Projects

Project funding: Slovenian Research Agency (ARRS)

The results of the proposed project will contribute to multiple scientific fields, including (i) systems and computational sciences, (ii) systems biology and genetics and (iii) biotechnology and agriculture. The developed procedures, models and data will be made accessible online. The application of novel machine learning approaches to industrially relevant areas, such as biotechnology, is a major EU research and development strategy, which also presents a positive feedback loop for further development of these methods by indicating the areas that require improved specific functionality. We will contribute with development and testing of (i) novel methods for model interpretation and (ii) inherently interpretable models, both of which are currently an important global R&D focus.

The problem of understanding how phenotypes arise from genotypes is among the top research frontiers of both the EC and the US National Science Foundation. Studying and testing the basic principles of gene expression will result in (i) enhanced predictive models, enabling computational testing of the effects of different combinations of DNA regions or motifs, and (ii) designs for novel molecular systems with target expression levels and phenotypic outcomes in plants. This can greatly accelerate experimental throughput and decrease development costs in biotechnology. In the case of metabolism, we will gain deeper insights into the stress-mitigating mechanisms of plants in response to environmental factors. As stress adaptation in plants is under the control of a complex metabolic and signaling network, the analysis will shed novel insights on the mechanisms that orchestrate extensive changes in gene expression and reprogramming of metabolism in response to pathogens.

Our focus on crop species will enable the direct translation of the new-found knowledge to agronomically important goals of improving crop productivity and resilience under field conditions. By identifying groups of genes that have key effects on metabolic and phenotypic outcomes, as well as solutions to control their gene expression, we have a high possibility of developing breakthrough methods for crop breeding. This aligns with and contributes to national and EU directives on food security (e.g. the EU Green deal Farm to Fork Strategy) that aim to create more sustainable food systems. More resistant crops can lower pollution by decreasing the amount of phytopharmaceutical substances used, and higher crop yields can positively impact biodiversity and climate change by lowering the amount of land used for agriculture.

Nationally, the project is expected to open multiple interdisciplinary research avenues in the technical and biological sciences, with import of foreign knowledge and collaborations with top research groups. The project also carries exceptional societal and economic impact, promoting national, EU and global incentives to address the problems of food security and crop improvement.

SICRIS