Computational systems biology group

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

Dr.sc.ing. Egils Stalidzāns

Dr.sc.ing. Agris Pentjušs

Dr.sc.comp. Atis Elsts

Dr.sc.ing. Elīna Dāce

Dr.sc.ing. Ivars Mozga

Dr.sc.ing. Vitālijs Komašilovs

M.sc. Jānis Kurlovičs

B.sc. Dārta Maija Zaķe

B.sc. Kristaps Bērziņš

B.sc. Rūdolfs Petrovs

B.sc. student Santa Prikule

 

Projects

2019 - 2022, Crypthecodinium cohnii and Zymomonas mobilis syntrophy for production of omega 3 fatty acid from byproducts of biofuel and sugar industry, funded by European Regional Development Fund (project No. 1.1.1.1/18/A/022) LV EN

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 (http://www.erasysapp.eu).

2012 - 2014, ERASynBio: Development and Coordination of Synthetic Biology in the European Research Area, funded by ERA-net (http://www.erasynbio.eu).

2009 - 2012, Establishment of Latvian interdisciplinary interuniversity scientific group of systems biology, funded by European Social Fund within activity 1.1.1.2. „Attraction of Human Resources to Science”.

 

Publications

2019

Dace, E., Stibe, A., Timma, L. (2019) A holistic approach to manage environmental quality by using the Kano model and social cognitive theory. Corporate Social Responsibility and Environmental Management, 1-14. https://doi.org/10.1002/csr.1828 

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. https://doi.org/10.1016/j.mbs.2018.11.002

2018

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. https://doi.org/10.1093/bib/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. https://doi.org/10.1042/BST20170263

2017

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. https://doi.org/10.1016/j.biosystems.2017.09.016

Elsts, A., Pentjuss, A., Stalidzans, E. (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics, 33, 2966-2967. https://doi.org/10.1093/bioinformatics/btx363

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. https://doi.org/10.1109/TCBB.2016.2550451

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. https://doi.org/10.1007/s10295-017-1946-8

2016

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. https://doi.org//10.1038/npjsba.2016.11

2015

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. https://www.bjmc.lu.lv/fileadmin/user_upload/lu_portal/projekti/bjmc/Contents/3_3_2_Meitalovs.pdf

2014

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. https://doi.org/10.3389/fmicb.2014.00042

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. https://www.bjmc.lu.lv/fileadmin/user_upload/lu_portal/projekti/bjmc/Contents/2_3_3_Mozga1.pdf

2013

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. https://doi.org/10.1109/CINTI.2013.6705218

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. https://doi.org/10.1109/CINTI.2013.6705232

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. https://doi.org/10.11592/bit.140502   

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. https://doi.org/10.1099/mic.0.071340-0

Mednis, M., Vigants A., (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information technology, 2(1), 1-5, https://doi.org/10.11592/bit.130501   

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. https://doi.org/10.1016/j.jbiotec.2013.02.014

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. http://www.tf.llu.lv/conference/proceedings2013/Papers/080_Meitalovs_J.pdf

2012

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. http://dx.doi.org/10.1109/CINTI.2012.6496792

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. https://doi.org/10.1109/CINTI.2012.6496737 

Kostromins A., Mozga I., Stalidzans E. (2012) ConvAn: a convergence analyzing tool for optimization of biochemical networks, Biosystems, 108(1–3), 73-77. https://doi.org/10.1016/j.biosystems.2011.12.004

Kostromins A., Stalidzans E. (2012) Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism, Biosystems, 109(2), 233-239. https://doi.org/10.1016/j.biosystems.2012.03.002

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. http://aict.itf.llu.lv/files/rakstkraj/2012/sulins_aict2012.pdf

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. http://dx.doi.org/10.11592/bit.121102

2011

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. https://ieeexplore.ieee.org/document/6150357

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.

 

Contacts

Head of the group

Dr.sc.ing. Egils Stalidzans

egils.stalidzans@lu.lv

Phone: +371 29575510

Biosystems.lv