2012
Cerepnalkoski D, Taškova K, Todorovski L, Atanasova N, Džeroski S. The influence of parameter fitting methods on model structure selection in automated modeling of aquatic ecosystems. Ecological Modelling. 2012 doi:10.1016/j.ecomodel.2012.06.001
Szomolay B, Shahrezaei V. Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles:the role of kinase-phosphatase complex formation. BMC Syst Biol. 2012 Apr 24;6(1):26. [Epub ahead of print] doi:10.1186/1752-0509-6-26
Taškova K, Silic J, Atanasova N, Džeroski S. Parameter estimation in a nonlinear dynamic model of an aquatic ecosystem with meta-heuristic optimization. Ecological Modelling. 2012. Feb 10;226:36-61 doi.org/10.1016/j.ecolmodel.2011.11.029
2011
Kupferschmidt K. Infectious disease. Taking a new shot at a TB vaccine. Science. 2011 Dec 16;334(6062):1488-90. DOI: 10.1126/science.334.6062.1488
Taškova K, Korošec P, Silic J, Todorovski L, Džeroski S. Parameter estimation with bio-inspired meta-heuristic optimization:modeling the dynamics of endocytosis. BMC Syst Biol. 2011 Oct 11;5:159. doi:10.1186/1752-0509-5-159
2010
Slavkov, I., Gjorgjioski, V., Struyf, J. & Dzeroski, S. Finding explained groups of time-course gene expression profiles with predictive clustering trees. Mol Biosyst 6, 729-740 (2010). DOI:10.1039/B913690H
Kocev D, Ženko B, Paul P, Todorovski L, Kuijl C, Neefjes J, Džeroski S. Predictive clustering relates gene annotations to phenotype properties extracted from images. In Proceedings of the Fourth International Conference on Bioinspired Optimization Methods and their Applications, BIOMA 2010. Editors: Bogdan Filipic, Jurij Silc Kluwer Academic Publishers PDF
Tashkova K, Korosec P, Silc J, Todorovski L, Džeroski S. Parameter estimation in an endocytosis model with bio-inspired optimization algorithms. In Proceedings of the Fourth International Conference on Bioinspired Optimization Methods and their Applications, BIOMA 2010. Editors: Bogdan Filipic, Jurij Silc Kluwer Academic Publishers. PDF
Džeroski S, Rogers S, Sanguinetti G. Proceedings of the Fourth International Workshop on Machine learning in system biology. 2010 PDF
Slavkov I, Aleksovski D, Savage N, Todorovski L, Walburg K.V, Ottenhoff T, Džeroski S. Discovering groups of gene with coordinated response to M. leprae infection. In Proceedings of the Fourth International Workshop on Machine learning in system biology. 2010 pages 163-66 PDF
Sašo Džeroski. Equation discovery for ecology and systems biology. The Annual Machine Learning Conference of Belgium and The Netherlands. BeneLearn 2010. PDF
2009
Todorovski & Dzeroski (2009) Inductive process-based modeling of endocytosis from time-series data. In Machine Learning in Systems Biology: Proceedings of the Third International Workshop. September 5-6, 2009, Ljubljana, Slovenia, (Julkaisusarja - Helsingin yliopisto. Tietojenkäsittelytieteen laitos, report B-2009-1). Helsinki University, Department of Computer Science, 2009, p175-176. PDF
Book Chapters
Dorhoi A, Reece S T, Kaufmann S H E. Immunity to Intracellular Bacteria. Fundamental Immunology, 7th edition. William Paul (Ed.). Wolters Kluwer. 2012. Chapter 40. - under revision, ISBN tbc
Barsacchi R, Sundaramurthy V, Korbee K, Neefjes J, Ottenhoff T, Scanu T, Zerial M. Manipulating the fight between Human Host Cells and Intracellular Pathogens. Systems Microbiology:Current Topics and Applications. Caister Academic Press. 2012. p77-94. ISBN: 978-1-908230-02-7
Books
Robertson B D, Wren B. Eds. Systems Microbiology:Current Topics and Applications. Caister Academic Press. 2012. ISBN: 978-1-908230-02-7.
Kaufmann Stefan H.E. Ed. The New Plagues-Pandemics and Poverty in a Globalized World. Haus Publishing. 2009. ISBN:978-1-906598-13-6.