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Projects
Current Projects
- 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
- 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
Selected publications
Curk T, Rot G, Zupan B: SNPsyn: detection and exploration of SNP-SNP interactions. Nucleic acids research, May 2011.
Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, Konig J, Hortobagyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE, Ule J: Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nature Neuroscience, February 2011.
Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe N, Rot G, Zupan B, Curk T, Ule J: iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions. PLOS Biology, October 2010.
König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner D, Luscombe N, Ule J: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Structural & Molecular Biology, July 2010.
Parikh A, Miranda R, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis W, Kuspa A, Shaulsky G: Conserved developmental transcriptomes in evolutionarily divergent species. Genome biology, March 2010.
Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B: dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics, August 2009, 10:265.
