dr. Miha Moškon

Miha Moškon is an associate professor at the University of Ljubljana, Faculty of Computer and Information Science. He received his BSc degree in Computer Science in 2007 and his PhD in 2012. He is interested in different aspects of modelling, design, and optimization of biological systems, especially in the context of their dynamical response. His main research interests have been recently directed towards accurate quantitative modelling and analysis of metabolic and gene regulatory networks and towards the computational design of synthetic biological systems, such as biological processor. He has coordinated and collaborated in several projects that were focused on the implementation of computational support systems for data management in experimental laboratories as well as within the clinical environment. He currently teaches the following courses at the University of Ljubljana: Computational Biology (PhD), Introduction to computer programming (BSc) and Digital Logic Design (BSc), and leads the laboratory practice for the course Unconventional information processing methods and platforms (MSc).

Research interests

  • systems biology
  • systems medicine
  • synthetic biology
  • unconventional computing
  • information processing in biological systems
  • modelling, analysis and design of biological systems
  • fuzzy logic
  • artificial life
  • optimization

Education and awards

  • coauthor of one of the best 10 research achievements of the University of Ljubljana in 2017 (for the work Large-scale computational models of liver metabolism: how far from the clinics)
  • certificate of recognition for young university teachers and associates (2016) - among the highest awards at the University of Ljubljana
  • advisor to the computational part of the Slovenian iGEM 2016 team - Best foundational advance prize at the iGEM World Championship (2016)
  • COBRA Exchange Programme award (2013)
  • PhD from computer science (2012)
  • advisor to the computational part of the Slovenian iGEM 2012 team - 1st runner up at the iGEM World Championship (2012)
  • advisor to the computational part of the Slovenian iGEM 2010 team - Grand Prize winners at the iGEM World Championship (2010)
  • BSc from computer science (2007)
  • Prešeren's award for the thesis on Fuzzy model of foraging behavior in a bird flocking simulation (2007)
  • Dean's awards from the University of Ljubljana, Faculty of Computer and information Science (2005 and 2006)
  • Zois scholarship for distinctly talented pupils and students (1998-2008)

Projects

ongoing

  • 2019 – 2022: Data integration framework for the assessments of the sustainable efficiency in Slovene neighbourhoods and settlements – Slovenian Research Agency, ARRS J5-1798 (PI at the Faculty of Computer and Information Science)
  • 2019 – 2022: Precision Medicine at the Interface of Translational Research and Systems Medicine (TranSYS), H2020-MSCA-ITN-2019 (comentor of a trainee)
  • 2018 – 2021: CholesteROR in metabolic liver disease – Slovenian Research Agency, ARRS J1-9176 (researcher)
  • From 2009 to 2023: Pervasive computing, Research Programme, P2-0359 (researcher).

finished

  • 2020: BioPrime: Establishment of information system for management of primer database, PKP – European Structural and Investment Funds (partner)
  • 2019: Establishment of open information system for the management of biological samples in the biobank repositories, PKP – European Structural and Investment Funds (coordinator)
  • 2019: Standardization of procedures for obtaining biological samples and information system for biobanks, SIPK – European Structural and Investment Funds (partner)
  • 2018: Computational support for identification of genetic predispositions and diagnostics of complex diseases, PKP – European Structural and Investment Funds (coordinator)
  • 2018: Information system for tracking and management of samples, material and chemicals in health sciences, SIPK – European Structural and Investment Funds (coordinator)
  • 2018: Genetic diagnostics of blood diseases, SIPK – European Structural and Investment Funds (partner)
  • 2017: Development of information system for tracking, analysis and management of laboratory samples in the field of functional genomics, PKP-3D 25-13-3 – European Structural and Investment Funds (coordinator).
  • 2017: Dark secrets of fast fashion, PKP-3D – European Structural and Investment Funds (partner).
  • From 2014 to 2017: Designed cellular logic, Basic Research and Application Project, J1-6740 (researcher).
  • From 2009 to 2012: Slovenian research agency - Computer vision for mobile computing and interaction. Basic Research and Application Project (researcher).
  • From 2006 to 2009: Iskratel ltd. – Optimization of resiliency and fast convergence in the Ethernet network environment. Industry-Funded Project (researcher).
  • From 2008 to 2010: TMG-BMC ltd. – Developing IT support for muscle diagnostics. Industry-Funded Project (researcher).
  • From 2006 to 2008: Slovenian Ministry of Defence - Introduction of fuzzy logic into the process of defence system management. Target Research programmes (researcher).

Other professional activities

  • editorial board member of Neural Computing and Application
  • reviewer for
    • PLoS Computational Biology
    • Nucleic Acids Research
    • Bioinformatics
    • BMC Systems Biology
    • BMC Bioinformatics
    • BMC Research Notes
    • Computational and Structural Biotechnology Journal
    • Computers in Biology and Medicine
    • Biochemistry and Biophysics
    • IEEE Transactions on Circuits and Systems
    • IEEE Transactions on Human Machine Systems
    • International Journal of Metaheuristics
    • Neural Computing and Applications
    • Mathematical Problems in Engineering
    • Journal of Advanced Transportation
    • Economic and Business Review
    • MDPI Metabolites
    • MDPI Molecules
    • MDPI Applied Sciences
  • co-chair of the 13th CFGBC Scientific Symposium - Taste of Genomics (Ljubljana, 21. 6. 2018)

PhD students

current

  • Žiga Pušnik: Context-specific inference of gene regulatory networks
  • Ana Halužan Vasle: Reservoir computing in biological systems

finished

  • Andrew Walakira: Personalized molecular signatures for modulating metabolic associated fatty liver disease and hepatocellular carcinoma (comentor, financed by H2020-MSCA-ITN-2019, finished in 2023)
  • Tanja Cvitanović: Application of SteatoNet to predict network disorders in liver metabolism (comentor) (finished in 2018)
  • Mattia Petroni: Computational methodology for enhanced sensitivity analysis of gene regulatory networks (finished in 2018) (thesis)

Contact and information