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Projects / Programmes source: ARIS

Functional Genomics and Biotechnology for Health

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Periods
January 1, 2022 - December 31, 2027
Research activity

Code Science Field Subfield
1.05.00  Natural sciences and mathematics  Biochemistry and molecular biology   
3.07.00  Medical sciences  Metabolic and hormonal disorders   

Code Science Field
1.06  Natural Sciences  Biological sciences 
3.02  Medical and Health Sciences  Clinical medicine 
Keywords
Functional genomics; systemic medicine of multifactorial disease; metabolism, steroid hormones, cholesterol, metabolic diseases, carcinogenesis; psychiatric disorders, circadian rhythm; polymorphism, mutations, biomarkers, nano-antibodies, stem cells, next generation sequencing (NGS)
Evaluation (rules)
source: COBISS
Evaluation of bibliographic research performance indicators according to ARIS methodology
Points
11,964.26
A''
951.27
A'
4,421.49
A1/2
7,448.84
CI10
27,014
CImax
698
h10
77
A1
40.43
A3
12.26
Data for the last 5 years (citations for the last 10 years) on November 30, 2023; A3 for period 2017-2021
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Database Linked records Citations Pure citations Average pure citations
WoS  1,026  32,091  29,352  28.61 
Scopus  1,038  35,743  32,845  31.64 
Researchers (35)
no. Code Name and surname Research area Role Period No. of publications
1.  55378  PhD Jerzy Adamski  Biochemistry and molecular biology  Researcher  2022 - 2023  414 
2.  38236  PhD Kaja Blagotinšek Cokan  Biochemistry and molecular biology  Researcher  2022 - 2023  43 
3.  18622  PhD Nataša Debeljak  Biochemistry and molecular biology  Researcher  2022 - 2023  237 
4.  18529  Dubravka Germ    Technical associate  2022 - 2023  0 
5.  55087  PhD John Michael Hancock  Biochemistry and molecular biology  Researcher  2022 - 2023  138 
6.  21395  PhD Petra Hudler  Medical sciences  Researcher  2022 - 2023  144 
7.  38279  PhD Ivana Jovchevska  Biochemistry and molecular biology  Researcher  2022 - 2023  87 
8.  52386  Eva Kočar  Biochemistry and molecular biology  Junior researcher  2022 - 2023  28 
9.  06135  PhD Radovan Komel  Biochemistry and molecular biology  Retired researcher  2022 - 2023  1,053 
10.  38540  Špela Kos    Technical associate  2022 - 2023  0 
11.  38237  PhD Katarina Kouter  Biochemistry and molecular biology  Researcher  2022 - 2023  78 
12.  55846  Gloria Krapež  Biochemistry and molecular biology  Junior researcher  2022 - 2023  7 
13.  51963  PhD Aleša Kristan  Biochemistry and molecular biology  Junior researcher  2022 - 2023  37 
14.  24392  PhD Katja Kristan  Pharmacy  Researcher  2022 - 2023  95 
15.  56259  Ajda Kunčič  Biochemistry and molecular biology  Junior researcher  2022 - 2023  26 
16.  11699  PhD Tea Lanišnik Rižner  Metabolic and hormonal disorders  Researcher  2022 - 2023  567 
17.  14305  PhD Mirjana Liović  Metabolic and hormonal disorders  Researcher  2022 - 2023  145 
18.  55843  Nika Marolt  Metabolic and hormonal disorders  Junior researcher  2022 - 2023  13 
19.  38391  PhD Renata Pavlič  Biochemistry and molecular biology  Junior researcher  2022 - 2023  38 
20.  55051  PhD Maja Pušić Novak  Human reproduction  Researcher  2022 - 2023  49 
21.  36486  PhD Pia Pužar Dominkuš  Biochemistry and molecular biology  Junior researcher  2022 - 2023  39 
22.  33223  PhD Lucija Raspor Dall'Olio  Biochemistry and molecular biology  Researcher  2022 - 2023  17 
23.  50630  PhD Rok Razpotnik  Biochemistry and molecular biology  Junior researcher  2022  22 
24.  22459  PhD Tadeja Režen  Neurobiology  Researcher  2022 - 2023  228 
25.  34353  PhD Marija Rogar  Biochemistry and molecular biology  Researcher  2022 - 2023  25 
26.  35360  PhD Sandra Ropret  Biochemistry and molecular biology  Researcher  2022 - 2023  15 
27.  06013  PhD Damjana Rozman  Biochemistry and molecular biology  Head  2022 - 2023  874 
28.  34259  PhD Maša Sinreih  Biochemistry and molecular biology  Researcher  2022 - 2023  83 
29.  50455  Cene Skubic  Biochemistry and molecular biology  Technical associate  2022 - 2023  59 
30.  53469  Iris Šalamon Arčan  Psychiatry  Junior researcher  2022 - 2023  28 
31.  33735  PhD Neja Šamec  Biochemistry and molecular biology  Researcher  2022 - 2023  82 
32.  37411  PhD Jana Tomc  Biochemistry and molecular biology  Researcher  2022 - 2023  22 
33.  55848  Hana Trček  Biochemistry and molecular biology  Junior researcher  2022 - 2023  15 
34.  27742  PhD Alja Videtič Paska  Medical sciences  Researcher  2022 - 2023  213 
35.  39126  PhD Alja Zottel  Biochemistry and molecular biology  Researcher  2022 - 2023  61 
Organisations (1)
no. Code Research organisation City Registration number No. of publications
1.  0381  University of Ljubljana, Faculty of Medicine  Ljubljana  1627066  45,347 
Abstract
Human diseases can be viewed as dynamic perturbations of complex, integrated, genetic, molecular and cellular networks, sensing and responding to the environment. Increasing evidence suggests that many seemingly unrelated multifactorial diseases, such as cancers, metabolic and hormonal diseases, and psychiatric disorders share some common roots, either in deviant metabolism, immune/ inflammatory response or indisturbed circadian clock. Such perspective emerges from the post-genome technologies and fuels a paradigm shift in classical medicine. In the upcoming period, our programe will be divided into three interconnecting work packages: 1) Disease mechanism and overlaps - with the aim to enhance molecular and cellular understanding of selected complex multifactorial disorders, and to identify common molecular / drug targets for drug repurposing; 2) Biomarkers for diagnostics and prognostics - using omics and systems approaches, aimed at constructing diagnostic and prognostic algorithms; 3) Therapeutics - design of new delivery systems and new treatment options, to contribute to personalized treatments. Disease mechanisms will be studied on complex multifactorial phenomena (carcinogenesis, deregulated metabolism or hormonal ballance, psychiatric phenomena, tissue injury and regeneration and also chemoresistance), with high clinical needs, including the COVID-19 co-occurence. We will upgrade our already rich technological repertoire of methods, model systems and original tools, such as 3D cultures, induced pluripotent stem cells, immortalized cell cultures modified by CRISPR / Cas9 or by lentiviral transduction, recombinant proteins, nanoantibodies, etc. Cells and clinical samples will be screened by classical and global omics high-throughput technologies, with corresponding data analysis. Whenever feasible, the 24-hour circadian behaviour will be considered as variable. For diseases which were so far investigated individually, the cross-validatation will be performed in at least one cohort from seemingly unrelated disease studied within the program. The added value of such integrative study will be in identification of potential common molecular players of mutifactorial disorders thus exposing common drug targets that would (may) allow drug repurposing. We will also upgrade the biobank based on international standards, and in collaboration with clinical and computational scientists in Slovenia and abroad further develop the information system for tracking, analysis and management of biological samples. The design of novel diagnostic and prognostic algorithms, delivery systems and treatment options will be provided in collaboration with private bodies. In conclusion, with addressing different types of complex disorders our know-how and methodologies will be applied to transfer the basic research results into the clinical and industrial settings. The broad range of collaborations in Slovenia and abroad assures our sicentific excellence.
Significance for science
The last decades have challenged us with novel technologies and abilities to look deep into the human genome and transcriptome of each individual, to screen for numerous metabolites in the blood, to search organs by imaging techniques, and much more. We can now collect data from all these measurements from humans, with different multifactorial diseases and in accordance with ethical rules store the data safely, locally, or remotely. Human data are growing exponentially. However, the technology and information booms have not yet sufficiently reached medicine and have so far barely influenced the clinical settings. Only a functional and global (systems) view on health and disease can bring a breakthrough to many multifactorial diseases for which we neither understand the complexity of disease causes, nor we can predict, diagnose, or cure the disease. Among such multifactorial conditions are metabolic and hormonal diseases (metabolism associated liver disease, endometriosis), cancers (liver, brain, endometrial, ovarian, breast, gastric), and psychiatric disorders (suicide), all with multiple environmental, metabolic and hormonal challenges. These diseases represent a major health burden in the developed societies. The burden is even amplified with the rise of the Covid-19 pandemics where patients with mentioned diseases are at highest risk. We can tackle these burdens if we accept that the combinations of interplaying genetic and environmental factors may have some common roots, even if they finally present in distinct diseases or phenotypes. Search for common roots is in the heart of our investigations and may be represented by deviant metabolism, changed immune/inflammatory response, or misaligned circadian clock. With the rise of functional genomics and its technologies the overlap of complex disease mechanisms can more easily be approached. For crucial steps forward, a biobank with international standards ia necessary, together with rich technological repertoire of classical and hight throughput methods and experimental models, and well defined clinical samples. The biobank with proper consents will allow re-use of clincial samples and studies of the disease cross-talks, whihc is important, since we hold strong domain expertise in differnet disease areas. We also hold a unique combination of expertises from genomics, epigenomics, proteomics, to metabolomics, together with classical biochemistry/molecular biology approaches. We are ready to tackle the challenges that rise from basic understanding of molecular players of diseases, and the disease overlaps, to investigating and providing the reliable biomarkers and novel therapeutic options. By applying the global approaches we will discover yet unknown molecular players of chosen diseases. The data obtained will enable novel, comprehensive insights into risk factors, mechanisms of development and progression of complex pathologies. This represents a basis for identification of diagnostic and prognostic biomarkers at any of the "omics" level, that can be, in collaboration with clinical partners, directly translated to the clinical setting. On the other side, collaboration with industry and other private bodies accelerates the development of new targeted drugs, especially as drug repurosing, and novel therapeutic approaches. The proposed program will provide break through discoveries in understanding the molecular causes and the interplay of different risk factors for complex diseases. Within the programme we will also ensure that the cutting edge post-genome technological developments are available and used in research. The nature of our research is highly interdisciplinary and uses new tools of functional genomics. The novel basic knowledge in biochemistry, molecular biology, and the functional genomic domains of health and disease, require also the knowledge of bioinformatics and modelling, that are being developed and used in the group. We perform our research with multiple scientific collaborations in Slovenia and abroad. Our scientific findings will have an impact on basic scientific knowledge of in all domains above, with use cases of selected metabolic and hormonal disorders, cancers and psychiatric diseases.
Significance for the country
Our program will tackle some of the most burning health challenges of today, taking into account also the Covid-19 disease and its burden in patients with other multifactorial pathologies. By providing novel biomarkers and treatment options, that all derive from the excellent basic research with discoveries and new knowledge in biomedicine, we can contribute significantly to reduction of the health cost. The immense progress in omics technologies has increased the power of research, so we are better equipped to unravel molecular roots and consequences of individual complex pathologies, as well as disease overlaps. The design of disease biomarkers and drug targets that permit drug repurposing, and the novel diagnostic and therapeutic approaches has a strong impact on economy and the society. The genomics and other omic approaches result in a variety of experimental data and biomedical knowledge resources that require close collaborations between biomedical and computational science. Only in such collaborative case the integrated data can be reused, leading to decrease in experimental costs and to an added value in biomedical knowledge. This will lead to the discovery of new biomedical knowledge, drugs and health care procedures. Despite most recent infrastructure investments, Slovenia is still lagging behind in the area of functional genomics and related interdisciplinary sciences, and is lacking sufficient expertise in their use in practice. The proposed program will continue to bridge this gap, by applying most novel post-genome experimental and computational approaches on biomedicaly relevant issue of multifactorial diseases, at the same time training also young scientists with the potential to present future leaders in the filed. The program will continue the battle against multifactorial disorders that are among the most challenging medical issues, such as components of metabolic syndrome, cancers, or psychiatric disorders. By expanding the knowledge on target diseases, this program will propose novel directions in therapeutic strategies and possibly identify novel drug targets. Open access to this new knowledge will boost the innovative capacity of pharmaceutical industries and/or small companies. By providing new health indicators and potentially developing personalized disease/drug risk predictors, by publishing developments on the web and other public media, this program will also contribute to the "health literacy" of citizens. We established a close cooperation with research groups at distinguished international institutions, such as ICGEB in Trieste, Italy, VUB and KU Leuvern in Belgium, Institut Pasteur in France, Babraham Institute in Cambridge, UK, DKFZ in Heidelberg, University of Leipzig, Helmholz Institute in Munich, all in Germany, Georgetown University and Vanderbilt University in USA, and others. With the proposed program, University of Ljubljana Faculty of Medicine continues to integrate its activities into the broader European efforts in development and usage of systems medicine (FP7 CASyM: Coordinated Actions Systems Medicine, that developed into EASyM - European Association for Systems Medicine), and production and analysis of high throughput medical relevant data (key roles in ELIXIR: ESFRI, a pan-European research; Slovenia became a full member of ELIXIR through efforts of our program group). Importantly, we are also among intiators of the Slovenian genome Project (started as Targeted Research Project in 2019) and have crucial positions in the 1+ Mio Genomes EU initiative, that aims at sequencing over 1 million of European Genomes until 2022.
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