Assoc. Prof. dr. Miha Moškon
Associate Professor
T: +386 1 479 8217
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Room: R3.61 - Kabinet
Description

I am an associate professor at the University of Ljubljana, Faculty of Computer and Information Science. My research is focused on the establishment and application of computational models and approaches for the analysis of biological systems in the context of systems biology and systems medicine applications. Recently, my research has encompassed the reconstruction and analysis of context-specific genome-scale metabolic models, and Boolean models of gene regulatory networks. Within the research group, we are working on different computational pipelines to automatise the reconstruction, analysis, and interpretation of such models. I am the author and the maintainer of the CosinorPy Python library (https://github.com/mmoskon/CosinorPy) devoted to analysis of rhythmic datasets, which presents a relatively large focus of my recent work. I have also been working on the analysis and interpretation of complex datasets using different machine learning models. For the last ten years, I have been working on the computational analysis and design of synthetic biological systems, especially in the context of their information processing capabilities. I have been working on the optimisation of synthetic circuits using different heuristical optimisation approaches. These have been applied especially in the context of the estimation of unknown kinetic parameter values and the evaluation of feasible parameter spaces for which the selected topology reflects the expected response. Our group has also been focused on alternative approaches for solving the parameter estimation problem, e.g., using fuzzy logic models.

 

I currently teach the following courses at the University of Ljubljana: Computational Biology (PhD), Introduction to computer programming (BSc) and Digital Logic Design (BSc). I lead laboratory practices for several different courses.

 

I serve as an Editorial board member of BMC Bioinformatics (BioMed Central, Springer Nature) and Neural Computing and Applications (Springer, Springer Nature). I frequently review papers for several journals, which include Nucleic Acids Research, Scientific Reports, Bioinformatics, Computers in Biology and Medicine, Computational and Structural Biotechnology Journal, Metabolites, PLoS Computational Biology, and others. Currently (until May 2023), I also serve as a guest editor of a special issue Integration and Analysis of Omics Data using Genome-scale Metabolic Models in Metabolites.

Awards
  • coauthor of one of the best 10 research achievements of the University of Ljubljana in 2022 (for the work An integrative approach to neighbourhood sustainability assessments using publicly available traffic data)
  • excellent research achievements by the Slovenian Research Agency (2022)
  • 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)
  • 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)
  • 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)
Projects
Past projects
Publications
  • MOŠKON, Miha, PUŠNIK, Žiga, STANOVNIK, Lidija, ZIMIC, Nikolaj, MRAZ, Miha. A Computational Design of a Programmable Biological Processor, BioSystems, 2022, vol. 221, 104778, DOI: 10.1016/j.biosystems.2022.104778.

  • PUŠNIK, Žiga, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Review and assessment of Boolean approaches for inference of gene regulatory networks, Heliyon, 2022, 8, e10222. DOI: 10.1016/j.heliyon.2022.e10222.

  • MOŠKON, Miha, MRAZ, Miha. Programmable evolution of computing circuits in cellular populations. Neural computing & applications. 2022. DOI: 10.1007/s00521-022-07532-7.

  • VELIKAJNE, Nina, MOŠKON, Miha. RhythmCount: a Python package to analyse the rhythmicity in count data. Journal of Computational Science. September 2022, vol. 63, 101758. DOI: 10.1016/j.jocs.2022.101758.

  • VEROVŠEK, Špela, JUVANČIČ, Matevž, PETROVČIČ, Simon, ZUPANČIČ, Tadeja, SVETINA, Matija, JANEŽ, Miha, PUŠNIK, Žiga, VELIKAJNE, Nina, MOŠKON, Miha. An integrative approach to neighbourhood sustainability assessments using publicly available traffic data. Computers, Environment and Urban Systems. July 2022, vol. 95, 101805. DOI: 10.1016/j.compenvurbsys.2022.101805.

  • REŽEN, Tadeja, MARTINS, Alexandre, MRAZ, Miha, ZIMIC, Nikolaj, ROZMAN, Damjana, MOŠKON, Miha. Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models. Computers in Biology and Medicine. June 2022, vol. 145, 105428. DOI: 10.1016/j.compbiomed.2022.105428.

  • ČELOFIGA, Andreja, KORES PLESNIČAR, Blanka, KOPRIVŠEK, Jure, MOŠKON, Miha, BENKOVIČ, Dominik, GREGORIČ KUMPERŠČAK, Hojka, Effectiveness of De-Escalation in Reducing Aggression and Coercion in Acute Psychiatric Units. A Cluster Randomized Study. Frontiers in Psychiatry. April 2022, vol. 13. DOI: 10.3389/fpsyt.2022.856153

  • WALAKIRA, Andrew, OCIRA, Junior, DUROUX, Diane, FOULADI, Ramouna, MOŠKON, Miha, ROZMAN, Damjana, VAN STEEN, Kristel, Detecting gene–gene interactions from GWAS using diffusion kernel principal components. BMC Bioinformatics. February 2022, vol. 23, no. 57. DOI: 10.1186/s12859-022-04580-7

  • JANEŽ, Miha, VEROVŠEK, Špela, ZUPANČIČ, Tadeja, MOŠKON, Miha. Citizen Science for Traffic Monitoring: Investigating the Potentials for Complementing Traffic Counters with Crowdsourced Data. Sustainability. January 2022, vol. 14, no. 622, pp. 1-18. DOI: 10.3390/su14020622

  • VEROVŠEK, Špela, ZUPANČIČ-STROJAN, Tadeja, JUVANČIČ, Matevž, PETROVČIČ, Simon, SVETINA, Matija, JANEŽ, Miha, PUŠNIK, Žiga, LEBAR BAJEC, Iztok, MOŠKON, Miha. The aspect of mobility and connectivity while assessing the neighbourhood sustainability. Academic journal of interdisciplinary studies. May 2021, vol. 10, no. 3, pp. 37-48. DOI: 10.36941/ajis

  • RAVNIK, Šimen, ŽABKAR, Ines, PROSENC ZMRZLJAK, Uršula, JOVCHEVSKA, Ivana, ŠAMEC, Neja, MOŠKON, Miha, VIDETIČ PASKA, Alja. OligoPrime : an information system for oligonucleotide management. Biomedical engineering and computational biology. Sep. 2021, vol. 12, pp. 1-9. DOI: 10.1177/11795972211041983.

  • WALAKIRA, Andrew, ROZMAN, Damjana, REŽEN, Tadeja, MRAZ, Miha, MOŠKON, Miha. Guided extraction of genome-scale metabolic models for the integration and analysis of omics data. Computational and Structural Biotechnology Journal. 2021, vol. 19, pp. 3521-3530. DOI: 10.1016/j.csbj.2021.06.009.

  • MOŠKON, Miha, PUŠNIK, Žiga, ZIMIC, Nikolaj, MRAZ, Miha. Field-programmable biological circuits and configurable (bio)logic blocks for distributed biological computing. Computers in Biology and Medicine. [Print ed.]. Jan. 2021, vol. 128, pp. 1-9. DOI: 10.1016/j.compbiomed.2020.104109.

  • MOŠKON, Miha, KOMAC, Roman, ZIMIC, Nikolaj, MRAZ, Miha. Distributed biological computation : from oscillators, logic gates and switches to a multicellular processor and neural computing applications. Neural computing & applications. Aug. 2021, vol. 33, no. 15, pp. 8923-8938. DOI: 10.1007/s00521-021-05711-6.

  • BLAGOTINŠEK COKAN, Kaja, URLEP, Žiga, MOŠKON, Miha, MRAZ, Miha, KONG, Xiang Y., ESKILD, Winnie, ROZMAN, Damjana, JUVAN, Peter, REŽEN, Tadeja. Common transcriptional program of liver fibrosis in mouse genetic models and humans. International journal of molecular sciences. 2021, vol. 22, iss. 2, pp. 1-21. DOI: 10.3390/ijms22020832.

  • KOVAČ, Urša, ŽUŽEK, Zala, RASPOR DALL'OLIO, Lucija, POHAR, Katka, IHAN, Alojz, MOŠKON, Miha, ROZMAN, Damjana, STARČIČ ERJAVEC, Marjanca. Escherichia coli affects expression of circadian clock genes in human hepatoma cells. Microorganisms. 2021, vol. 9, iss. 4, pp. 1-14. DOI: 10.3390/microorganisms9040869.

  • PUŠNIK, Žiga, MOŠKON, Miha. Integracija strukturnih omejitev pri izpeljavi gensko regulatornih omrežij. Uporabna informatika. 2021, vol. 29, no. 1, pp. 25-29, ISSN 1318-1882. https://uporabna-informatika.si/index.php/ui/article/view/110.

  • MOŠKON, Miha. CosinorPy : a Python package for cosinor-based rhythmometry. BMC bioinformatics. Oct. 2020, vol. 21, pp. 1-12. DOI: 10.1186/s12859-020-03830-w.

  • JUKAN, Nermin, ZAGORŠEK, David, LAZAREVIČ, Julija, PRELOŽNIK-ZUPAN, Irena, DEBELJAK, Nataša, MOŠKON, Miha. ViDis : a platform for constructing and sharing of medical algorithms. Journal of computational biology. Jun. 2020, vol. 27, no. 6, pp. 941-947. DOI: 10.1089/cmb.2019.0238.

  • PUŠNIK, Žiga, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Computational analysis of viable parameter regions in models of synthetic biological systems. Journal of biological engineering. Sep. 2019, vol. 13, pp. 1-21. DOI: 10.1186/s13036-019-0205-0.

  • MAGDEVSKA, Lidija, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha, Initial state perturbations as a validation method for data-driven fuzzy models of cellular networks, BMC Bioinformatics, Vol. 19, No. 333, 2018. DOI: 10.1186/s12859-018-2366-0.
  • CVITANOVIĆ TOMAŠ, Tanja, MOŠKON, Miha, MRAZ, Miha, ROZMAN, Damjana. Computational modelling of liver metabolism and its applications in research and the clinics. Acta chimica slovenica. June 2018, vol. 65, no. 2, pp. 253-265. DOI: 10.17344/acsi.2018.4461
  • CVITANOVIĆ TOMAŠ, Tanja, URLEP, Žiga, MOŠKON, Miha, MRAZ, Miha, ROZMAN, Damjana. LiverSex computational model : sexual aspects in hepatic metabolism and abnormalities. Frontiers in physiology. Apr. 2018, vol. 9, pp. 1-12. DOI: 10.3389/fphys.2018.00360
  • BORDON, Jure, MOŠKON, Miha, ZIMIC, Nikolaj, MRAZ, Miha. Semi-quantitative modelling of gene regulatory processes with unknown parameter values using fuzzy logic and Petri nets. Fundamenta informaticae. 2018, vol. 160, no. 1/2, pp. 81-100. DOI: 10.3233/FI-2018-1675.
  • MOŠKON, Miha, ZIMIC, Nikolaj, MRAZ, Miha. Grohar : automated visualization of genome-scale metabolic models and their pathways. Journal of computational biology. May 2018, vol. 25, no. 5, pp. 505-508. DOI: 10.1089/cmb.2017.0209.
  • VASYLCHENKOVA, Anastasiia, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Classical mechanics approach applied to analysis of genetic oscillators. IEEE/ACM transactions on computational biology and bioinformatics. May/Jun. 2017, vol. 14, no. 3, pp. 721-727. DOI: 10.1109/TCBB.2016.2550456
  • MAGDEVSKA, Lidija, PUŠNIK, Žiga, MRAZ, Miha, ZIMIC, Nikolaj, MOŠKON, Miha. Computational design of synchronous sequential structures in biological systems. Journal of computational science. Jan. 2017, vol. 18, pp. 24-31. DOI: 10.1016/j.jocs.2016.11.010
  • REJC, Živa, MAGDEVSKA, Lidija, TRŠELIČ, Tilen, OSOLIN, Timotej, VODOPIVEC, Rok, MRAZ, Jakob, PAVLIHA, Eva, ZIMIC, Nikolaj, CVITANOVIĆ TOMAŠ, Tanja, ROZMAN, Damjana, MOŠKON, Miha, MRAZ, Miha. Computational modelling of genome-scale metabolic networks and its application to CHO cell cultures. Computers in Biology and Medicine. Sep. 2017, vol. 88, pp. 150-160, DOI: 10.1016/j.compbiomed.2017.07.005.
  • CVITANOVIĆ TOMAŠ, Tanja, REICHERT, Matthias C., MOŠKON, Miha, MRAZ, Miha, LAMMERT, Frank, ROZMAN, Damjana. Large-scale computational models of liver metabolism : how far from the clinics?. Hepatology. 2017, vol. 66, no. 4, pp. 1323-1334. DOI: 10.1002/hep.29268.
  • BIZJAK, Manca, ZIMIC, Nikolaj, MRAZ, Miha, MOŠKON, Miha. Computational framework for modeling multiple noncooperative transcription factor binding and its application to the analysis of nuclear factor kappa B oscillatory response. Journal of computational biology. Dec. 2016, vol. 23, no. 12, pp. 923-933. DOI: 10.1089/cmb.2016.0065
  • BORDON, Jure, MOŠKON, Miha, ZIMIC, Nikolaj, MRAZ, Miha. Fuzzy logic as a computational tool for quantitative modelling of biological systems with uncertain kinetic data. IEEE/ACM transactions on computational biology and bioinformatics. [Print ed.]. 2015, vol. 12, no. 5, pp. 1199-1205. DOI: 10.1109/TCBB.2015.2424424.
  • PETRONI, Mattia, ZIMIC, Nikolaj, MRAZ, Miha, MOŠKON, Miha. Stochastic simulation algorithm for gene regulatory networks with multiple binding sites. Journal of computational biology. Mar. 2015, vol. 22, no. 3, pp. 218-226. DOI: 10.1089/cmb.2014.0064.

 

Dr. Moškon's full bibiliography is available at https://bib.cobiss.net/bibliographies/si/webBiblio/bib201_20211014_183240_a110484579.html

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