Publications

Papers

Warning: Preprint versions of some papers might differ from the published versions of the papers. According to the Copyright Transfer Agreements which are required by some journals, we cannot replace here some preprint versions with the published versions. The published version of each manuscript is available online on the corresponding journal webpage.

2018

Akberdin I. R., Thompson M., Hamilton R., Desai N., Alexander D., Henard C. A., Guarnieri M. T., Kalyuzhnaya M. G. (2018). Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. Scientific reports, 8(1):2512, doi:10.1038/s41598-018-20574-z.
Akberdin I.R., Omelyanchuk N.A., Fadeev S.I., Leskova N.E., Oschepkova E.A., Kazantsev F.V., Matushkin Yu.G., Afonnikov D.A., Kolchanov N.A. (2018). Pluripotency gene network dynamics: system views from parametric analysis. PLOS One, doi: 10.1371/journal.pone.0194464.

2017

Kazantsev F., Akberdin I., Lashin S. , Ree N., Timonov V., Ratushny A., Khlebodarova T., Likhoshvai V. (2017). MAMMOTH: A NEW DATABASE FOR CURATED MATHEMATICAL MODELS OF BIOMOLECULAR SYSTEMS. J. Bioinform. Comput. Biol., doi: 10.1142/S0219720017400108.

2016

Klimenko A. I., Mustafin Z. S., Chekantsev A. D., Zudin R. K., Matushkin Y. G., & Lashin S. A. (2016). A review of simulation and modeling approaches in microbiology. Russian Journal of Genetics: Applied Research, 6(8), 845-853.
Klimenko A. I., Matushkin Y. G., Kolchanov N. A., & Lashin S. A. (2016). Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study. BMC microbiology, 16(1), S10.
Zakhrtsev M., Medvedeva I., Orlov Y., Akberdin I., Krebs O., & Schulze W. X. (2016). Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. BMC Plant Biology, 16(1), 262.
Demidenko A., Akberdin I. R., Allemann M., Allen E. E., & Kalyuzhanaya M. G. (2016). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G (B1). Frontiers in Microbiology, 7, 2167.

2015

Klimenko A. I., Matushkin Y. G., Kolchanov N. A., & Lashin S. A. (2015). Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor. BMC evolutionary biology, 15(1), S3.

2014

Ivanisenko N. V., Mishchenko E. L., Akberdin I.R., Demenkov P. S., Likhoshvai V. A., Kozlov K. N., Todorov D.I., Gursky V.V., Samsonova M.G., Samsonov A.M., Clausznitzer D., Kaderali L., Kolchanov N.A., Ivanisenko V. A. (2014). A New Stochastic Model for Subgenomic Hepatitis C Virus Replication Considers Drug Resistant Mutants. PloS one, 9(3), e91502.
Akberdin I.R., Ivanisenko N. V., Kazantsev F.V., Oschepkova E.A., Omelyanchuk N.A., Matushkin Yu.G., Afonnikov D.A. (2014). Modeling of regulatory mechanisms for mESC self-renewal: kinetic and stochastic approaches. Mathematical Biology and Bioinformatics, 9(2), pp.504-517. SI: Kinetic model, Stochastic model.
Lashin S. A., Klimenko A. I., Mustafin Z. S., Kolchanov N. A., & Matushkin Y. G. (2014). HEC 2.0: improved simulation of the evolution of prokaryotic communities. Mathematical Biology and Bioinformatics, 9(2), 585-596.

2013

SUPPLEMENTARY MATERIAL for Likhoshvai V.A., Khlebodarova T.M. (2013) Mathematical modeling of bacterial cell cycle: the problem of coordinating genome replication with cell growth. J. Bioinform. Comput. Biol., DOI: 10.1142/S0219720014500097.
Akberdin I.R., Kazantsev F.V., Ermak T.V., Timonov V.S., Khlebodarova T.M., Likhoshvai V.A. (2013). In silico cell: challenges and perspectives. Mathematical Biology and Bioinformatics, 8(1), pp. 295-315.
Khlebodarova T.M., Kogai V.V., Akberdin I.R., Ri N.A., Fadeev S.I., Likhoshvai V.A. (2013). Modeling of Nitrite Utilization in E. coli Cells: Flux Analysis . Mathematical Biology and Bioinformatics, 8(1), pp. 276-294.
Likhoshvai V.A., Khlebodarova T.M. (2013). Coordination of Cell Growth and DNA Replication: A Mathematical Model. Mathematical Biology and Bioinformatics, 8(1), pp. 66-92.
N.V. Ivanisenko, E.L. Mishchenko, I.R. Akberdin, P.S. Demenkov, V.A. Likhoshvai, K.N. Kozlov, D.I. Todorov, M.G. Samsonova, A.M. Samsonov, N.A. Kolchanov, V.A. Ivanisenko (2013). Replication of the subgenomic HCV replicon in the presence of the NS3 protease inhibitors: a stochastic model. Biophysics (Russian), 58(5), pp. 758–774.

2012

Mironova V.V., Novoselova E.S., Doroshkov A.V., Kazantsev F.V., Omelyanchuk N.A., Kochetov A.V., Mjolsness E., Likhoshvai V.A. Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance. Annals of botany, 110 (2). pp.349-360. doi: 10.1093/aob/mcs 069, Supplementary materials.
E.L. Mishchenko, N.V. Ivanisenko, I.R. Akberdin, P.S. Demenkov, V.A. Likhoshvai, N.A. Kolchanov, V.A. Ivanisenko. (2012). Suppression of subgenomic Hepatitis C Virus RNA replicon replication in huh-7 cells by the NS3 protease inhibitor sch5030334: a stochastic mathematical model. Russian Journal of Genetics: Applied Research, 16(2), pp. 339-347.
F.V. Kazantsev, I.R. Akberdin, N.L. Podkolodnyy, V.A. Likhoshvai. (2012). New facilities of the MGSmodeller. Russian Journal of Genetics: Applied Research, 16(4/1), pp. 799-804.
Lashin S. A., Matushkin Y. G., Suslov V. V., & Kolchanov N. A. (2012). Computer modeling of genome complexity variation trends in prokaryotic communities under varying habitat conditions. Ecological modelling, 224(1), 124-129.
Lashin S. A. & Matushkin Y. G. (2012). Haploid evolutionary constructor: new features and further challenges. In silico biology, 11(3, 4), 125-135.

2010

Lashin S.A., Suslov V.V., Matushkin Yu.G. Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity // Journal of Bioinformatics and Computational Biology, 2010, V 8, N. 3, p. 627-643.
Mironova VV, Omelyanchuk NA, Yosiphon Guy, Fadeev SI, Kolchanov NA, Mjolsness E., Likhoshvai VA How acropetal auxin flow determines cell fate specification along the central axis in root development. BMC Systems Biology. 2010, 4:98.
V. A. Likhoshvai, T. M. Khlebodarova, M. T. Ree, and N. A. Kolchanov Metabolic Engineering in Silico. Applied Biochemistry and Microbiology, 2010, Vol. 46, No. 7, pp. 671–687.

2009

I.R. Akberdin, F.V. Kazantsev, N.A. Omelyanchuk, V.A. Likhoshvai (2009). Mathematical model of auxin metabolism in meristem cells of plant shoots. VOGiS Herald journal, Vol. 13, 1, pp. 170-176.
F.V. Kazantsev, I.R. Akberdin, K.D. Bezmaternykh, V.A. Likhoshvai (2009). The tool for automatic generation of gene network’s mathematical models. VOGiS Herald journal, Vol. 13, 1, pp. 163-170
V.A. Likhoshvai, N.A. Omelyanchuk, V.V. Mironova, F.V. Kazantsev, I.R. Akberdin, V.K. Korolev, S.I. Fadeev, N.A. Kolchanov (2009). Modeling of auxin regulated kateral organ initiation in Arabidopsis thaliana L.. VOGiS Herald journal, Vol. 13, 1, pp. 176-186.
I.R Akberdin, F.V. Kazantsev, V.A. Likhoshvai, S.I. Fadeev, I.A. Gainova, V.K. Korolev, A.E. Medvedev (2009). Computer system of modules integration for automatic construction and numerical analysis of molecular genetic systems. SEMR, Vol. 6, pp. 440-456.
N. A. Omelyanchuk, V. V. Mironova , N. A. Kolchanov. Plant Developmental Genetics: Integrating Data from Different Experiments in Databases. Russian Journal of Genetics, 2009, Vol. 45, No. 11, pp. 1302–1316.

2008

G. G. Lazareva, V. V. Mironova, N. A. Omelyanchuk, I. V. Shvab, V. A. Vshivkov, D. N. Gorpinchenko, S. V. Nikolaev and N. A. Kolchanov. Mathematical modeling of plant morphogenesis // Numerical Analysis and Applications. 2008. V. 1. № 2. P. 123-134

2007

Axenovich T.I., Zorkoltseva I.V., Akberdin I.R., Beketov S.V., Kashtanov S.N., Zakharov I.A., Borodin P.M.Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora). Heredity. 2007 Feb, Vol. 98, 2, pp. 99-105. PMID: 17006530
Akberdin I.R., Ozonov E.A., Mironova V.V., Omelyanchuk N.A., Likhoshvai V.A., Gorpinchenko D.N., Kolchanov N.A. (2007). A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT OF PRIMARY SHOOT MERISTEMS OF ARABIDOPSIS THALIANA. Journal of Bioinformatics and Computational Biology, Vol. 5, 02B, pp. 641-650. PMID: 17636867
V. A. Likhoshvai, N. A. Omel’yanchuk, V. V. Mironova, S. I. Fadeev, E. D. Mjolsness and N. A. Kolchanov. Mathematical model of auxin distribution in the plant root. Russian Journal of Developmental Biology. 2007. V. 38, № 6. p. 446–456.

2006

Akberdin I. R., Ozonov E. A., Mironova V.V., Gorpinchenko D. N., Omelyanchuk N. A., Likhoshvai V. A., Kolchanov N. A. A Cellular Automaton Model of Morphogenesis in Arabidopsis thaliana. Biophysics, Vol.51, 7, pp. 91-94.
Zorkoltseva I.V., Akberdin I.R., Kulikova A.V, Knyazev S.V,Borodin P.M, Axenovich T.I. (2006) Changes in litter size in Kerry Blue Terrier dogs with abnormal dentition. Russian Journal of Genetics, Vol. 42, 3, pp. 339-340
N. A. Omelyanchuk, V. V. Mironova, E. M. Zalevsky, I. S. Shamov, A. S. Poplavsky, N. L. Podkolodny, D. K. Ponomaryov, S. V. Nikolaev, E. D. Mjolsness, E. M. Meyerowitz, and N. A. Kolchanov A Systems Approach to Morphogenesis in Arabidopsis thaliana: I. AGNS Database // Biofizika, 2006 V.51, Suppl.1, p. 75-83.
S. V. Nikolaev, S. I. Fadeev, A. V. Penenko, V. V. Lavrekha, V. V. Mironova, N. A. Omelyanchuk, E. D. Mjolsness, and N. A. Kolchanov A Systems Approach to Morphogenesis in Arabidopsis thaliana: II. Modeling the Regulation of Shoot Apical Meristem Structure // Biofizika, 2006 V.51, Suppl.1, p. 83-90.
I. R. Akberdin, E. A. Ozonov, V. V. Mironova, D. N. Gorpinchenko, N. A. Omelyanchuk, V. A. Likhoshvai, and N. A. Kolchanov A Cellular Automaton Model of Morphogenesis in Arabidopsis thaliana // Biofizika, 2006 V.51, Suppl.1 p. 91-94

Abstracts2011

Akberdin I.R., Kazantsev F.V., Ree M.T., Ree N.A.,Timonov V.S., Oshchepkova E.A., Ratushny A.V., Khlebodarova T.M., Likhoshvai V.A.MGSmodelsDB – a new database of mathematical models of Escherichia coli cell subsystems // Proceedings of the VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia. 2011. Vol. 2, p. 397.
Likhoshvai V.A.,Ri M.T., V. V. Kogai, Khlebodarova T.M., and S. I. Fadeev. Modelling of de novo biosynthesis of purines and pyrimidines in E. coli cells // Proceedings of the VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia. 2011, pp385-386.