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Computational Systems Biology Lab (CSBL)
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02.11.2017
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  1. Head - Dr.sc.ing. Egils Stalidzans

egils.stalidzans@lu.lv

Phone: +371 29575510

 

Dr.sc.ing. Egils Stalidzans 

www.biosystems./egils

Dr.sc.ing. Agris Pentjuss

 

Dr.sc.ing. Martins Mednis

www.biosystems.lv/martins

Dr.sc.ing. Ivars Mozga

 

Dr.sc.ing. Jurijs MeitalovsDārta Maija ZaķeKatrīna Daila Neiburga

 

Scientific interests

-         stoichiometric and kinetic modeling and optimisation of metabolism,

-         metabolic reconstructions,

-         modeling of signaling networks,

-         modeling of microbial communities,

-         software development.

 Projects

2018 - 2021, RHODOLIVE: Biovalorization of olive oil mill wastewater to microbial lipids and other products via Rhodotula glutinis fermentation, (ERA-net CoBioTech 1-st call). Our task is the modeling and optimization of metabolic networks.

2015 – 2018, LEANPROT: Systems biology platform for the creation of lean-proteome Esherichia coli strains, (EraSysApp 2nd call). SILICON platform development (combined genome scale modelling and Single Cell model platform).

2015 – 2018, SMARTPLANTS: Control of Engineered Metabolism by Flowering and Temperature Triggered Plant Regulatory Networks, (EraSynBio 2nd call). Development of Arabidopsis thaliana stoichiometric genome scale model and isorpenoid pathway kinetic model.

2013-2016 Metabolic engineering of Zymomonas mobilis respiratory chain (536/2012), funded by Latvian Council of Science

2013-2015 ERA–net project on systems biology (http://www.erasysapp.eu).
2012-2014 ERA–net project on synthetic biology (http://www.erasynbio.eu).

2009 – 2012 European Social Fund project “Establishment of Latvian interdisciplinary interuniversity scientific group of systems biology” within activity 1.1.1.2. „Attraction of Human Resources to Science” (http://www.sysbio.lv).

 Publications

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. doi: 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, accepted

2017

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., 2017. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. arXiv, arxiv.org/abs/1710.04038

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 Vol. 162, 128-134.

Elsts, A., Pentjuss, A., Stalidzans, E. (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics Vol. 33, p.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 Trans. Comput. Biol. Bioinforma. 14, 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. J. Ind. Microbiol. Biotechnol. Vol. 44, p. 1177–1190.

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, Vol.2, 16011.

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

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. doi: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.

 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 19-20, Budapest, Hungarypp.345-350. doi:10.1109/CINTI.2013.6705218

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. doi:10.11592/bit.140502    

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 19-20, Budapest, pp.411-418, doi:10.1109/CINTI.2013.6705232

Rutkis, R., Kalnenieks, U., Stalidzans, E., & Fell, D. A. (2013). Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology (Reading, England),  159(Pt 12), 2674–89 , doi: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), pp 1-5, doi:10.11592/bit.130501 Full text    

Pentjuss A., Odzina I., Kostromins A., Fell D., Stalidzans E., Kalnenieks U. Biotechnological potential of respiring Zymomonas mobilis: a stoichiometric analysis of its central metabolism, Journal of Biotechnology, Volume 165, 2013, pp 1-10.Full text available at: http://dx.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” (pp. 435–440). Jelgava, Latvia.

 2012

Stalidzans E., Kostromins A., Sulins J., Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. "13th IEEE International Symposium on Computational Intelligence and Informatics", Budapest, Hungary, 20.-22. November 2012, pp 365-369.Full text available at:http://dx.doi.org/10.1109/CINTI.2012.6496792

Kostromins A., Mozga I., Stalidzans E. ConvAn: a convergence analyzing tool for optimization of biochemical networks, Biosystems, Volume 108, Issues 1–3, April–June 2012, pp 73-77, ISSN 0303-2647, 10.1016/j.biosystems.2011.12.004.Full text available at: http://dx.doi.org/10.1016/j.biosystems.2011.12.004

Kostromins A., Stalidzans E. Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism, Biosystems, Volume 109, Issue 2, August 2012, pp 233-239, ISSN 0303-2647, 10.1016/j.biosystems.2012.03.002.Full text available at: http://dx.doi.org/10.1016/j.biosystems.2012.03.002

Sulins J., Stalidzans E. 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, ISBN 978-9984-48-065-7, pp 312-316.Full text available at:http://aict.itf.llu.lv/files/rakstkraj/2012/sulins_aict2012.pdf

Mednis, M., Brusbardis, V., Galvanauskas, V. Comparison of genome-scale reconstructions using ModeRator, Proceedings of 13th IEEE International Symposium on Computational Intelligence and Informatics, Budapest, 2012, pp 79-84 doi:10.1109/CINTI.2012.6496737 

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, vol 1(1), pp 14-18 doi:10.11592/bit.121102 Full text 

 2011

Mozga I., Stalidzans E. Convergence Dynamics of Biochemical Models To The Global Optimum, 3rd IEEE International Conference on e-Health and Bioengineering, EHB 2011 – Proceedings, pp. 227-230. Full text available at: ehb2011_mozga.pdf

Mozga I., Stalidzans E. Optimization protocol of biochemical networks for effective collaboration between industry representatives, biologists and modellers, 9th International Industrial Simulation Conference (ISC'2011), Venice, Italy, 2011. pp. 91–96.Full text available at: isc2011_mozga_stalidzans.pdf