Dr Katerina Taškova

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Research Fellow (Data Science)

Phone: +64 9 921 9999 – ext: 5126

Email: katerina.taskova@aut.ac.nz

Qualifications:

  • 2012 – PhD in Computer Science, International Postgraduate School Jožef Stefan, Slovenia
  • 2005 – BsC (Hons) in Electrical Engineering, major in Computer Science, Information Technology and Automation, Faculty of Electrical Engineering, St. Cyril and Methodius University, Macedonia

Memberships and Affiliations:

Biography:

  • Oct 2014 – May 2018,   Postdoctoral Researcher, Computational Biology and Data Mining Group, Faculty of Biology, Johannes Gutenberg-Universität Mainz (JGU); Institute of Molecular Biology gGmbH, Germany.
  • Oct 2017 – Feb 2018,   Visiting Researcher, Centre for Computational Evolution, The University of Auckland, New Zealand.
  • Dec 2014,   Visiting Researcher, Theoretical Cell Science Group, Department of Cell Growth and Differentiation, Center for iPS Research and Application, Kyoto University, Japan.
  • Aug 2012 – Sep 2014,   Postdoctoral Researcher, Software Engineering and Bioinformatics Group, Institute for Computer Science, JGU, Germany
  • Mar – Apr 2014,   Visiting Researcher, Machine Learning Group, Computer Science Department, University of Waikato, New Zealand.
  • Jan 2007 – Jun 2011,   Young Researcher, Computer Systems Department, Jožef Stefan Institute, Slovenia
  • Jan – Mar 2009,   Visiting PhD Student, Chair for Computation in Engineering, Technische Universität München, Germany.
  • 2005 – Oct 2006,   Teaching Assistant, Faculty of Informatics, European University – Republic of Macedonia (EURM), Macedonia.

Teaching Areas:

  • Bioinformatics (JGU)
  • Programming (JGU)
  • Computer organization (EURM)

Research Areas:

  • Bioinformatics
  • Data mining
  • Machine learning
  • Metaheuristic optimization
  • Mathematical modeling

Current Research Projects:

  • At-Birth Predictive Risk Modelling Project – develop algorithms to predict the risk of abuse and neglect for children born in Allegheny County (United States) from linked administrative data.

Publications:

Articles in Peer-Reviewed Journals

  1. Theobald, J., Ghanem, A., Wallisch, P., Banaeiyan, A. A., Andrade-Navarro, M. A., Taškova, K., Haltmeier, M., Kurtz, A., Becker, H., Reuter, S., Mrowka, R., Cheng, X. and Wölfl, S. (2018). Liver-Kidney-on-Chip To Study Toxicity of Drug Metabolites. ACS Biomaterials Science & Engineering, 4.1, pp. 78–89.
  2. Taškova, K., Fontaine, J.-F., Mrowka, R. and Andrade-Navarro, M. A. (2017). Evaluation of In Vivo and In Vitro Models by Comparison of Toxicogenomics Data with the Literature. Methods, 132, pp. 569–577.
  3. Benedik, B., Taškova, K., Tavčar, J. and Duhovnik, J. (2015). Prediction of Vacuum Cleaner Motor Brush Life: A Regression Approach. IET Electric Power Applications, 9.9, pp. 569–577.
  4. Dietzen, M., Kalinina, O. V., Taškova, K., Kneissl, B., Hildebrandt, A.-K., Jaenicke, E., Decker, H., Lengauer, T. and Hildebrandt, A. (2015). Large Oligomeric Complex Structures can be Computationally Assembled by Efficiently Combining Docked Interfaces. Proteins: Structure, Function, and Bioinformatics, 83.10, pp. 1887–1899.
  5. Šilc, J., Taškova, K. and Korošec, P. (2015). Data Mining-Assisted Parameter Tuning of a Search Algorithm. Informatica, 39.2, pp. 169–176.
  6. Čerepnalkoski, D., Tashkova, K., Todorovski, L., Atanasova, N. and Džeroski, S. (2012). The Influence of Parameter Fitting Methods on Model Structure Selection in Automated Modeling of Aquatic Ecosystems. Ecological Modelling, 245.1, pp. 136–165.
  7. Tashkova, K., Šilc, J., Atanasova, N., and Džeroski, S. (2012). Parameter Estimation in a Nonlinear Dynamic Model of an Aquatic Ecosystem with Meta-heuristic Optimization. Ecological Modelling, 226.1, pp. 36–61.
  8. Tashkova, K., Korošec, P. and Šilc, J. (2011). A Distributed Multilevel Ant-Colony Algorithm for the Multi-Way Graph Partitioning. International Journal of Bio-Inspired Computation 3.5, pp. 286–296.
  9. Tashkova, K., Korošec, P., Šilc, J., Todorovski, L. and Džeroski, S. (2011). Parameter Estimation with Bio-Inspired Meta-Heuristic Optimization: Modeling the Dynamics of Endocytosis. BMC Systems Biology, 5.1, pp. 159.
  10. Taškova, K., Korošec, P., and Šilc, J. (2008a). A Distributed Multilevel Ant Colonies Approach. Informatica, 32.3, pp. 307–317.
  11. Taškova, K., Stojanova, D., Bohanec, M. and Džeroski, S. (2007). A Qualitative Decision-Support Model for Evaluating Researchers. Informatica, 31.1, pp. 479–486.

Articles in Peer-Reviewed Conferences and Workshops

  1. Tashkova, K., Korošec, P. and Šilc, J. (2012). Exploring the Parameter Space of a Search Algorithm. Proceedings of the 5th International Conference on Bioinspired Optimization Methods and their Application (BIOMA 2012), May 24–25, 2012, Bohinj, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 151–162.
  2. Korošec, P., Tashkova, K. and Šilc, J. (2010). The Differential Ant-Stigmergy Algorithm for Large-Scale Global Optimization. Proceedings of the IEEE Congress on Evolutionary Computation (CEC2010), July 18–23, 2010, Barcelona, Spain. IEEE, pp. 1–8.
  3. Tashkova, K., Korošec, P., Šilc, J., Todorovski, L. and Džeroski, S. (2010a). Parameter Estimation in an Endocytosis Model. Proceedings of the 4th International Workshop on Machine Learning in Systems Biology (MLSB 2010), October 15–16, 2010, Edinburgh, Scotland, pp. 75–80.
  4. Tashkova, K., Korošec, P., Šilc, J., Todorovski, L. and Džeroski, S. (2010b). Parameter Estimation in an Endocytosis Model Using Bioinspired Optimization Algorithms. Proceedings of the 4th International Conference on Bioinspired Optimization Methods and their Application (BIOMA 2010), May 20–21, 2010, Ljubljana, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 67–82.
  5. Taškova, K., Korošec, P. and Šilc, J. (2010). A Distributed Multilevel Ant-Colony Approach for Finite Element Mesh Decomposition. Parallel Processing and Applied Mathematics, 8th International Conference, PPAM 2009, Wroclaw, Poland, September 2009. Revised Selected Papers, Part II. Vol. 6068. Lecture Notes in Computer Science. Springer-Verlag, pp. 398–407.
  6. Čerepnalkoski, D., Taškova, K., Todorovski, L. and Dzeroski, S. (2008). Inducing Process-Based Models of Dynamic Systems from Multiple Data Sets. European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD 2008): Proceedings of Induction of Process Models (IPM 2008), September 15-19, 2008, Antwerp, Belgium. University of Antwerp, Antwerp, Belgium, pp. 5–12.
  7. Taškova, K., Korošec, P. and Šilc, J. (2008). A Distributed Multilevel Ant Colonies Approach for Graph Partitioning. Proceedings of the 3rd International Conference on Bioinspired Optimization Methods and their Applications (BIOMA 2008), October 13–14, 2008, Ljubljana, Slovenia. Ed. by B. Filipič and J. Šilc. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 41–57.
  8. Čerepnalkoski, D., Dzeroski, S., Taškova, K. and Todorovski, L. (2007). Learning Generic Models of Dynamic Systems. Proceedings of the 10th International Multi-Conference Information Society (IS 2007), October 8-12, 2007, Ljubljana, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 186–189.
  9. Stojanova, D., Taškova, K., Bohanec, M. and Džeroski, S. (2007). A Qualitative Decision-Support Model for Evaluating Researchers. Proceedings of the 10th International Multi-Conference Information Society (IS 2007), October 8-12, 2007, Ljubljana, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 60–63.
  10. Stojanova, D., Panov, P., Kobler, A., Džeroski, S. and Taškova, K. (2006). Learning to Predict Forest Fires with Different Data Mining Techniques. Proceedings of the 9th International Multi-Conference Information Society (IS 2006), October 9-14, 2006, Ljubljana, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 255–258.
  11. Taškova, K., Panov, P., Kobler, A., Džeroski, S. and Stojanova, D. (2006). Predicting Forest Stand Properties from Satellite Images with Different Data Mining Techniques. Proceedings of the 9th International Multiconference Information Society (IS 2006), October 9-14, 2006, Ljubljana, Slovenia. Jožef Stefan Institute, Ljubljana, Slovenia, pp. 259–262.

Abstracts in Peer-Reviewed Conferences and Workshops

  1. Taškova, K., Fontaine, J.-F. and Andrade-Navarro, M. A. (2017). Evaluation of In Vivo and In Vitro Models of Drug Effects by Comparison to Literature-derived Phenotype Data. The 5th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2017, April 26-28, 2017, Granada, Spain.
  2. Taškova, K. and Andrade-Navarro, M. A. (2016). Rank Aggregation-Based Prioritization of Drug-Response Genes in Toxicogenomics data. The 15th European Conference on Computational Biology, ECCB 2016, September 3-7, 2016, The Hague, The Netherlands.
  3. Taškova, K., Carnini, M., Rao, S. and Hildebrandt, A. (2014). Exploring the Space of Co-Optimal Alignments for Template-Based Protein Model Quality Assessment. The 13th European Conference on Computational Biology, ECCB 2014, September 7-10, 2014, Strasbourg, France.
  4. Dietzen, M., Kalinina, O., Taškova, K., Kneissl, B., Jaenicke, E., Decker, H., Lengauer, T. and Hildebrandt, A. (2013). Three-Dimensional Modelling of Macromolecular Assemblies by Efficient Combination of Pairwise Dockings. The 21st International Conference on Intelligent Systems for Molecular Biology/The 12th European Conference on Computational Biology, ISMB/ECCB 2013, July 21-23, 2013, Berlin, Germany.
  5. Tashkova, K., Šilc, J., Atanasova, N. and Džeroski, S. (2011b). Parameter Identification in a Nonlinear Dynamic Model of an Aquatic Ecosystem with a Metaheuristic Optimization Approach. The 7th European Conference on Ecological Modelling (ECEM 2011), 30 May – 2 June 2011, Riva del Garda, Italy.
  6. Taškova, K., Korošec, P. and Šilc, J. (2009). Parameter Estimation in an Endocytosis Model with Metaheuristic Optimization Algorithms. Data 2 Dynamics Workshop (D2D), September 23–25, 2009, Freising, Germany.

Doctoral Dissertation

  1. Tashkova, K. (2012). Parameter Identification in Nonlinear Dynamic Systems with Meta-Heuristic Approaches. PhD thesis. International Postgraduate School Jožef Stefan, Ljubljana, Slovenia.