University of Ljubljana, Slovenia
The University of Ljubljana (UL) is the oldest and the largest higher education and research institution in Slovenia. University has its seat in picturesque and vibrant city of Ljubljana, one of the smallest European capitals. It hosts 23 faculties and three academies that are attended by over 40.000 undergraduate and over 7.000 graduate students. The University of Ljubljana fosters basic, applied and developmental research, and strives to achieve excellence and the highest quality as well as to fulfil the highest ethical criteria in all areas of the sciences and arts. The participation in ITFoM will be coordinated through its Faculty of Computer and Information Science, an ingeneering school with extensive experience in computational and data analytics approaches and applications in biomedicine.
Previous experience and profile of staff members
Blaz Zupan, Janez Demsar and Tomaz Curk are all members of Bioinformatics Laboratory. Blaz Zupan's research is focused on the development and use of artificial intelligence and data mining approaches in biomedicine. His expertise is computational phenotyping and development of tools for modelling of relations between gene sequence, expression, and mutant-based phenotypes. With Janez Demsar, he shares interest in data visualization, analytics and biomedical data mining. They are both principal authors of Orange, a popular Python-based open-source data mining suite. Demsar and Zupan will be joined with Tomaz Curk, who specializes in gene sequence analysis and discovery of relations between sequence, expression and phenotypes. Bioinformatics Laboratory is an experienced designer of practical bioinformatics software tools that include mutant-based inference of regulatory pathways, GenePath, interactive web-based gene expression profile browser dictyExpress and web-based application for gene interaction analytics SNPSyn.
Five recent publications relevant to the project
1) Zagar L, Mulas F, Garagna S, Maurizio Z, Bellazzi R, Zupan B (2011) Stage prediction of embryonic stem cell differentiation from genome-wide expression data, Bioinformatics 27(18):2546-2553.
2) 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 (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43, Nature Neuroscience 14(4):452-458.
3) Stajdohar M, Mramor M, Zupan B, Demsar J (2010) FragViz: visualization of fragmented networks, BMC Bioinformatics 11 (457).
4) 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.
5) Zupan B, Demsar J (2008) Open-source tools for data mining. Clinics in Laboratory Medicine 28(1):37-54, 2008.