2020

  • 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. https://doi.org/10.3390/su12187389

  • 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. https://doi.org/10.3390/min10060558

  • Stalidzans, E., Zanin, M., Tieri, P., Castiglione, F., Polster, A., Scheiner, S., Pahle, J., Stres, B., List, M., Baumbach, J., Lautizi, M., VanSteen, 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. https://doi.org/10.1089/nsm.2020.0002

  • Timma, L., Dace, E., Trydeman Knudsen, M. (2020) Temporal Aspects in Emission Accounting - Case Study of Agriculture Sector. Energies, 13, 800. https://doi.org/10.3390/en13040800
     

  • 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, pp. 430–443.  https://doi.org/10.1002/csr.1828

2019

  • 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, pp. 639–702. https://doi.org/10.1038/s41596-018-0098-2

  • 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 metabolism. Frontiers in Microbiology, 10, 2533. https://doi.org/10.3389/fmicb.2019.02533
     

  • 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, Vol. 307, pp. 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, Vol. 46 (2), pp. 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, Vol. 162, pp.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), pp. 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, Vol. 44(8), pp. 1177–1190.  https://doi.org/10.1007/s10295-017-1946-8


2016

  • Mednis, M., Vilums, S., Stalidzans, E., (2016). TraSe: Real-time two-dimensional ball tracking and control system. Int. J. Electr. Eng. Educ. 53, pp. 145–155. https://doi.org/10.1177/0020720915611141

  • 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
     

  • Zacepins, A., Kviesis, A., Stalidzans, E., Liepniece, M., Meitalovs, J. (2016) Remote detection of the swarming of honey bee colonies by single-point temperature monitoring, Biosystems Engineering, Vol. 148, p. 76–80.  https://doi.org/10.1016/j.biosystemseng.2016.05.012


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. View full text.

  • Kviesis, A., Zacepins, A. (2015). System Architectures for Real-time Bee Colony Temperature Monitoring. Procedia Computer Science, Vol. 43, pp.86–94. View full text.


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
     

  • Zacepins A., Meitalovs J., (2014) Implementation of multi-node temperature measurement system for bee colonies online monitoring Proceedings of 15th International Carpathian Control Conference (ICCC), May 28–30, 2014, pp. 695–698. Velke Karlovice. Read more.

  • 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. View full text.

  • Pentjuss, A., & Kalnenieks, U. (2014). Assessment of Zymomonas mobilis biotechnological potential in ethanol production by flux variability analysis. Biosystems and Information Technology, 3(1), pp. 1–5. View full text.


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, pp. 345–350.  https://doi.org/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, Vol. 3(1), pp.1–5. View full text. 
     

  • 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, pp. 411–418.  https://doi.org/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, Vol. 159, pp. 2674–2689. View full text.

  • Mednis, M., Vigants A., (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information technology, 2(1), pp. 1–5. View full text. 

  • 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, Vol. 165, pp. 1–10.  https://doi.org/10.1016/j.jbiotec.2013.02.014

  • Stalidzans, E., & Berzonis, A. (2013). Temperature changes above the upper hive body reveal the annual development periods of honey bee colonies. Computers and Electronics in Agriculture, Vol. 90,  pp.1–6. https://doi.org/10.1016/j.compag.2012.10.003

  • 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, pp. 435–440. View full text. 


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, pp. 365–369. Read more.

  • Kostromins A. Altfluxes: COBRA Toolbox extension for flux variability analysis of stoichiometric models of metabolism. 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. 294–299. View full text.

  • Rove Z., Mednis M., Odzina I. Biochemical networks comparison tool. 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. 306–311. View full text.

  • Rubina T., Stalidzans E. Evolution of alternative control loops of biological systems. 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. 317–324. View full text.

  • 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, pp. 312–316. View full text.

  • Vilums S., Grigs O. Application of functional state modelling approach for yeast saccharomyces cerevisae batch fermentation state estimation. 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 300–305. View full text.

  • Vilums, S., Kozlinskis, E., & Brusbardis, V. (2012). Application of functional state modelling approach for yeast Sacharomyces cerevisiae fed-batch fermentation modelling. 6th International Conference on Application of Information and Communication Technologies (AICT), pp. 1–5. IEEE. Read more.

  • 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

  • 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), pp. 14–18. View full text.

  • Mednis, M., Rove, Z., and Galvanauskas, V. (2012). ModeRator - a software tool for comparison of stoichiometric models. The 7th IEEE International Symposium on Applied Computational Intelligence and Informatics, pp. 97–100. Read more.


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. View full text.

  • 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. View full text.

  • I. Odziņa, R. Rutkis, U. Kalnenieks. In silico engineering of biochemical network of Zymomonas mobilis adaptation for glycerol conversion into bioethanol. The 10th International Scientific Conference Engineering for Rural development 2011, Vol. 10, May 26–27, 2011, Jelgava 2011. pp. 272–276.  View full text.

  • J. Meitalovs. Development of chemostat supply system during fermentation process. 10th International Scientific Conference Engineering for Rural development 2011, Vol. 10, May 26–27, 2011, Jelgava 2011. pp. 115–120.  View full text.

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

2010

  • Rubina T., Stalidzans E. Software tools for structure analysis of biochemical networks, In Proceedings of Applied Information and Communication Technologies 2010, April 22–23, 2010, Jelgava, Latvia, pp. 33–49. View full text.

  • Rubina T., Stalidzans E. Topological features and parameters of Biochemical Network Structures, 8-th International Industrial Simulation Conference 2010, Budapest, pp. 228–236. View full text.

  • Zacepins A., Meitalovs J., Stalidzans E. Model Based Real Time Automated Temperature Control System for Risk Minimization in Honey Bee Wintering Building, 8-th International Industrial Simulation Conference 2010, Budapest, pp. 245–247. View full text.


2009

  • Meitalovs J., Histjajevs A., Stalidzans E. Automatic Microclimate Controlled Beehive Observation System, 8th International Scientific Confernce ‘Enginieering for Rural Development’ May 28–29, 2009 Jelgava, Latvia, pp. 265–271. View full text.


2008

  • Osadcuks V., Stalidzans E. Metabolic Activity Assessment Specialised Microclimate Chamber with Control System, In Proceedings of Applied Information and Communication Technologies 2008, April 10–11, 2008, Jelgava, Latvia, pp. 78–85. View full text.

  • Stalidzans E., Mozga I., Modular Approach Teaching Systems Biology to Monodisciplinary Specialists in European Project „MOSBIO”. In proceedings of Applied Information and Communication Technologies 2008, April 10–11, 2008, Jelgava, Latvia, pp. 141–145. View full text.


2007

  • Mozga I., Grunde-Zeiferts U., Sudars S., Stalidzans E. Life cycles and competition in modelling of artificial and biological control system. ESM 2007, Malta, 23.–26. October 2007, pp. 533–536. View full text.

  • Stalidzans E. Markovics Z., Krauze A., Bilinskis V., Berzonis A. Modeling of bee wintering building profitability. Journal of Apicultural Science, Vol.51 No.2, 2007, pp. 25–31. View full text.


2006

  • Stalidzans E. Control of biological objects as collaboration of biological and artificial control systems. Proceedings of International conference 'Engineering for rural development', May 17–20, 2006, Latvia, Jelgava. pp. 204–208. View full text.

  • Stalidzāns E., Grunde-Zeiferts U., Brusbārdis V. Classification of nodes transforming topological model of biological process to a dynamic functional model. International conference "Information technologies in rural development", Jelgava, Latvia.  October 19–20, 2006, pp 158–163. View full text.

  • Stalidzāns E., Markovičs Z. Expert survey on topological model development for microclimate control in wintering bee colony. International conference "Information technologies in rural development", Jelgava, Latvia. October 19–20, 2006, pp. 149–157. View full text.

  • Žukova T., Stalidzāns E., Systems biology - interaction science of biology and information technology. International conference "Information technologies in rural development", Jelgava, Latvia. October 19–20, 2006, pp. 120–130. View full text.


2005

  • Stalidzans E., Z. Markovitch. Development of dynamic model for a biological system under conditions of insufficient information. In Proceedings of ITAFE-05 International Congress on Information Technology in Agriculture, Food and Environment, October 12–14, 2005, Adana, Turkey, pp. 337–344. View full text.

  • Stalidzans E., Z. Markovitch. Methodology of control system development for biological systems under information insufficiency. European Modelling Simulation Symposium EMSS 2005, Marseille, France, October 20 – 22, 2005. pp. 169–175.  View full text.

Institute of Microbiology and Biotechnology, University of Latvia Jelgavas iela 1, Riga
LV-1004, Latvia

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