I lecture and perform research in machine learning, data mining and decision support, and apply these to problems in bioinformatics and systems biology. My current major interests are data fusion and reconstruction of gene networks.
I run Bioinformatics Lab and enjoy participating in its software projects that include a data mining suite Orange, a web-based gene expression analytics dictyExpress, and next generation sequencing pipeline PIPA. Our first popular web application was GenePath: check it out, it is almost ten years old but still runs!
Here is how to find my office in the main Faculty building.
Office Hours:
Every Monday from 9:00 to 10:00.
Courses:
Laboratory:
Activities and Events
In 2013, I am serving on program committees of ECML PKDD, AIME in ACM BCB. I am an associate editor of IEEE Transactions on Information Technology in Biomedicine, 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
Closed Projects
- A next-generation analytics toolbox for integrated high-throughput genomic data analysis, Bilateral Collaboration Project, BI-US/11-12-020, 2011−2012
- 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.
- Microarray data mining with visual programming, Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, Zupan B. Bioinformatics, 21(3):396-398, 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
Present: Lan Žagar, Anže Starič, Marko Toplak, Črt Gorup.
Past: Lan Umek, Minca Mramor, Martin Žnidaršič, Curk Tomaž, Peter Juvan.
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