I am a professor at the Faculty of Computer and Information Science, where I lecture on subjects that mostly include machine learning, data mining and decision support. My primary research interest are data mining, machine learing and data visualization, and applications of these in bioinformatics and systems biology. I am co-author of open-source data mining software Orange, which features Python scripting and visual programming, and GenePath, an epistasis analysis system which can be used to infer genetic networks from a set of experimental data. Our most recent web application is dictyExpress, a Web 2.0 software for Dictyostelium gene expression data analytics.
Office Hours:
Every Thursday from 13:00 to 14:00.
Courses:
Laboratory:
Activities and Events
Member of program committees of IV10 in 2010, and AIME, IDAMAP, EvoBIO, OSDM, CBMS in MLSB, all in 2009. I am an associate editor of IEEE Transactions on Information Technology in Biomedicine, Current Bioinformatics, Open Bioinformatics Journal in Informatica Medica Slovenica.
Education
- B.Sc., 1991, Faculty of Electrical Engineering, University of Ljubljana
- M.Sc., 1993, University of Houston, Department of Computer Science
- Ph.D., 1997, Faculty of Computer and Information Science, University of Ljubljana
Projects
Current Projects
- Qualitative modeling from data, Basic Research and Application Project, J2-2194 (B), 2009−2012
- Data and knowledge integration methods for network systems biology, Basic Research and Application Project, J2-2197, 2009−2012
- , Research Programme, P2-0209, 2009−2014
- Computational methods and tools for functional and chemogenomics of Dictyostelium, Bilateral Collaboration Project, BI-ZDA/08-10-73, 2008−2010
- Knowledge technology approaches in drug discovery: analysis and experiment planning in high-throughput genetics, Basic Research and Application Project, L2-1112, 2008−2010
Closed Projects
- Computational Phenomics, Basic Research and Application Project, J2-9699, 2007−2009
- Knowledge discovery and visualization methods for textual data, Bilateral Collaboration Project, PROTEUS 07-08, 2007−2008
- Preventive effects of antioxidants on development of hyperlipidemia and atherosclerosis in the animal model of obesity, Target Research programmes, V3-0365, 2006−2008
- Knowledge technologies and decision support in health information portals, Target Research programmes, V2-0221, 2006−2008
- X-MEDIA: Large Scale Knowledge Sharing and Reuse Across Media, European Project (Framework Programmes), FP6-26978, 2006−2010
- Artificial intelligence approaches to knowledge discovery in functional genomics, Bilateral Collaboration Project, BI-IT/05-08-011, 2006−2009
- Artificial intelligence approaches to knowledge discovery in functional genomics, Bilateral Collaboration Project, BI-IT/05-08-011, 2006−2009
- STEROLTALK: Functional genomics of complex regulatory networks from yeast to human: cross talk of sterol homeostasis and drug metabolism, European Project (Framework Programmes), LSHG-CT-2005-512096, 2005−2008
- Artificial Intelligence Approaches for Knowledge Discovery in Functional Genomics, Bilateral Collaboration Project, 2005−2006
- Artificial intelligence and inteligent systems, Research Programme, P2-0209, 2004−2008
- ASPIC: Argumentation Service Platform with Integrated Components, European Project (Framework Programmes), IST-002307, 2004−2007
- Artificial Intelligence Approaches for Knowledge Discovery , Basic Research and Application Project, J2-3387 (C), 2001−2004
Selected publications
- Toplak M, Curk T, Demsar J, Zupan B (2010) Does replication groups scoring reduce false positive rate in SNP interaction discovery?. BMC Genomics, 11: 58.
- Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, A. EO, E. JS, C. DQ, Zupan B, Shaulsky G, Kuspa A (2009) Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Current Biology, 19 (7): 567-572.
- Franco-Duarte R, Umek L, Zupan B, Schuller D (2009) Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection. Yeast, 26 (12): 675-692.
- Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B (2009) dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics, 10: 265.
- Curk T, Petrovic U, Shaulsky G, Zupan B (2009) Rule-based clustering for gene promoter structure discovery. Methods of Information in Medicine, 48 (3): 229-235.
- Zupan B, Demsar J (2008) Open-source tools for data mining. Clinics in Laboratory Medicine, 28 (1): 37-54.
- Mramor M, Leban G, Demsar J, Zupan B (2007) Visualization-based cancer microarray data classification analysis. Bioinformatics, 23 (16): 2147-2154.
- Leban G, Zupan B, Vidmar G, Bratko I (2006) VizRank: Data Visualization Guided by Machine Learning. Data Mining and Knowledge Discovery, 13 (2): 119-136.
- Juvan P, Demsar J, Shaulsky G, Zupan B (2005) GenePath: from mutations to genetic networks and back. Nucleic Acids Res, 33 (Web Server Issue). W749-W752.
- Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsky G (2005) Epistasis analysis with global transcriptional phenotypes. Nature Genetics, 37 (5): 471-477.
- Jakulin A, Mozina M, Demsar J, Bratko I, Zupan B (2005) Nomograms for Visualizing Support Vector Machines. In: SIGKDD'05 Chicago, August 2005, Illinois, USA.
- Leban G, Bratko I, Petrovic U, Curk T, Zupan B (2004) VizRank: Finding Informative Data Projections in Functional Genomics by Machine Learning. Bioinformatics, 21 (3): 413-414.
- Mozina M, Demsar J, Kattan MW, Zupan B (2004) Nomograms for Visualization of Naive Bayesian Classifier. In: European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), September 20-24, 2004, Pisa.
- Jakulin A, Bratko I, Smrke D, Demsar J, Zupan B (2003) Attribute Interactions in Medical Data Analysis. In: 9th Conference on Artificial Intelligence in Medicine in Europe (AIME 2003), October 18-22, 2003, Protaras, Cyprus.
- Zupan B, Demsar J, Bratko I, Juvan P, Halter J, Kuspa A, Shaulsky G (2003) GenePath: a System for Automated Construction of Genetic Networks from Mutant Data. Bioinformatics, 19 (3): 383.
- Zupan B, Demsar J, Kattan MW, Beck JR, Bratko I (2000) Machine learning for survival analysis: a case study on recurrence of prostate cancer. Artificial Intelligence in Medicine, 20 (1): 59-75.
Graduate Students
Minca Mramor, Lan Umek, Marko Toplak, Lan Žagar, Gregor Rot.
