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. I am also a visiting professor at Department of Molecular and Human Genetics, Baylor College of Medicine.
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.
Here is how to find my office in the main Faculty building.
Office Hours:
Every Monday from 11:00 to 12:00.
Courses:
Laboratory:
Activities and Events
In 2012, I am serving on program committees of ECML PKDD, ICDM and ICML Workshop on Machine Learning for Health Care Applications. I am an associate editor of IEEE Transactions on Information Technology in Biomedicine, Current Bioinformatics, BMC Cancer, and Informatica Medica Slovenica.
Projects
Current Projects
- CARE-MI - Cardio repair european multidisciplinary initiative, European Project (Framework Programmes), 242038, 2010−2015
- Artificial intelligence and inteligent systems, Research Programme, P2-0209, 2009−2014
- Growth and defense trade-offs in multitrophic interaction between potato and its two major pests, Basic Research and Application Project, J4-4165, 2011−2014
- Functional genomics of potato-PVY interactions, Basic Research and Application Project, J1-4268, 2011−2014
- Functional genomics of cholesterol homeostasis: the role of lanosterol 14alpha-demethylase in development of metabolic disorders, Basic Research and Application Project, J7-4053, 2011−2014
- Combination of next generation sequencing and metagenomic analysis in the diagnostics of severe hop stunting, Basic Research and Application Project, J4-4153, 2011−2014
- FightingDrugFailure, European Project (Framework Programmes), PITN-GA-2009-238132, 2010−2013
- CLIP - Mapping functional protein-RNA interactions to identify new targets for oligonucleotide-based therapy , International Project, ERC (2010) A/203738, 2010−2013
- A next-generation analytics toolbox for integrated high-throughput genomic data analysis, Bilateral Collaboration Project, BI-US/11-12-020, 2011−2012
Closed 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
- Knowledge technology approaches in drug discovery: analysis and experiment planning in high-throughput genetics, Basic Research and Application Project, L2-1112, 2008−2010
- X-MEDIA: Large Scale Knowledge Sharing and Reuse Across Media, European Project (Framework Programmes), FP6-26978, 2006−2010
- Computational Phenomics, Basic Research and Application Project, J2-9699, 2007−2009
Selected publications
- NIMFA: A Python Library for Nonnegative Matrix Factorization, Zitnik M, Zupan B. Journal of Machine Learning Research, 13:849-853, 2012.
- Stage prediction of embryonic stem cell differentiation from genome-wide expression data, Zagar L, Mulas F, Garagna S, Maurizio Z, Bellazzi R, Zupan B. Bioinformatics, 27(18):2546-2553, 2011.
- Subgroup discovery in data sets with multi-dimensional responses, Umek L, Zupan B. Intelligent Data Analysis, 15(4):533-549, 2011.
- Characterizing the RNA targets and position-dependent splicing regulation by TDP-43, Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, Konig J, Hortobágyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, Ule J. Nature Neuroscience, 14(4):452-458, 2011.
- iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution, Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. Journal of Visualized Experiments, 50:2638, 2011.
- SNPsyn: detection and exploration of SNP-SNP interactions, Curk T, Rot G, Zupan B. Nucleic Acids Res, 39 (Suppl ). W444-9, 2011.
- miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors, Crippa S, Cassano M, Messina G, Galli D, Galvez BG, Curk T, Altomare C, Ronzoni F, Toelen J, Gijsbers R, Debyser Z, Janssens S, Zupan B, Zaza A, Cossu G, Sampaolesi M. J Cell Biol, 193:1197-1212, 2011.
- New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data, Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D, Shaulsky G. BMC Bioinformatics, 11:163, 2010.
- iCLIP predicts the dual splicing effects of TIA-RNA interactions, Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J. PLoS Biology, 8 (10). e1000530, 2010.
- FragViz: visualization of fragmented networks, Stajdohar M, Mramor M, Zupan B, Demsar J. BMC Bioinformatics, 11 (457), 2010.
- Inference of the Molecular Mechanism of Action from Genetic Interaction and Gene Expression Data, Mattiazzi M, Curk T, Krizaj I, Zupan B, Petrovic U. OMICS A journal of Integrative Biology, 14(4):357-367, 2010.
- iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution, Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. Nature Structural & Molecular Biology, 17:909-915, 2010.
- Conserved developmental transcriptomes in evolutionarily divergent species, Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G. Genome Biology, 11:R35, 2010.
- Does replication groups scoring reduce false positive rate in SNP interaction discovery?, Toplak M, Curk T, Demsar J, Zupan B. BMC Genomics, 11:58, 2010.
- Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium, Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, Strassmann JE, Queller DC, Zupan B, Shaulsky G, Kuspa A. Current Biology, 19(7):567-572, 2009.
- Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection, Franco-Duarte R, Umek L, Zupan B, Schuller D. Yeast, 26(12):675-692, 2009.
- dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface, Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B. BMC Bioinformatics, 10:265, 2009.
- Rule-based clustering for gene promoter structure discovery, Curk T, Petrovic U, Shaulsky G, Zupan B. Methods of Information in Medicine, 48(3):229-235, 2009.
- Predictive data mining in clinical medicine: Current issues and guidelines, Bellazzi R, Zupan B. Internation Journal of Medical Informatics, 77(2):81-97, 2008.
- Open-source tools for data mining, Zupan B, Demsar J. Clinics in Laboratory Medicine, 28(1):37-54, 2008.
- Towards knowledge-based gene expression data mining, Bellazzi R, Zupan B. Journal of Biomedical Informatics, 40(6):787-802, 2007.
- Visualization-based cancer microarray data classification analysis, Mramor M, Leban G, Demsar J, Zupan B. Bioinformatics, 23(16):2147-2154, 2007.
- VizRank: Data Visualization Guided by Machine Learning, Leban G, Zupan B, Vidmar G, Bratko I. Data Mining and Knowledge Discovery, 13(2):119-136, 2006.
- GenePath: from mutations to genetic networks and back, Juvan P, Demsar J, Shaulsky G, Zupan B. Nucleic Acids Res, 33 (Web Se). W749-W752, 2005.
- Epistasis analysis with global transcriptional phenotypes, Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsky G. Nature Genetics, 37(5):471-477, 2005.
- VizRank: Finding Informative Data Projections in Functional Genomics by Machine Learning, Leban G, Bratko I, Petrovic U, Curk T, Zupan B. Bioinformatics, 21(3):413-414, 2004.
- Nomograms for Visualization of Naive Bayesian Classifier, Mozina M, Demsar J, Kattan MW, Zupan B. In: European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), September 20-24, 2004, Pisa, 2004.
- Attribute Interactions in Medical Data Analysis, Jakulin A, Bratko I, Smrke D, Demsar J, Zupan B. In: 9th Conference on Artificial Intelligence in Medicine in Europe (AIME 2003), October 18-22, 2003, Protaras, Cyprus, 2003.
- GenePath: a System for Automated Construction of Genetic Networks from Mutant Data, Zupan B, Demsar J, Bratko I, Juvan P, Halter J, Kuspa A, Shaulsky G. Bioinformatics, 19(3):383, 2003.
- Machine learning for survival analysis: a case study on recurrence of prostate cancer, Zupan B, Demsar J, Kattan MW, Beck JR, Bratko I. Artificial Intelligence in Medicine, 20(1):59-75, 2000.
Graduate Students
Lan Umek, Marko Toplak, Lan Žagar, Gregor Rot, Črt Gorup, Anže Starič.
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