- tures with pathways using multiple high- throughput data. Abstracts of the 2009 Joint RE- COMB Satellite Conference on Regulatory Ge- nomics - Systems Biology - Dream4, Boston, USA, 2-6 December 2009 p. 291.