Jonatan Taminau

About | CV | Research | Teaching | Publications | Supplementary Information

• [2000-2004] Master in Computer Science, Vrije Universiteit Brussel (VUB)
• [2004-2005] Advanced Studies Master of Science in Bio-Informatics, Katholieke Universiteit Leuven (KULeuven)
• [2005-2007] Researcher Chemoinformatics, Silicos NV
• [2008-????] Ph.D. student supervised by Prof. Dr. Ann Nowé at the Computational Modeling Lab (CoMo), Vrije Universiteit Brussel (VUB)

See also: linkedin

I'm currently working on the In Silico Wet Lab Research project initiated in the framework of the Brussels Impulse Programme for ICT, which is supported by ISRIB, the Institute for the encouragement of Scientific Research and Innovation of Brussels, and by the Brussels Capital Region.

In this project I'm mostly involved in Work Package 4: Data Mining. I will analyse gene expression data (from multiple sources) using new machine learning techniques. The purpose of this research will be to incorporate domain-specific information into these new methods.

Opgaven:

• taak01 (deadline: 27 Oktober 2010)
• taak02 (deadline: 29 November 2010)
• taak03 (deadline: 20 December 2010)
• project (deadline: 14 Januari 2011 | 28 Augustus 2011)

Extra:

• Makefile
• character.txt
• equipment.txt
• code_pointers.cpp

Book Chapters

[2010, incollection | www | bibTeX]

J. Taminau, S. Meganck, C. Lazar, D. Y. Weiss-Solis, A. Coletta, N. Walker, H. Bersini, and A. Nowé, "Sequential Application of Feature Selection and Extraction for Predicting Breast Cancer Aggressiveness," , Chan, J. H., Ong, Y.-S., and Cho, S.-B., Eds., Springer Berlin Heidelberg, 2010, vol. 115, pp. 46-57.

[2009, incollection | www | bibTeX]

Y. Gómez, R. Bello, A. Nowé, E. Casanovas, and J. Taminau, "Multi-colony ACO and Rough Set Theory to Distributed Feature Selection Problem," , Omatu, S., Rocha, M., Bravo, J., Fernández, F., Corchado, E., Bustillo, A., and Corchado, J., Eds., Springer Berlin / Heidelberg, 2009, vol. 5518, pp. 458-461.

Journals and Lecture Notes

[2012, article | bibTeX]

C. Lazar, J. Taminau, S. Meganck, D. Steenhoff, A. Coletta, C. Molter, V. de Schaetzen, R. Duque, H. Bersini, and A. Nowe, "A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 99, iss. PrePrints, 2012.

[2011, article | bibTeX]

J. Taminau, D. Steenhoff, A. Coletta, S. Meganck, C. Lazar, V. de Schaetzen, R. Duque, C. Molter, H. Bersini, A. Nowé, and D. Y. Weiss Solís, "InSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO," Bioinformatics, vol. 27, iss. 22, pp. 3204-3205, 2011.

[2009, article | www | bibTeX]

J. Taminau, S. Meganck, D. Y. Weiss-Solis, W. C. G. van Staveren, G. Dom, D. Venet, H. Bersini, V. Detours, and A. Nowé, "Validation of Merging Techniques for Cancer Microarray Data Sets," Australian Journal of Intelligent Information Processing Systems, vol. 10, iss. 4, pp. 4-11, 2009.

[2008, article | www | bibTeX]

J. Taminau, G. Thijs, and H. De Winter, "Pharao: Pharmacophore alignment and optimization," Journal of Molecular Graphics and Modeling, vol. 27, iss. 2, pp. 161-169, 2008.

Refereed Conference

[2011, conference | bibTeX]

J. Taminau, R. Hillewaere, S. Meganck, D. Conklin, A. Nowé, and B. Manderick, "Applying Subgroup Discovery for the Analysis of String Quartet Movements," in Proc. Proceedings of the 23rd Benelux Conference on Artificial Intelligence, Ghent, Belgium, 2011, pp. 435-437.

[2010, conference | bibTeX]

J. Taminau, S. Meganck, and A. Nowé, "Validation of Merging Techniques for Cancer Microarray Data Sets," in Proc. The 22nd Benelux Conference on Artificial Intelligence, Luxembourg, Luxembourg, 2010.

[2009, conference | bibTeX]

J. Taminau, R. Hillewaere, S. Meganck, D. Conklin, A. Nowé, and B. Manderick, "Descriptive Mining of Folk Music: A Testcase," in Proc. The 21st Benelux Conference on Artificial Intelligence, Eindhoven, The Netherlands, 2009, pp. 377-379.

Refereed Workshop

[2010, inproceedings | bibTeX]

J. Taminau, R. Hillewaere, S. Meganck, D. Conklin, A. Nowé, and B. Manderick, "Applying Subgroup Discovery for the Analysis of String Quartet Movements," in Proc. Third International Workshop on Machine Learning and Music, Firenze, Italy, 2010.

[2009, inproceedings | bibTeX]

J. Taminau, R. Hillewaere, S. Meganck, D. Conklin, A. Nowé, and B. Manderick, "Descriptive Subgroup Mining of Folk Music," in Proc. Second International Workshop on Machine Learning and Music, Bled, Slovenia, 2009, pp. 1-6.

* J. Taminau, G. Thijs, H. De Winter and W. Langenaecker, “De Novo and Fast-Follower Design of Novel Therapeutic Compounds using Cosmos™”, Poster at 4th Joint Sheffield Conference on Chemoinformatics, Sheffield (UK), 18-20 Jun 2007. (abstract) (poster)

* J. Taminau, “Subgroup Discovery in Bioinformatics,” Cuba-Flanders Workshop on Machine Learning and Knowledge Discovery, Santa Clara (Cuba), 3-5 February 2010.

* D. Venet, S. Meganck, J. Taminau, L. Abdessemed, D. Weiss, A. Coletta, N. Walker, D. Steenhoff, F. Rousseau, J. Schymkowitz, A. Nowé, V. Detours and H. Bersini, “The InSilico Database: An Efficient Starting Point for Genomic Data Analysis”, Poster at European Human Genetics Conference, Gothenburg (Sweden), 12-15 Jun 2010. (abstract)

* J. Taminau, C. Lazar, S. Meganck and A. Nowé, “Feature Extraction on Breast Cancer Signatures”, Poster spotlight talk at Cancer Bioinformatics Workshop, Cambridge (UK), 2-4 Sep 2010. (program) (view)

* J. Taminau, S. Meganck, D. Y. Weiss-Solis, W.C.G. Van Staveren, G. Dom, D. Venet, H. Bersini, V. Detours and A. Nowé, “Comparison of validation methods for merging cancer microarray data sets”, Poster at 9th European Conference on Computational Biology, Ghent (Belgium), 26-29 Sep 2010. (abstract)

* D. Venet, A. Coletta, J. Taminau, D. Steenhoff, L. Bentabet, N. Walker, S. Meganck, J.B. Delgado, V. de Schaetzen, F. Savagner, F. Rousseau, J. Schymkowitz, “InSilico DB: an efficient starting point for the analysis of curated human Affymetrix gene expression microarray datasets in GenePattern”, Late Breaking Poster at 9th European Conference on Computational Biology, Ghent (Belgium), 26-29 Sep 2010. (abstract)

* J. Taminau, Seminar Talk, Machine Learning Group @ UCL, 02 Dec 2010. (slides)

Supplementary information for several submissions and/or papers can be found here:

AJIIPS_2010 (Australian Journal of Intelligent Information Processing Systems)

CBW_2010 (Cancer Bioinformatics Workshop, Cambridge )

ECCB_2010 (European Conference on Computational Biology, Ghent)