University Of Ljubljana, Faculty of Medicine

Short Name: UL

Country: SL

Organization description:

University of Ljubljana (Univerza v Ljubljani, UL) is the oldest, largest and central education and scientific research institution in Slovenia as well as internationally best-ranked university in Slovenia, being among the top 500 universities according to the ARWU Shanghai ranking, Times THES-QS and WEBOMETRICS rankings. UL was founded in 1919 and encompasses 23 faculties, 3 art academies and 3 associated members.

Study: By number of students, UL ranks among the largest HEI in Europe with more than 40.000 undergraduate and postgraduate students. It covers all ISCED areas in the first and second cycle study programs and leads the way in some new developments in technology and research (cognitive science, nanotechnologies, environmental sciences, biomedicine etc.). By number of employees, UL ranks as medium-sized HEI and employs approximately 5.700 employees, with more than 3.500 academic staff. UL is renowned for its quality social, natural sciences, and technical study programmes, structured in accordance with the Bologna Declaration. The projects keep pace with the latest developments in the areas of arts, sciences and technology at home and abroad.

HR excellence: from 2008, UL is committed to respect the principles of the European Charter for Researchers and the Code of Conduct for Recruitment of Researchers, which led to the award of the “HR Excellence in Research” in 2013.

Research activity: UL is very active in national and international R&D and educational programmes, and creates almost half of the research results of Slovenia. In 2018, UL researchers worked in 307 research groups on 163 national research programmes, 331 national research projects with more than

4.105 registered researchers. According to data from the database Web of Knowledge, Thomson- Reuters, UL teachers and researchers regularly contribute almost 50% of all internationally acclaimed scientific publications from the Republic of Slovenia. Ethics in research and responsible research work are the bases of research and development work at the UL.

International research: UL is also very active in international research and education programs. In the programming period 2007-2013 UL altogether cooperated in 745 European projects, including 163 FP7 projects, which rank UL on the first place in the EU-13 countries among the research organisations (source MIRRIS). In 2018, UL was involved in 458 European projects, including 98 running ERASMUS+ KA2 projects and 33 projects in the European territorial cooperation programme. UL was involved in 90 running HORIZON2020 projects, including 4 ERC grants and 15 Marie Sklodowska Curie Actions.

TTO: To protect the university intellectual property developed through the public financed research projects and to improve the technology transfer from the university to the industry, a central university Technology Transfer Office was established in 2007. University develops and accelerates the research also through the University Committee for R&D, and Committee for Innovation, which consist of representatives of most propulsive Faculties. University Incubator and Institute for Innovation and Development and the Slovenian Innovation Hub are three other units in which University of Ljubljana supports innovation and development in different ways along with laboratories and other research units within Faculties.

UL has close ties with Slovenian companies and foreign enterprises. Our partners include multinational corporations and the most successful Slovenian companies. As UL is fully aware of the importance of knowledge and skills in obtaining its own financial sources, it is increasingly developing the market oriented activities every year.

The EURAXESS contact point supports openness to foreign researchers and the international flow of researchers and the UL’s inclusion in the EURAXESS network of Slovenia

Facilities:

System for statistical analysis of medical data, Central servers and network equipment-National Data Archive, High-throughput sequencing platform equipment, Illumina MiSeq and MiniSeq

Other European projects: UL is very active in national and international R&D and educational programmes. In 2017, UL altogether cooperated in 444 EU projects, among them in 70 Horizon 2020 projects. In terms of the number of research projects, UL ranks among the top of universities and research organizations from the new EU Member States (EU 13). In the period 2007-2013 UL cooperated in 745 EU projects, including 163 FP7 projects, which places UL on the first place among the organisations in the EU 13 member states. In the last 10 years UL was also involved in many other research, development and educational projects financed by European union (CIP, COST, EUREKA, TEMPUS, LLP, DAPHNE, SafeInternet, LIFE+, CULTURE, etc.).

By participating in development projects financed with EU Structural Funds, the UL contributes significantly to the infrastructure development, structural change and economic development of Slovenia. UL is also very active in the projects financed by Structural Funds in Slovenia (ERDF, ESF), INTERREG and Transnational Cooperation Programme. It holds 2 Centres of Excellence and is partner in 6 other Centres of Excellence. It also cooperates with the industry partners in all 7

Competence centres and in one Development centre of Slovenian industry, all financed by ERDF.

Role in the project:

Institute for Biostatistics and Medical Informatics (IBMI) at the Faculty of Medicine University of Ljubljana offers bioinformatics tools, services and research counselling for scientists, medical centers, private companies and government institutions. We perform data analysis on standard and on in-house developed workflows for a wide range of bioinformatics issues, including NGS, RNA-Seq and microarray analysis. Additionally, IBMI is the leading research organization in the world regarding Literature-Based Discovery (LBD) solutions for both research and clinical applications. LBD is a novel paradigm in contemporary science that tries to solve big data problem through mining biomedical literature and infer plausible hypotheses based of facts hidden in literature (mostly by parsing MEDLINE, the leading biomedical bibliographic database). IBMI stuff developed and now maintains well-known BITOLA system for LBD. IBMI also offers automated interpretation for raw microarray and NGS data through in-house developed workflows and tools for LBD.

University of Ljubljana (UL), Faculty of Medicine will also participate in the project with its expertise in NGS and personalized medicine of rare diseases in the field of haematology, including establishment of familial erythrocytosis (FE) genetic diagnosis panel using genome wide techniques.

Key personnel:

Brane Leskošek

Brane Leskošek, PhD, male, is Head of Node of ELIXIR Slovenia (ELIXIR-SI) and an Assistant Professor of Medical Informatics and Bioinformatics. He is active in ELIXIR and other ESFRI’s life science (coordination) activities and is PI in national and international projects, e.g. H2020 ELIXIR-

EXCELERATE. ELIXIR is an intergovernmental organisation that brings together life science resources (including databases, software tools, training materials, cloud storage and supercomputers) from across Europe and coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. His expertise lays in different fields of biomedical informatics like clinical research informatics, web-based tools for data management and data curation (e.g. for distributed clinical studies or health registries), bioinformatics analyses, medical informatics ontologies, standards and standardization (SNOMED-CT, HL7, OpenEHR), e-learning and telepharmacology. He is a national representative of Slovenia in the 1M Genomes declaration group. He published close to 30 peer- reviewed papers and reviews in international journals, along with numerous conference papers and professional papers.

Polonca Ferk

Polonca Ferk, PhD, female, is an Assistant Professor of Pharmacology and Toxicology. Her PhD thesis focused on genetic variability in patients with polycystic ovary syndrome. Her research is mainly focused on genetics of reproductive health, pharmacogenomics and (epi)genomic approaches in cancer diseases along with their pharmacological treatment. She is an active member in ELIXIR- SI, oriented mainly in wet lab activities, leading the establishment of single-cell genomics/transcriptomics infrastructure in Slovenia. She is also a representative of Slovenia for rare diseases use case working group in 1M Genomes declaration. She published more than 30 peer- reviewed papers and reviews in international journals, along with numerous conference papers.

Andrej Kastrin

Andrej Kastrin, PhD, male, is a post-doctoral researcher at IBMI and member of bioinformatics group of ELIXIR-SI. He is focused on classification and discretization of high-dimensional DNA data sets, in close co-operation with functional genomics researchers. He also works on biomedical text mining in general and literature-based discovery (LBD). As data scientist, he participated in the EU projects GENEPARK (FP7) and PRACE (FP7). Currently he is the principal investigator of the national LBD project aiming towards automated and fluid interpretation of NGS results through LBD. Andrej has published about 30 peer-reviewed papers in international journals, along with numerous conference papers.

Nataša Debeljak

Nataša Debeljak, PhD, female, is Associated Professor of Biochemistry and Molecular Biology. She is currently leading national project focusing on NGS diagnosis of rare disease Familial Erythrocitosys. In past she leaded national research project, industry project and NSF-NATO postdoctoral project. She is currently involved in CASyM (www.casym.eu), COST-OpenMultiMed and national projects. As Senior Research Fellow at Institute of biochemistry her research focuses on the role of erythropoietin (Epo) and its receptor in tissue-protection, familial erythrocytosis (FE) and establishment of FE genetic diagnosis panel using genome wide techniques. She published over 20 papers and reviews.

Main publications and awards:

Publications:

Pérez-Wohlfeil E, Torreno O, Bellis LJ, Fernandes P, Leskošek B, Trelles O. Training bioinformaticians in High Performance Computing. Heliyon, 2018; 4 (12): 1-18.

Leskošek B, Pajntar M. Lightweight application for generating clinical research information systems: MAGIC. Wiener Klinische Wochenschrift, 2015; 127 (5): 228-234.

Kastrin A, Ferk P, Leskošek B. Predicting potential drug-drug interactions on topological and semantic similarity features using statistical learning. PLoS ONE, 2018; 13 (5): e0196865.

Kastrin A, Rindflesch TC, Hristovski D. Link prediction on a network of cooccurring MeSH terms: Towards literature-based discovery. Methods of Information in Medicine, 2016; 55 (4): 340-346.

Hojnik M, Dobovišek L, Knez Ž, Ferk P. A synergistic interaction of 17-[beta]-estradiol with specific cannabinoid receptor type 2 antagonist/inverse agonist on proliferation activity in primary human osteoblasts. Biomedical Reports, 2015; 3 (4): 554-558.

Rožman JŽ, Ferk P, Frković-Grazio S, Leskošek B, Geršak K. Risk factors for HR- and HER2- defined breast cancer in Slovenian postmenopausal women. Climacteric, 2012; 15 (1): 68-74.

Ferk P, Pohar Perme M, Geršak K. Insulin gene polymorphism in women with polycystic ovary syndrome. Journal of International Medical Research, 2008; 36 (6): 1180-1187.

Vočanec D, Prijatelj T, Debeljak N, Kunej T. Genetic variants of erythropoietin (EPO) and EPO

receptor genes in familial erythrocytosis. Int J Lab Hematol, 2019; 41 (2): 162-167 [Review].

Zanin M, Chorbev I, Stres B, Stalidzans E, Vera J, Tieri P, Castiglione F, Groen D, Zheng H, Baumbach J, Schmid JA, Basilio J, Klimek P, Debeljak N, Rozman D, Schmidt HHHW. Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Brief Bioinform, 2017 [Epub ahead of print].

Ilkovičová L, Trošt N, Szentpéteriová E, Solár P, Komel R, Debeljak N. Overexpression of the erythropoietin receptor in RAMA 37 breast cancer cells alters cell growth and sensitivity to tamoxifen. Int J Oncol, 2017; 51 (2): 737-746.