Research intrest
Various methods of network clustering have been applied to reveal modular organisation in protein interaction networks (PINs). However, those clustering methods are mostly based on topological properties of the network. Therefore, we are focusing on developing methods for deriving functional modules from PINs using both structural information and domain knowledge from Gene Ontology. The modules obtained by these integrated methods are characterised by high functional cohesiveness among their members. Besides deriving modular structure, we also use the proposed methods to shed light on how the functional strength of interactions affects our view of global structural organization.
Publications
Carlsson, J., Davidsson, S., Helenius, G., Karlsson, M., Lubovac, Z., Andrén, O., Olsson, B. and Klinga Levan, K. A miRNA expression signature that separate between normal and malignant prostate tissues. Submitted to Cancer Cell International.
Carlsson, J., Helenius, G., Karlsson, M., Lubovac, Z., Andrén, O., Olsson, B., and Klinga-Levan, K. (2010). Validation of suitable endogenous control genes for expression studies of miRNA in prostate cancer tissues, Cancer Genet Cytogenet. 15;202(2):71-5.
Linde, J., Olsson, B., Lubovac, Z. (2010) Network Properties for Ranking Predicted miRNA Targets in Breast Cancer. Adv Bioinformatics. 2009:182689. Epub 2010 Mar 7.
Lubovac, Z. (2009) Investigating topological and functional features of multimodular proteins, J Biomed Biotechnol. 2009:472415. Epub 2009 Dec 30.
Zichner, T., Lubovac, Z. and Olsson, B. (2008) Temporal Analysis of Oncogenesis Using MicroRNA Expression Data. In: Proceedings of the German Conference on Bioinformatics, Lecture notes in Informatics, 136:128-137, Bonner Köllen Verlag.
Lubovac, Z. (2008) Identifying Functionally and Topologically Cohesive Modules in Protein Interaction Networks. PhD thesis, Heriot-Watt University, Edinburgh, UK.
Lubovac, Z., Corne, D., Gamalielsson, J., and Olsson B. (2007) Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity, In Hochreither, S. and Wagner, R. (eds), Proceedings of Bioinformatics Reserach and Development BIRD, Berlin, Germany, March 12-14, LNBI 4414: 185-198, Springer Verlag.
Lubovac, Z., Gamalielsson, J., and Olsson, B. (2006) Combining functional and topological properties to identify core modules in protein interaction networks. PROTEINS:Structure, Function, and Bioinformatics 64(4):948-959.
Lubovac, Z., Olsson, B., and Gamalielsson, J. (2006) Weighted Clustering Coefficient for Identifying Modular Formations in Protein-Protein Interaction Networks, In Proceedings of the Third International Conference on Bioinformatics and Computational and Systems Biology, Prague, Czech Republic, August 25-27, 122-127.
Lindlöf, A. and Lubovac, Z. (2005) Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks. In Silico Biology 5:239-249, IOS Press.
Lubovac, Z., Olsson, B., and Gamalielsson, J. (2005) Combining topological characteristics and domain knowledge reveals functional modules in protien interaction networks. In Sagot, M-F., and Guimaraes, K.S. (eds), Proceedings of CompBioNets - Algorithms and Computational Methods for Biochemical and Evolutionary Networks, Lyon, France, December 5-7, 93-106, College Publications.
Lubovac, Z., Gamalielsson, J., Olsson, B. and Lindlöf, A. (2005) Exploring protein networks with a semantic similarity measure across Gene Ontology, In Proceedings of the 6th International Symposium on Computational Biology and Genome Informatics, USA, July 21-26, 1203-1208.
Jonsson, P., Laurio, K., Lubovac, Z., Olsson, B. and Andersson, M.L. (2002) Using functional annotation to improve clusterings of gene expression patterns, In Caulfield, H.J., Chen, S-H., Cheng, H-D., Duro, R., Honavar, V., Kerre, E.E., Lu, M., Grana Romay, M., Shih, T.K., Ventura, D., Wang, P.P. and Yang, Y. (eds.), Proceedings of the 6th Joint Conference on Information Sciences, 1257-1262. Association for Intelligent Machinery.
Jonsson, P., Laurio, K., Lubovac Z., Olsson, B. and Andersson, M.L. (2002) Using functional annotation to improve clusterings of gene expression data, Information Sciences, 145(3-4): 183-194. (revised version of previous)
Lubovac, Z., Olsson, B., Jonsson, P., Laurio, K. and Andersson, M.L. (2001) Biological and statistical evaluation of gene expression profiles, In D'Attellis, C.E., Kluev, V.V and Mastorakis, N.E. (eds.), Proceedings of Mathematics and Computers in Biology and Chemistry, 149-155. WSES Press.