selected publications
In Preparation
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Memorizing in biological circuits: An unnecessary step in the synthetic biology research agenda?
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A dictionary of linguistic terms for modelling gene regulatory networks in biological systems using Fuzzy logic
- M. Mraz and M. Moškon, Selected Chapters from Computational Biology
- Non-expandability of non-overlapping codes subject to DNA-related constraints
In Review
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Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon. SAILoR: Structure-Aware Inference of Logic Rules.
Published
2024
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L. Stanovnik, M. Moškon, M. Mraz, In search of maximum non-overlapping codes, Designs, codes and cryptography. 2024 (paper), DOI: 10.1007/s10623-023-01344-z.
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M. Moškon, U. Kovač, L. Raspor Dall'Olio, K. Geršak, G. Kavšek, E. Bojc, A. Trojner-Bregar, D. Rozman, Circadian characteristics of term and preterm labors, Scientific reports. Vol. 14, 2024 (paper), DOI:10.1038/s41598-024-54490-2.
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A. Halužan Vasle, M. Moškon, Synthetic biological neural networks : from current implementations to future perspectives, Biosystems. Vol. 237, 2024 (paper), DOI:10.1016/j.biosystems.2024.105164.
2023
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A. Walakira, C. Skubic, N. Nadižar, D. Rozman, T. Režen, M. Mraz, M. Moškon, Integrative computational modeling to unravel novel potential biomarkers in hepatocellular carcinoma, Computers in Biology and Medicine, 106957, 2023 (paper), DOI: 10.1016/j.compbiomed.2023.106957.
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E. Kočar, S. Katz, Ž. Pušnik, P. Bogovič, G. Turel, C. Skubic, T. Režen, F. Strle, V. A. P. Martins dos Santos, M. Mraz, M. Moškon, D. Rozman, COVID-19 and cholesterol biosynthesis : towards innovative decision support systems, iScience. Vol. 26, 2023 (paper), DOI: 10.1016/j.isci.2023.107799.
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M. Moškon, T. Režen, Context-specific genome-scale metabolic modelling and its application to the analysis of COVID-19 metabolic signatures, Metabolites. Vol. 13, 126, 2023 (paper), DOI: 10.3390/metabo13010126.
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M. Moškon, T. Režen, M. Juvančič, Š. Verovšek, Integrative Analysis of Rhythmicity: From Biology to Urban Environments and Sustainability, International Journal of Environmental Research and Public Health. Vol. 20, 2023 (paper), DOI: 10.3390/ijerph20010764.
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L. Stanovnik, M. Mraz, Naslavljanje DNA-pomnilnikov, Uporabna informatika. Vol. 4, 2023. (paper)
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L. Sevčnikar, J. Nastran, V. Drofenik, A. Trobec, U. Vajngerl, H. Kifle, A. Pivaš, L. Kovač, D. Popovski, M. Jan, A. Halužan Vasle, T. Režen, M. Starčič Erjavec, S. Moškon, M. Juvančič, Š. Verovšek, M. Moškon, Analiza možnosti uporabe odprtih podatkov pri določanju okoljskih vplivov na razvoj bolezni. Proceedings of the 32nd International Electrotechnical and Computer Science Conference ERK 2023 (paper)
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E. Kočar, S. Katz, Ž. Pušnik, P. Bogovič, G. Turel, C. Skubic, T. Režen, F. Strle, M. Mraz, M. Moškon, D. Rozman, Intracellular cholesterol synthesis in COVID-19. presented at the 18th CFGBC Symposium, Ljubljana, 1st June 2023 (abstract)
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E. Kočar, S. Katz, Ž. Pušnik, P. Bogovič, G. Turel, C. Skubic, T. Režen, F. Strle, V. A. P. Martins dos Santos, M. Mraz, M. Moškon, D. Rozman, Assessing the potential of cholesterol-related sterols in predicting the progression of COVID-19 disease. presented at the 15th Meeting of the Slovenian Biochemical Society with International Participation, Portorož, 20-23 September 2023 (abstract)
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M. Moškon, A modeler’s perspective on the design and analysis of biological systems : from synthetic biology to systems medicine applications. Presented at the 15th Meeting of the Slovenian Biochemical Society with International Participation, Portorož, 20-23 September 2023 (abstract)
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A. Halužan Vasle, M. Moškon, The hitchhiker's guide to synthetic biological neural networks. Presented at the 18th CFGBC Symposium, Ljubljana, 1st June 2023 (abstract)
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M. JERŠE, E. Kočar, C. Skubic, M. Moškon, J. Šmon, L. Dolenc-Grošelj, D. Rozman, Evaluating circadian rhythm disturbances in obstructive sleep apnea : molecular insights into circadian gene and hormone patterns. Presented at the 18th CFGBC Symposium, Ljubljana, 1st June 2023 (abstract)
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A. Trobec, U. Vajngerl, H. Kifle, A. Pivaš, J. Nastran, L. Sevčnikar, L. Kovač, V. Drofenik, D. Popovski, M. Jan, A. Halužan Vasle, T. Režen, M. Starčič Erjavec, M. Juvančič, Š. Verovšek, M. Moškon, Health, environmental and urban databases for integrative data analysis of health risk assessment. Presented at the 18th CFGBC Symposium, Ljubljana, 1st June 2023 (abstract)
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M. JERŠE, E. Kočar, C. Skubic, M. Moškon, J. Šmon, L. Dolenc-Grošelj, D. Rozman, Exploring circadian rhythm disturbances in obstructive sleep apnea : identification of molecular biomarkers from buffy coat and plasma using RNA expression analysis and LC-MS. Presented at Biochemistry and molecular genetics in medicine, Ljubljana 6th-7th July 2023 (abstract)
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A. Walakira, C. Skubic, N. Nadižar, D. Rozman, B. Breznik, T. Režen, M. Mraz, M. Moškon, Integrative computational modeling to identify genes relevent in hepatocellular carcinoma. Presented at Biochemistry and molecular genetics in medicine, Ljubljana 6th-7th July 2023 (abstract)
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A. Trobec, U. Vajngerl, H. Kifle, A. Pivaš, J. Nastran, L. Sevčnikar, L. Kovač, V. Drofenik, D. Popovski, Damjan, M. Jan, A. Halužan Vasle, T. Režen, M. Starčič Erjavec, M. Juvančič, Š. Verovšek, M. Moškon, Assessing the application of open-source data in determining environmental health risks. Presented at Cutting Edge 2023, Ljubljana, 21st September 2023 (abstract)
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A. Halužan Vasle, M. Moškon, Sinteznobiološke nevronske mreže. Presented at Četrti Doktorski dan Bi(o)znanosti? Ljubljana, 7th June 2023 (abstract)
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D. Rozman, A. Walakira, C. Skubic, N. Nadižar, T. Režen, K. Blagotinšek Cokan, E. Kočar, M. Mraz, M. Moškon, Unraveling potential biomarkers of metabolism associated liver disease and hepatocellular carcinoma. Presented at Discovering new knowledge and technology in life sciences and drug discovery : learning from the past, knowing the future, Shizuoka, 2023 ( abstract)
2022
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M. Moškon, Ž. Pušnik, L. Stanovnik, M. Mraz, N. Zimic, A Computational Design of a Programmable Biological Processor, BioSystems, 104778, 2022 (paper), DOI: 10.1016/j.biosystems.2022.104778.
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Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon Review and assessment of Boolean approaches for inference of gene regulatory networks, Heliyon, 8, e10222, 2022 (paper), DOI: 10.1016/j.heliyon.2022.e10222.
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M. Moškon and M. Mraz, Programmable evolution of computing circuits in cellular populations, Neural Computing & Applications, 2022 (paper), DOI: 10.1007/s00521-022-07532-7.
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T. Režen, A. Martins, M. Mraz, N. Zimic, D. Rozman, M. Moškon, Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models, Computers in Biology and Medicine. 105428, 2022 (paper), DOI: 10.1016/j.compbiomed.2022.105428.
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A. Walakira, J. Ocira, D. Duroux, R. Fouladi, M. Moškon, D. Rozman, K. Van Steen, Detecting gene–gene interactions from GWAS using diffusion kernel principal components, BMC Bioinformatics. Vol. 23, 2022 (paper), DOI: 10.1186/s12859-022-04580-7.
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Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon, Evaluation of Boolean network inference approaches, presented at the 17th CFGBC Symposium, Ljubljana, 6 June 2022 (abstract)
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M. Moškon, A. Walakira, T. Režen, D. Rozman, M. Mraz, GEMs and MEMs: Interpreting transcriptomics data with genome-scale metabolic modelling in
combination with model extraction methods, presented at the 17th CFGBC Symposium, Ljubljana, 6 June 2022 (abstract)
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E. Kočar, Ž. Pušnik, C. Skubic, P. Bogovič, G. Turel, N. Resnik, F. Strle, M. Mraz, M. Moškon, D. Rozman, Cholesterol-related sterols as early predictors of COVID-19 disease severity and their role in the SARS-COV2 spike interaction, presented at the 17th CFGBC Symposium, Ljubljana, 6 June 2022 (abstract)
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A. Walakira, C. Skubic, N. Nadižar, D. Rozman, T. Režen, M. Mraz, M. Moškon, Cholesterol and Vitamin E are important in hepatocellukar carcinoma, presented at the 17th CFGBC Symposium, Ljubljana, 6 June 2022 (abstract)
2021
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Š. Ravnik, I. Žabkar, U. Prosenc Zmrzljak, I. Jovčevska, N. Šamec, M. Moškon, A. Videtič Paska, OligoPrime: An Information System for Oligonucleotide Management, Biomedical Engineering and Computational Biology. Vol. 12, pp. 1-9, 2021 (paper), DOI: 10.1177/11795972211041983.
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A. Walakira, D. Rozman, T. Režen, M. Mraz, M. Moškon, Guided extraction of genome-scale metabolic models for the integration and analysis of omics data, Computational and Structural Biotechnology Journal. 2021 (paper), DOI: 10.1016/j.csbj.2021.06.009.
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M. Moškon, R. Komac, N. Zimic, M. Mraz. Distributed biological computation : from oscillators, logic gates and switches to a multicellular processor and neural computing applications, Neural computing & applications. 2021 (paper), DOI: 10.1007/s00521-021-05711-6.
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M. Moškon, Ž. Pušnik, N. Zimic, M. Mraz, Field-programmable biological circuits and configurable (bio)logic blocks for distributed biological computing. Computers in Biology and Medicine. Jan. 2021, vol. 128 (paper), DOI: 10.1016/j.compbiomed.2020.104109.
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Ž. Pušnik, M. Moškon, Integration of structural constraints into the gene regulatory network inference. Uporabna informatika. 2021, vol. 29, no. 1, pp. 25-29 (paper).
- K. Blagotinšek Cokan, Ž. Urlep, M. Moškon, M. Mraz, X. Y. Kong, W. Eskild, D. Rozman, P. Juvan, T. Režen, Common transcriptional program of liver fibrosis in mouse genetic models and humans. International journal of molecular sciences. 2021, vol. 22, iss. 2 ( paper), DOI: 10.3390/ijms22020832.
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U. Kovač, Z. Žužek, Raspor Dall'Olio Lucija, K. Pohar, A. Ihan, M. Moškon, D. Rozman, M. Starčič Erjavec, Escherichia coli affects expression of circadian clock genes in human hepatoma cells. Microorganisms. 2021, vol. 9, iss. 4 (paper), DOI: 10.3390/microorganisms9040869.
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Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon, Incorporation of motif information in the gene regulatory network inference, presented at the 16th CFGBC Scientific Virtual Symposium, Ljubljana, 17 June 2021 (abstract)
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C. Skubic, P. Ivanuša, A. Walakira, Ž. Vičič, M. Moškon, M. Mraz, D. Rozman, Transcriptome landscape of HepG2 cells with deleted late genes of cholesterol synthesis : focus on RORC and the circadian clock., V: Molecules of life : towards new horizons : FEBS 2021 : the 45th FEBS Congress : 3-8 July 2021, Ljubljana, Slovenia (abstract).
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K. Blagotinšek Cokan, M. Perše, J. Jeruc, G. Lorbek, Ž. Urlep, C. Skubic, P. Juvan, T. Režen, M. Moškon, M. Mraz, W. Eskild, M. Matz-Soja, W. Spindelbock, D. Rozman, The molecular crosstalk between diminished cholesterol synthesis and chronic liver disease in mice and humans., FEBS open bio. 2021, vol. 11, suppl. 1, str. 502-503. ISSN 2211-5463 (abstract).
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Z. Žužek, U. Kovač, L. Raspor Dall'Olio, K. Pohar, A. Ihan, M. Moškon, D. Rozman, M. Starčič Erjavec, Escherichia coli affects expression of circadian clock genes in human hepatoma cells, V: Molecules of life : towards new horizons : FEBS 2021 : the 45th FEBS Congress : 3-8 July 2021, Ljubljana, Slovenia (abstract).
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L. Raspor Dall'Olio, U. Kovač, Z. Žužek, K. Pohar, A. Ihan, M. Moškon, M. Starčič Erjavec, D. Rozman, Escherichia coli affects expression of circadian clock genes in human hepatoma cells, V: Abstracts : virtual symposium. 16th CFGBC Symposium, 17th June 2020, Ljubljana. Ljubljana: Faculty of Medicine, 2021 (abstract)
2020
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M. Moškon, CosinorPy : a Python package for cosinor-based rhythmometry. BMC bioinformatics, Oct. 2020, vol. 21 (full paper).
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N. Jukan, D. Zagoršek, J. Lazarovič, I. Preložnik Zupan, N. Debeljak, M. Moškon, ViDis: a platform for constructing and sharing of medical algorithms, Journal of Computational Biology, Jun. 2020, vol. 27, no. 6, pp. 941-947(preprint)
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K. Blagotinšek Cokan, P. Juvan, M. Moškon, Ž. Urlep, M. Mraz, X. Y. Kong, W. Eskild, D. Rozman, T. Režen, Transcriptional and metabolic rearrangements in liver fibrosis, V: Abstracts : virtual symposium. 15th CFGBC Symposium, 15th June 2020, Ljubljana. Ljubljana: Faculty of Medicine, 2020 (abstract).
- A. Walakira, J. Ocira, D. Duroux, R. Fouladi, M. Moškon, D. Rozman, K. Van Steen, Detecting gene-gene interactions from GWAS using diffusion kernel principal components, V: TranSYS Online Training School, 22nd - 27th, November 2020 : abstracts. Ljubljana: University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, 2020 (abstract).
- T. Režen, M. Moškon, D. Rozman, From experimental to computational models, V: TranSYS Online Training School, 22nd - 27th, November 2020 : abstracts. Ljubljana: University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, 2020 (abstract).
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R. Komac, Computational design of multicellular synchronous processing structures, MSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assoc. prof. dr. Miha Moškon) (thesis)
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D. Miškić, Overview and comparison of computational approaches for the analysis of rhythmicity in gene expression data, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assoc. prof. dr. Miha Moškon) (thesis)
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J. Nastran, Robustness assessment of the biological processor using hyperellipsoids, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assoc. prof. dr. Miha Moškon) (thesis)
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M. Ajster, Web application for the analysis and visualisation of circadian data using CosinorPy, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assoc. prof. dr. Miha Moškon) (thesis)
2019
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Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon, Computational analysis of viable parameter regions in models of synthetic biological systems, Journal of Biological Engineering, 13, Article number: 75, 2019 (full paper).
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D. Rozman, T. Cvitanović Tomaš, M. Moškon, M. Mraz, Sexual aspects of liver metabolism: A computational approach, Journal of Hepatology, Vol. 70, pp. e545, 2019 (doi:10.1016/S0618-8278(19)31080-1) (abstract).
- N. Debeljak, J. Lazarevič, D. Miskič, L. Vermiglio, A. Kopitar, A. Solarovič, M. Sever, M. Fink, T. Pajič, S. A. Doma, M. Moškon, I. Preložnik Zupan, Characterization of erythrocytosis and a proposed diagnostic algorithm in Slovenia, Slovenian Medical Journal, Vol. 88 No. 5-6, 2019: May – June (doi:10.6016/ZdravVestn.2880) (full paper).
- L. Magdevska, A mathematical model describing the circadian clock influences on cholesterol biosynthesis, MSc Thesis, University of Ljubljana, Master of Science in Computers and Mathematics (supervisor: assist. prof. dr. Miha Moškon, co-supervisor: prof. dr. Miha Mraz)
- N. Vodopivec, Integration of standards and guidelines into the open source information management systems for biobanks, MSc Thesis, Université Grenoble Alpes, Master of Science in Informatics at Grenoble, Master Informatique, Specialization Artificial Intelligence and the Web (supervisor: assist. prof. dr. Miha Moškon) (thesis)
- M. Moškon, N. Debeljak, A. Videtič Paska, T. Režen, Towards the development of a comprehensive open information solution for small biobanks, invited lecture at the 14th CFGBC Scientific Symposium, Ljubljana, 11 June 2019 (abstract)
- R. Komac, M. Mraz, N. Zimic, M. Moškon, Computational design of synchronized bacterial counters, presented at the 14th CFGBC Scientific Symposium, Ljubljana, 11 June 2019 (abstract)
- Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon, Constraint-based inference of gene regulatory networks, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- L. Jerman, M. Moškon, D. Rozman, M. Mraz, Integration of circadian clock effects into a cholesterol biosynthesis model, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- M. Smerkol, J. Šteblaj, Ž. Klaneček, M. Mraz, N. Zimic, M. Moškon, Computational analysis of parametric variability influnece on the dynamics of synchronized cellular populations, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- U. Kovač, K. Malovrh, M. Moškon, T. Režen, D. Rozman, Lipids around the clock: findings from different human cell lines, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- Z. Žužek, U. Kovač, K. Pohar, M. Moškon, A. Ihan, D. Rozman, M. Starčič Erjavec, Selection of Escherichia coli strains and pre-assays needed to study the effect of bacteria on human hepatoma cell lines, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- Ž. Drakulić, C. Skubic, M. Moškon, D. Rozman, Altered cholesterol synhtesis pathway influences the circadian rhythm of mouse embryonic fibroblasts, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- N. Jukan, S. Moškon, N. Debeljak, T. Režen, A. Videtič Paska, M. Moškon, GDPR and biobanking: ensuring compliance with the law, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- Kity Požek, Tina Turel, Tilen Burjek, Eva Drnovšek, Andrej Gorjan, Roman Komac, Nejka Kotnik, Vid Rotvejn Pajič, Sara Tekavec, David Zagoršek, Jurij Bon, Nataša Debeljak, Miha Moškon, Alja Videtič Paska, Tadeja Režen, StandBioBank: standardization of information systems for management of samples and data for research laboratories, presented at the Symposium "Systems Medicine in Clinical Practice", Ljubljana, 10-11 June 2019 (book of abstracts)
- A. Kristan, J. Gašperšič, P. Hudler, D. Germ, T. Režen, D. Rozman, T. Kunej, T. Pajič, M. Fink, S. Anžej Doma, Š. Žula, I. Preložnik Zupan, R. Količ, T. Marčac Grahek, M. Moškon, N. Debeljak, Implementation of a new diagnostic strategy for familial erythrocytosis in Slovenia, presented at the European Human Genetics Conference, Gothenburg, Sweden, 15-18 June 2019 (abstract)
- N. Nadižar, T. Režen, N. Debeljak, A. Videtič Paska, D. Rozman, M. Moškon, BiOpenBank : open source solution for management of biological samples and sample associated data in small biobanks presented at 13th Meeting of the Slovenian Biochemical Society with International Participation, Dobrna 24-27 September 2019
- L. Bohinc, K. Požek, T. Burjek, E. Drnovšek, M. Fabjančič, A. Gorjan, F. Grčar, N. Jukan, R. Komac, N. Kotnik, J. Lazarevič, V. Rotvejn Pajič, A. Povše, N. Pucihar, S. Tekavec, T. Turel, G. Vrhovnik, D. Zagoršek, J. Bon, S. Moškon, N. Debeljak, T. Režen, A. Videtič Paska, M. Moškon Development of an open information system for sample management in biomedical research studies and in a biobank repository presented at 13th Meeting of the Slovenian Biochemical Society with International Participation, Dobrna 24-27 September 2019
- M. Moškon, T. Režen, N. Debeljak, A. Videtič Paska, BiOpenBank information systems and its integration into the analysis of genetic predispositions in psychiatric disorders, Cognitive science: proceedings of the 22nd International Multiconference Information Society - IS 2019, 10 October 2019, volume B. Ljubljana: Institut "Jožef Stefan", 2019. pp. 36-38 (proceedings)
2018
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L. Magdevska, M. Mraz, N. Zimic, M. Moškon, 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) (full paper).
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T. Cvitanović Tomaš, Ž. Urlep, M. Moškon, M. Mraz, D. Rozman, LiverSex Computational Model: Sexual Aspects in Hepatic Metabolism and Abnormalities, Frontiers in Physiology, Vol. 9, pp. 360, 2018 (doi:10.3389/fphys.2018.00360) (full paper).
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M. Moškon, N. Zimic, M. Mraz, Grohar: automated visualisation of genome-scale metabolic models and their pathways, Journal of Computational Biology, Vol. 25, No. 5, pp 505-508, 2018 (doi:10.1089/cmb.2017.0209) (abstract, full paper, Bitbucket repository).
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J. Bordon, M. Moškon, N. Zimic, and M. Mraz, Semi-quantitative modeling of gene regulatory processes with unknown parameter values using Fuzzy logic and Petri nets, Fundamenta Informaticae, Vol. 160, No. 1-2, pp. 81-100, April 2018
(abstract, full paper).
- T. Cvitanović Tomaš, M. Moškon, M. Mraz, D. Rozman, Computational modelling of liver metabolism and its applications in research and the clinics, Acta Chimica Slovenica, Vol 65, No. 2, pp. 253-265, 2018 (doi:10.17344/acsi.2018.4461) (full paper).
- M. Moškon, N. Zimic, M. Mraz, Visualisation and analysis of metabolic networks with GROHAR, invited lecture at the 13th CFGBC Scientific Symposium, Ljubljana, 20-21 June 2018 (abstract)
- L. Magdevska, M. Mraz, N. Zimic, M. Moškon, Towards a sex-dependent mathematical model of mammalian circadian clock, presented at the 13th CFGBC Scientific Symposium, Ljubljana, 20-21 June 2018 (abstract)
- T. Cvitanović, M. Moškon, M. Mraz, D. Rozman, Systems approaches for the analysis of sex and alcohol related influences on liver metabolism, presented at the 13th CFGBC Scientific Symposium, Ljubljana, 20-21 June 2018 (abstract)
- N. Jukan, D. Zagoršek, I. Preložnik Zupan, N. Debeljak, M. Moškon, ViDis: Web-Based Tool For The Visualisation Of Diagnostic Algorithms, presented at the 13th CFGBC Scientific Symposium, Ljubljana, 20-21 June 2018 (abstract)
- M. Moškon, T. Cvitanović Tomaš, M. Mraz, D. Rozman, invited Hands-on tutorial on object-oriented modelling of large-scale metabolic models at the 2nd Conference of the European Association of Systems Medicine, Utrecht,7 November 2018
- M. Moškon, N. Zimic, M. Mraz, Grohar – Computational Tool for the Analysis, Visualisation and Alignment of Metabolic Networks, presented at the 2nd Conference of the European Association of Systems Medicine, Utrecht,7-9 November 2018
- N. Jukan, D. Zagoršek, I. Preložnik Zupan, N. Debeljak, M. Moškon, ViDis: Web-based platform for constructing and sharing visualizations of diagnostic algorithms, presented at the 2nd Conference of the European Association of Systems Medicine, Utrecht,7-9 November 2018
- N. Nadižar, M. Moškon, D. Rozman, iSymbiol: Information system for storage and management of biological samples, presented at the 2nd Conference of the European Association of Systems Medicine, Utrecht,7-9 November 2018
- M. Petroni, Computational methodology for enhanced sensitivity analysis of gene regulatory networks, PhD Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (thesis)
- T. Cvitanović Tomaš, Analysis of System Disorders in Liver Metabolism with the SteatoNet Model, PhD Thesis, University of Ljubljana, Faculty of Medicine (advisors: prof dr. Damjana Rozman and assist. prof. dr. Miha Moškon) (abstract)
- Ž. Pušnik, Computational analysis of viable parameter spaces in high-dimensional dynamical models of biological systems, MSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (abstract)
- N. Jukan, Development of web platform for visualization and sharing of medical algorithms, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (abstract, ViDis)
- N. Nadižar, Information system for management of biological samples, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (abstract)
2017
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Ž. Rejc, L. Magdevska, T. Tršelič, T. Osolin, R. Vodopivec, J. Mraz, E. Pavliha, N. Zimic, T. Cvitanović, D. Rozman, M. Moškon, and M. Mraz, Computational modelling of metabolic networks and its application to CHO cell cultures, Computers in Biology and Medicine, Vol. 88, pp. 150-160, September 2017 (doi:10.1016/j.compbiomed.2017.07.005) (article, sciencedirect).
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T. Cvitanović, M. C. Reichert, M. Moškon, M. Mraz, F. Lammert, and D. Rozman, Large-scale computational models of liver metabolism: how far from the clinics, Hepatology, Vol. 66, No. 4, pp. 1323-1334, 2017 (doi: 10.1002/hep.29268) (NCBI)
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L. Magdevska, Ž. Pušnik, M. Mraz, N. Zimic, and M. Moškon, Computational design of synchronous sequential structures in biological systems, Journal of Computational Science, Vol.18, pp. 24-31, Jan. 2017 (doi:10.1016/j.jocs.2016.11.010) (article supplementary text, sciencedirect).
- A. Vasylchenkova, M. Mraz, N. Zimic, and M. Moškon, Classical mechanics approach applied to analysis of biological oscillators, IEEE/ACM Transactions of Computational Biology and Bioinformatics Vol. 14, No. 3, pp. 721-727. May/Jun. 2017 (doi:10.1109/TCBB.2016.2550456) (abstract, full paper, code).
- L. Magdevska and M. Moškon, Application of fuzzy temporal logic to biological systems modelling, lecture at 4th International Synthetic & Systems Biology Summer School - SSBSS 2017, Robinson College, University of Cambridge, UK, 17-21 July 2017 (abstract)
- T. Cvitanović, Ž. Urlep, M. Moškon, M. Mraz, D. Rozman, LiverSex: In Silico Study Of Sexual Aspects In Liver Metabolism, presented at Systems Medicine Conference in Slovenia: National Awareness Event, 12th CFGBC Symposium and Systems Medicine Workshop, Ljubljana, 8-9 June 2017 (abstract)
- L. Magdevska, M. Mraz, N. Zimic, M. Moškon, Automatization Of Fuzzy Inference System Describing The Dynamics Of MAPK Cascade, presented at Systems Medicine Conference in Slovenia: National Awareness Event, 12th CFGBC Symposium and Systems Medicine Workshop, Ljubljana, 8-9 June 2017 (abstract)
- Ž. Pušnik, M. Mraz, N. Zimic, M. Moškon, Viable Parameter Space Analysis Of Dynamic Biological Models, presented at Systems Medicine Conference in Slovenia: National Awareness Event, 12th CFGBC Symposium and Systems Medicine Workshop, Ljubljana, 8-9 June 2017 (abstract)
- Ž. Rejc, T. Tršelič, J. Mraz, N. Zimic, M. Mraz, M. Moškon, In Silico Analysis Of CHO Metabolism In Dependence On The Medium Composition, presented at Systems Medicine Conference in Slovenia: National Awareness Event, 12th CFGBC Symposium and Systems Medicine Workshop, Ljubljana, 8-9 June 2017 (abstract)
- J. Bordon, Modelling simple biological switching systems using fuzzy logic and extended Petri nets, PhD Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: prof. dr. Miha Mraz) (abstract)
- S. Gazvoda, Overview of Agent-Based Tools for Modelling of Biological Systems and their Application to the Analysis of Multi-Cellular Biological Oscillator, MSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (abstract)
- L. Magdevska, Fuzzy modelling of biological systems and its application to the analysis of MAPK signalling pathway, BSc Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: assist. prof. dr. Miha Moškon) (abstract)
2016
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M. Bizjak, M. Mraz, N. Zimic, and M. Moškon, Computational framework for modelling multiple non-cooperative transcription factor binding and its application to the analysis of NF-κB oscillatory response, Journal of Computational Biology, Vol. 23, Issue 12, pp. 923-933, 2016 (doi:10.1089/cmb.2016.0065) (abstract, preprint, paper , code).
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M. Moškon, N. Zimic, and M. Mraz, Implementation of binary memory in simple biological circuits, Journal of Electrical Engineering and Computer Science, Vol. 83, No. 4, pp. 194-200, 2016 (full paper)
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Ž. Pušnik, L. Magdevska, M. Mraz, N. Zimic, and M. Moškon, Computational framework for global sensitivity analysis of high-dimensional and poorly connected parameter spaces, presented at The IET/SynbiCITE Engineering Biology Conference, London, UK, December, 13-15, 2016 (link, paper).
- T. Cvitanović, M. Moškon, M. Mraz, and D. Rozman, SteatoNet model to investigate the gender component of liver related pathologies. in Proceedings of the 1st Conference of the European Association of Systems Medicine, Berlin, Germany, October 26-28, 2016 (conference proceedings [password: EASyMBerlin2016])
- T. Štular, M. Žerovnik, M. Mraz, T. Cvitanović, N. Zimic, and M. Moškon, Computational framework for the analysis of biological oscillators and its application to p53-Mdm2 interaction. in Proceedings of the 1st Conference of the European Association of Systems Medicine, Berlin, Germany, October 26-28, 2016 (conference proceedings [password: EASyMBerlin2016], poster)
- D. Rozman, T. Cvitanović, and M. Moškon, Tackling liver disease: an object oriented modelling approach: hands-on tutorial at Modelling and bioinformatics for personalised medicine, 2nd SysBioMed, 1st Conference of the European Association of Systems Medicine, Berlin, Germany, October 26, 2016.
- T. Cvitanović, M. Moškon, M. Mraz, and D. Rozman, SteatoNet as a computational model for prediction of gender-based liver-related diseases, in Proceedings of the 5th EMTRAIN PhD Workshop, Berlin, Germany, April 26-27, 2016 (abstract, poster).
- T. Cvitanović, M. Moškon, M. Mraz, Ž. Urlep, and D. Rozman, SteatoNet as a predictive and gender-based liver metabolic model, in Proceedings of the 6th Conference on Systems Biology of Mammalian Cells, Munich, Germany, April 6-8, 2016 (SBMC 2016 Program, abstract).
- T. Cvitanović, M. Moškon, M. Mraz, and D. Rozman, Use of SteatoNet as a predictive tool to disclose the complexity of gender-based liver-related diseases, in ELIXIR-SI launch & 11th CFGBC Symposium Proceedings.
- L. Magdevska, Ž. Pušnik, M. Mraz, N. Zimic, and M. Moškon, Design of synchronous transcription based biological memory, in ELIXIR-SI launch & 11th CFGBC Symposium Proceedings.
- Ž. Pušnik, L. Magdevska, M. Mraz, N. Zimic, and M. Moškon, Global sensitivity analysis of biological models with high-dimensional and poorly connected parameter spaces, in ELIXIR-SI launch & 11th CFGBC Symposium Proceedings.
- J. Bordon, N. Zimic, M. Moškon, and M. Mraz, Evaluating the kinetic parameters for quantitative models in systems biology , in ELIXIR-SI launch & 11th CFGBC Symposium Proceedings.
- T. Osolin, Translation of biologic models to SBML format, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2016 (abstract)
2015
- J. Bordon, N. Zimic, M. Moškon, and M. Mraz, Fuzzy logic as a computational tool for quantitative modelling of biological systems with uncertain kinetic data, IEEE/ACM Transactions of Computational Biology and Bioinformatics, Vol. 12, No. 5, pp. 1199-1205, 2015 (doi: 10.1109/TCBB.2015.2424424) (abstract, full paper, code).
- M. Petroni, N. Zimic, M. Mraz, and M. Moškon, Stochastic simulation algorithm for gene regulatory networks with multiple binding sites, Journal of Computational Biology, Vol. 22, No. 3, pp. 218-226, 2015 (doi: 10.1089/cmb.2014.0064) (abstract, full paper).
- T. Cvitanović, A. Belič, M. Mraz, M. Moškon, and D. Rozman, Application of SteatoNet to predict network disorder in cholesterol metabolism, poster presented at Advanced Lecture Course on Computational Systems Biology, Aussois, France, April 6-11, 2015 (poster).
- M. Moškon and M. Mraz, Novel approaches for computational analysis of biological oscillators, in 10th CFGBC Symposium Proceedings.
- M. Bizjak, M. Mraz, N. Zimic, and M. Moškon Explicit modelling of binding site clusters in NF-kB oscillatory response, in 10th CFGBC Symposium Proceedings.
- M. Petroni, M. Mraz, N. Zimic and M. Moškon, A parallel algorithm for stochastic multiscale simulation of gene regulatory networks with multiple binding sites, in 10th CFGBC Symposium Proceedings.
- M. Bizjak, M. Mraz, N. Zimic, and M. Moškon, Computational approaches for quantitative modeling of gene regulatory networks with multiple transcription factor DNA binding site repeats, in Synthetic Systems Biology Summer School 2015, Taormina, Italy, July 5-9, 2015 (poster).
- T. Cvitanović, M. Moškon, M. Mraz, A. Belič, and D. Rozman, Validation of SteatoNet for prediction the network disorder in liver in order of personalized medicine, in 10th CFGBC Symposium Proceedings.
- T. Cvitanović, M. Moškon, M. Mraz, A. Belič, and D. Rozman, Validation of SteatoNet for prediction the liver network disorders, in FEBS3+ Meeting Book of Abstracts , September 16-19, 2015, Portorož, Slovenia.
2014
- M. Moškon and M. Mraz, Systematic Approach to Computational Design of Gene Regulatory Networks with Information Processing Capabilities, IEEE/ACM Transactions of Computational Biology and Bioinformatics, Vol. 11, Issue 2, 2014 (doi: 10.1109/TCBB.2013.2295792) (abstract, full paper, code)
- M. Stražar, N. Zimic, M. Mraz, and M. Moškon, An adaptive genetic algorithm for parameter estimation of biological oscillator models to achieve target quantitative system response, Natural Computing, Vol. 13, No. 1., 119-127, Mar.2014 (abstract, full paper)
- M. Moškon, J. Bordon, M. Mraz, N. Zimic, and M. Petroni, Computational approaches in synthetic and systems biology, book chapter in Recent Advances in System Biology, Nova Science Publishers Inc., USA, January, 2014, ISBN: 978-1-62948-736-6, pp. 131-155 (abstract, book, Amazon)
- J. Bordon, M. Moškon, and M. Mraz, Overcoming Unknown Kinetic Data for Quantitative Modelling of Biological Systems Using Fuzzy Logic and Petri Nets, in PETRI NET 2014 CEUR Workshop Proceedings.
- M. Moškon and M. Mraz, Recent approaches for the modelling and computational design of biological information processing structures, in 9th CFGBC Symposium Proceedings.
- J. Bordon, M. Moškon, N. Zimic, and M. Mraz, Quantitative modelling of a 3-gene repressilator with uncertain kinetic data using fuzzy logic, in 9th CFGBC Symposium Proceedings.
- M. Petroni, M. Mraz, N. Zimic, and M. Moškon, Multiscale stochastic simulation algorithm for complex gene regulatory networks, in 9th CFGBC Symposium Proceedings.
2013
- M. Moškon, N. Zimic, M. Stražar, and M. Mraz, Comparison of selected performances of biological and electronic information processing structures, Przegląd Elektrotechniczny (Electrical Review), Vol.2013, No. 2a, 166-169, 2013 (abstract)
- D. Vučko, M. Mraz, N. Zimic, and M. Moškon, Hybrid discrete agorithm for the modelling of gene regulatory networks, Biosystems and Information Technology, Vol. 2, Issue 2, 32-36, 2013 (full paper)
- J. Bordon, M. Moškon, and M. Mraz, Semi-quantitative modelling of biological systems with extended Fuzzy Petri nets, CEUR workshop proceedings, vol. 988, 2013 (abstract)
- M. Petroni, I. Lebar Bajec, M. Moškon, M. Mraz, D. Paoli, and C. E. Traverso, Glaucoma management system : a clinical report on 409 eyes, supported by a mobile software application for interactive assessing and guiding the diagnosis and treatment of Glaucoma, World Glaucoma Congress, July 17-20, 2013, (book of abstracts)
- S. Petrović, Development of a modular framework for computational modelling approaches, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2013 (abstract)
- M. Somrak, Computational modelling of treatment with in situ biological drug production, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2013 (abstract)
- M. Stražar, Parallel Evolutionary Algorithm for Knowledge Discovery from a Model of a Gene Regulatory Network, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2013 (abstract)
- D. Vučko, Hybrid approach for the modelling of gene regulatory networks, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2013 (abstract)
2012
- M. Moškon and M. Mraz, Modelling and analysing the information processing capabilities of simple biological systems, Mathematical Modelling and Analysis, Vol. 17, 467-484, 2012 (abstract, full paper)
- J. Bordon, M. Moškon, and M. Mraz, Modeling gene regulatory networks using Petri Nets, Journal of Electrical Engineering and Computer Science, Vol. 79, Number 4, 189-192, 2012 (full paper)
- M. Moškon and M. Mraz, Modeling as the essential step in construction of biological computer structures, International Journal of Computer Theory and Engineering , Vol. 4, 556-560, 2012 (abstract)
- M. Moškon, Computer structures perspective on switching dynamics of simple biological systems, PhD Thesis, University of Ljubljana, Faculty of Computer and Information Science (advisor: prof. dr. Miha Mraz) (abstract)
- M. Petroni, L. Canciani, M. Mraz, and M. Moškon, A qualitative method for parameter estimation in gene regulatory networks using extended Kalman filtering, Proceedings of 21th Electrotechnical and Computer Science Conference (ERK 2012), 39-42, 2012 (full paper)
- J. Bordon, M. Moškon, and M. Mraz, Modeling gene regulatory networks using Petri Nets, Proceedings of 21th Electrotechnical and Computer Science Conference (ERK 2012), 43-46, 2012 (full paper)
2011
- M. Moškon and M. Mraz, Analyzing the Information Processing Capabilities of Gene Expression based Logic, ICCSIT2011: proceedings, Vol. 3, 297-300, 2011 (abstract)
- M. Moškon, Metrics for evaluation of data processing capabilities of biological systems, Proceedings of 20th Electrotechnical and Computer Science Conference (ERK 2011), 3-6, 2011 (abstract)
- M. Petroni, Gene regulatory networks as dataflow processing platforms, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2011 (advisor: prof. dr. Nikolaj Zimic) (abstract)
- J. Bordon, Qualitative analysis of biological oscillators as processing structures, Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2011 (advisor: prof. dr. Miha Mraz) (abstract)
2009
- M. Moškon, M. Avbelj, N. Zimic, and M. Mraz, Toward in vivo digital synchronous sequential circuits, WSEAS Transactions on Circuits and Systems, Vol. 8, 301-310,2009 (full paper)
- M. Moškon, M. Avbelj, R. Jerala, N. Zimic, and M. Mraz, A model of the RS memmory-cell realization in biological systems, Journal of Electrical Engineering and Computer Science, Vol. 76, 223-228,2009 (abstract)
- M. Moškon, M. Avbelj, N. Zimic, and M. Mraz, Towards the realization of synchronous sequential biological circuits, Recent advances in mathematics and computers in biology and chemistry : proceedings of the 10th WSEAS International Conference on Mathematics and Computers in Biology and Chemistry (MCBC'09), 136-141,2009 (abstract)
2008
- B. Cvetković, Feasibility analysis of realization of primitive computer structures based on DNA assembly elements. Thesis, University of Ljubljana, Faculty of Computer and Information Science, 2008 (advisor: prof. dr. Miha Mraz) (abstract)