Mathematical modeling can tell us what is possible and what impossible and the reasons why. It is extremely useful to avoid unnecessary experiments from the long list of opportunities.

Modeling sheds the light on something that is not obvious, thus allowing to conduct LESS USELESS experiments.


COMPUTATIONAL SYSTEMS BIOLOGY GROUP uses mathematical modeling to find the way how interactions of components form a biological system. The SCIENTIFIC INTERESTS OF THE GROUP include:

  • stoichiometric and kinetic modeling and optimization of metabolism,
  • metabolic reconstructions,
  • modeling of signaling networks,
  • modeling of microbial communities, and
  • software development

in the areas of:

  • microbial biotechnology,
  • medicine, and
  • environment.


Team Egils Stalidzāns Agris Pentjušs Atis Elsts Elīna Dāce Ivars Mozga Vitālijs Komašilovs

PhD student Jānis Kurlovičs Dārta Maija Zaķe student Kristaps Bērziņš Santa Prikule




2020 - 2023, Waste2Surf: Sustainable Microbial Valorisation of Waste Lipids into Biosurfactants, funded by the European Regional Development Fund (project No. LV EN

2020 - 2023, DeSTInation: Decision Support Tool for an Integrated Food Waste Valorisation System, funded by the European Regional Development Fund (project No.
 An assessment of waste amount and management in Latvia till 2035

2020 - 2023, UpWaste: Sustainable up-cycling of agricultural residues: modular cascading waste conversion system, funded by the European Commission Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI) Sustainable and Resilient Agriculture for Food and Non-food Systems (FACCE SURPLUS) call.

2019 - 2022, Crypthecodinium cohnii and Zymomonas mobilis syntrophy for production of omega 3 fatty acid from byproducts of biofuel and sugar industry, funded by the European Regional Development Fund (project No. LV EN

2019 - 2021, ZYMMODEL: Production potential of top building block chemicals by Zymomonas mobilis: stoichiometric analysis, funded by the European Regional Development Fund (project No.

2018 - 2020, Mathematical model of pharmacokinetics for personalized optimization of metformin therapy, funded by Latvian Council of Science (project No: lzp-2018/2-0088).

2018 - 2021, RHODOLIVE: Biovalorization of olive oil mill wastewater to microbial lipids and other products via Rhodotula glutinis fermentation, funded by Horizon 2020 research and innovation programme ERA-net CoBioTech (1-st call) (grant No. 722361). 

2015 - 2018, SMARTPLANTS: Control of Engineered Metabolism by Flowering and Temperature Triggered Plant Regulatory Networks, funded by FP7 EraSynBio (2nd call). 

2015 - 2018, LEANPROT: Systems biology platform for the creation of lean-proteome Esherichia coli strains, funded by FP7 EraSysApp (2nd call). 

2013 - 2016, Metabolic engineering of Zymomonas mobilis respiratory chain, funded by Latvian Council of Science (grant No. 536/2012).

2013 - 2015, ERASysAPP: Systems Biology applications, funded by ERA-net (

2012 - 2014, ERASynBio: Development and Coordination of Synthetic Biology in the European Research Area, funded by ERA-net (

2009 - 2012, Establishment of Latvian interdisciplinary interuniversity scientific group of systems biology, funded by European Social Fund within activity „Attraction of Human Resources to Science”.




Timma L., Dace E., Kristensen T., Trydeman Knudsen M. (2020) Dynamic Sustainability Assessment Tool: Case Study of Green Biorefineries in Danish Agriculture. Sustainability, 2020, 12(18), 7389.

Burlakovs J., Vincevica-Gaile Z., Krievans M., Jani Y., Horttanainen M., Pehme K.-M., Dace E., Setyobudi R.H., Pilecka J., Denafas G., Grinfelde I., Bhatnagar A., Rud V., Rudovica V., Mersky R.L., Anne O., Kriipsalu M., Ozola-Davidane R., Tamm T., Klavins M. (2020) Platinum Group Elements in Geosphere and Anthroposphere: Interplay among the Global Reserves, Urban Ores, Markets and Circular Economy. Minerals, 2020, 10(6), 558.

Stalidzans E., Zanin M., Tieri P., Castiglione F., Polster A., Scheiner S., Pahle J., Stres B., List M., Baumbach J., Lautizi M., Van Steen K., Schmidt H.H.H.W. (2020) Mechanistic modeling and multiscale applications for precision medicine: theory and practice. Network and Systems Medicine, 3(1), 36-56.

Timma L., Dace E., Trydeman Knudsen M. (2020) Temporal Aspects in Emission Accounting—Case Study of Agriculture Sector. Energies, 13, 800.

Dace E., Stibe A., Timma L. (2020) A holistic approach to manage environmental quality by using the Kano model and social cognitive theory. Corporate Social Responsibility and Environmental Management, 27, 430-443. 


Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S.N., Richelle, A., Heinken, A., Haraldsdottir, H.S., Keating, S.M., Vlasov, V., Wachowiak, J., Magnusdottir, S., Ng, C.Y., Preciat, G., Zagare, A., Chan, S.H.J., Aurich, M.K., Clancy, C.M., Modamio, J., Sauls, J.T., Noronha, A., Bordbar, A., Cousins, B., Assal, D.C. El, Ghaderi, S., Ahookhosh, M., Guebila, M. Ben, Apaolaza, I., Kostromins, A., Le, H.M., Ma, D., Sun, Y., Valcarcel, L. V., Wang, L., Yurkovich, J.T., Vuong, P.T., Assal, L.P. El, Hinton, S., Bryant, W.A., Artacho, F.J.A., Planes, F.J., Stalidzans, E., Maass, A., Vempala, S., Hucka, M., Saunders, M.A., Maranas, C.D., Lewis, N.E., Sauter, T., Palsson, B.Ø., Thiele, I., Fleming, R.M. (2019) Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. Nature Protocols, 14, 639-702.

Stalidzans E., Landmane K., Sulins J., Sahle S. (2019) Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs. Mathematical Biosciences, 307, 25-32.

Kalnenieks U., Balodite E., Strähler S., Strazdina I., Rex J., Pentjuss A., Fuchino K., Bruheim P., Rutkis R., Pappas K.M., Poole R. K. (2019). Improvement of acetaldehyde production in zymomonas mobilis by engineering of its aerobic metabolismFrontiers in Microbiology10, 2533.


Zanin, M., Chorbev, I., Stres, B., Stalidzans, E., Vera, J., Tieri, P., Castiglione, F., Groen, D., Zheng, H., Baumbach, J., Schmid, J.A., Basilio, J., Klimek, P., Debeljak, N., Rozman, D., Schmidt, H.H.H.W., (2018) Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Briefings in Bioinformatics, bbx160.

Stalidzans E., Seiman A., Peebo K., Komasilovs V., Pentjuss A. (2018) Model based metabolism design: constraints for kinetic and stoichiometric models, Biochemical Society Transactions, 46 (2), 261-267.


Komasilovs V., Pentjuss A., Elsts A., Stalidzans E. (2017) Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model. Biosystems,162, 128-134.

Elsts, A., Pentjuss, A., Stalidzans, E. (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics, 33, 2966-2967.

Stalidzans, E., Mozga, I., Sulins, J., Zikmanis, P., (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(4), 978–985.

Pentjuss, A., Stalidzans, E., Liepins, J., Kokina, A., Martynova, J., Zikmanis, P., Mozga, I., Scherbaka, R., Hartman, H., Poolman, M.G., Fell, D.A., Vigants, A., (2017) Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. Journal of Industrial Microbiology & Biotechnology, 44(8), 1177–1190.


Cvijovic, M., Höfer, T., Aćimović, J., Alberghina, L., Almaas, E., Besozzi, D., Blomberg, A., Bretschneider, T., Cascante, M., Collin, O., de Atauri, P., Depner, C., Dickinson, R., Dobrzynski, M., Fleck, C., Garcia-Ojalvo, J., Gonze, D., Hahn, J., Hess, H., Hollmann, S., Krantz, M., Kummer, U., Lundh, T., Martial, G., dos Santos, V.M., Mauer-Oberthür, A., Regierer, B., Skene, B., Stalidzans, E., Stelling, J., Teusink, B., Workman, C.T., Hohmann, S. (2016) Strategies for structuring interdisciplinary education in Systems Biology: an European perspective. npj Systems Biology and Applications, 2, Article number: 16011.


Meitalovs J., Stalidzans E. (2015) Impact of Thermodynamic Constraint to the Solution Space of Metabolic Pathway Design Using sAnalyzer Tool. Baltic Journal of Modern Computing, 3(3), pp.164-178.


Kalnenieks, U., Pentjuss, A., Rutkis, R., Stalidzans, E., Fell, D. A. (2014) Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies. Frontiers in Microbiology, 5, 42.

Mozga I., Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing, 2(3), pp.150-159.


Rubina T., Stalidzans E. (2013) BINESA – a software tool for evolution modelling of biochemical networks structure. In Proceedings of IEEE 14th International Symposium on Computational Intelligence and Informatics (CINTI), November 19-21, 2013, Budapest, Hungary. INSPEC Accession Number: 14030108, 345-350.

Rubina T., Mednis M., Stalidzans E. (2013) Agreement assessment of biochemical pathway models by structural analysis of their intersection. In Proceedings of IEEE 14th International Symposium on Computational Intelligence and Informatics (CINTI), November 19-21, 2013, Budapest, Hungary, INSPEC Accession Number: 14030115, 411-418.

Pentjuss, A., Kalnenieks, U. (2013) Assessment of Zymomonas mobilis biotechnological potential in ethanol production by flux variability analysis. Biosystems and Information Technology, 3(1), 1–5.   

Rutkis, R., Kalnenieks, U., Stalidzans, E., & Fell, D. A. (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology, 159, 2674-2689.

Mednis, M., Vigants A., (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information technology, 2(1), 1-5,   

Pentjuss A., Odzina I., Kostromins A., Fell D., Stalidzans E., Kalnenieks U. (2013) Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism. Journal of Biotechnology, 165, 1-10.

Meitalovs, J., Stalidzans, E. (2013) Connectivity analysis of metabolites in synthetic metabolic pathways. In Proceedings of the 12th International Scientific Conference “Engineering for Rural Development”, May 23-25, 2013, Jelgava, Latvia, 435–440.


Stalidzans E., Kostromins A., Sulins J. (2012) Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. In Proceedings of IEEE 13th International Symposium on Computational Intelligence and Informatics, Budapest, Hungary, November 20-22, 2012. INSPEC Accession Number: 13446430, 365-369.

Mednis, M., Brusbardis, V., Galvanauskas, V. (2012) Comparison of genome-scale reconstructions using ModeRator. In Proceedings of IEEE 13th International Symposium on Computational Intelligence and Informatics, Budapest, Hungary, November 20-22, 2012. INSPEC Accession Number: 13446376, 79-84. 

Kostromins A., Mozga I., Stalidzans E. (2012) ConvAn: a convergence analyzing tool for optimization of biochemical networks, Biosystems, 108(1–3), 73-77.

Kostromins A., Stalidzans E. (2012) Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism, Biosystems, 109(2), 233-239.

Sulins J., Stalidzans E. (2012) Corunner: multiple optimization run manager for Copasi software. In Proceedings of the International Scientific Conference "Applied Information and Communication Technologies", April 26-27, 2012, Jelgava, Latvia, 312-316.

Mednis, M., Aurich, M.K., (2012) Application of string similarity ratio and edit distance in automatic metabolite reconciliation comparing reconstructions and models, Biosystems and Information technology, 1(1), 14-18.


Mozga I., Stalidzans E. (2011) Convergence Dynamics of Biochemical Models To The Global Optimum. In Proceedings of 2011 E-Health and Bioengineering Conference (EHB), Iasi, Romania, November 24-26, 2011. INSPEC Accession Number: 12542531.

Mozga I., Stalidzans E. (2011) Optimization protocol of biochemical networks for effective collaboration between industry representatives, biologists and modellers. 9th International Industrial Simulation Conference (ISC'2011), Venice, Italy, June 6-8, 2011, 91–96.



Head of the group Egils Stalidzans

Phone: +371 29575510