/Publications
Publications 2020-02-05T18:03:09+00:00

Publications

 

Our team’s publications include our research using systems pharmacology, systems biology approaches with different methods of mechanistic modeling, agent based modeling, pharmacokinetic and pharmacodynamic modeling, pharmacometrics, papers on modern modeling software tools developed in collaboration and with our participation, papers on different diseases areas including immunology, oncology, infectious diseases, neurodegenerative diseases, respiratory diseases, endocrine diseases, papers on molecular biology problems and model based drug development methodology and others.

2019

  • Sokolov SS, Vorobeva MA, Smirnova AI, Smirnova EA, Trushina NI, Galkina KV, Severin FF and Knorre DA (2020) LAM Genes Contribute to Environmental Stress Tolerance but Sensibilize Yeast Cells to Azoles. Front. Microbiol. 11:38. doi: 10.3389/fmicb.2020.00038. Read more
  • G. Helmlinger, V. Sokolov, K. Peskov, K.M. Hallow, Yu. Kosinsky, V. Voronova, L. Chu, T. Yakovleva, I. Azarov, D. Kaschek, A. Dolgun, H. Schmidt, D.W. Boulton, R.C. Penland. (2019) Quantitative Systems Pharmacology: An Exemplar Model Building Workflow with Applications in Cardiovascular, Metabolic and Oncology Drug Development, CPT: Pharmacometrics and Systems Pharmacology. doi: 10.1002/psp4.12426
  • Victor Sokolov, Gabriel Helmlinger, Catarina Nilsson, Kirill Zhudenkov, Stanko Skrtic, Bengt Hamrén, Kirill Peskov, Eva Hurt-Camejo, and Rasmus Jansson-Löfmark. Comparative quantitative systems pharmacology modeling of anti-PCSK9 therapeutic modalities in hypercholesterolemia. J Lipid Res. 2019 Sep; 60(9): 1610–1621. doi: 10.1194/jlr.M092486. Read more
  • Tatiana Yakovleva, Victor Sokolov, Lulu Chu, Weifeng Tang, Peter J. Greasley, Helena Peilot Sjögren, Susanne Johansson, Kirill Peskov, Gabriel Helmlinger, David W. Boulton, Robert C. Penland. Comparison of the urinary glucose excretion contributions of SGLT2 and SGLT1: A quantitative systems pharmacology analysis in healthy individuals and patients with type 2 diabetes treated with SGLT2 inhibitors. Diabetes Obes Metab. 2019 Aug 18. doi: 10.1111/dom.13858. Read more
  • Azarov, I., Peskov, K., Helmlinger, G., & Kosinsky, Y. (2019). Role of T Cell-To-Dendritic Cell Chemoattraction in T Cell Priming Initiation in the Lymph Node: An Agent-Based Modeling Study. Frontiers in Immunology, 10, 1289. doi: 10.3389/fimmu.2019.01289. Read more
  • Busse D, Tang W, Scheerer MF, Danne T, Biester T, Sokolov V, Boulton DW and Parkinson J. Comparison of pharmacokinetics and the exposure-response relationship of dapagliflozin between adolescent/young adult and adult patients with type 1 diabetes mellitus. Br J Clin Pharmacol. 2019. Ms no. MP-00894-18.R2. Read more
  • Kirill Peskov, Ivan Azarov, Lulu Chu, Veronika Voronova, Yury Kosinsky, Gabriel Helmlinger. Quantitative mechanistic modelling in support of pharmacological therapeutics development in immuno-oncology. Front. Immunol. doi: 10.3389/fimmu.2019.00924. Read more
  • Sokolov V, Yakovleva T, Ueda S, Parkinson J, Boulton D W, Penland R C, Tang W. Urinary glucose excretion after dapagliflozin treatment: An exposure-response modelling comparison between Japanese and non-Japanese patients diagnosed with type 1 diabetes mellitus. Diabetes Obes Metab. 2019; 21:829–836. Read more

2018

  • Al‐Khaifi, S. Straniero V. Voronova, D. Chernikova, V. Sokolov, C. Kumar, B. Angelin, M. Rudling. Asynchronous rhythms of circulating conjugated and unconjugated bile acids in the modulation of human metabolism. Journal of Internal Medicine, 2018, 284; 546-559. Read more
  • Snezhkina AV, Lukyanova EN, Kalinin DV, Pokrovsky AV, Dmitriev AA, Koroban NV, Pudova EA, Fedorova MS, Volchenko NN, Stepanov OA, Zhevelyuk EA, Kharitonov SL, Lipatova AV, Abramov IS, Golovyuk AV, Yegorov YE, Vishnyakova KS, Moskalev AA, Krasnov GS, Melnikova NV, Shcherbo DS, Kiseleva MV, Kaprin AD, Alekseev BY, Zaretsky AR, Kudryavtseva AV. Exome analysis of carotid body tumor. BMC Med Genomics (2018) Feb 13; 11(Suppl 1):17. Read more
  • Avdeev S.N., Nenasheva N.M., Zhudenkov K.V., Petrakovskaya V.A., Izyumova G.V. Prevalence, morbidity, phenotypes and other characteristics of severe bronchial asthma in the Russian Federation. Russian Pulmonology. 2018; 28(3):341-358. (In Russ.) Read more
  • Voronova V, Zhudenkov K, Penland RC, Boulton DW, Helmlinger G, Peskov K. Exenatide effects on gastric emptying rate and the glucose rate of appearance in plasma: A quantitative assessment using an integrative systems pharmacology model. Diabetes Obes Metab. 2018; 20:2034–2038. Read more
  • Yu. Kosinsky, S. Dovedi, K. Peskov, V. Voronova, L. Chu, H. Tomkinson, N. Al-Huniti, D. Stanski, G. Helmlinger. (2018) Radiation and PD-(L)1 treatment combinations: immune response and dose optimization via a predictive systems model, Journal for ImmunoTherapy of Cancer (2018) 6:17. Read more

2017

  • Helmlinger, G., Al-Huniti, N., Aksenov, S., Peskov, K., Hallow, K. M., Chu, L., Boulton, D., Eriksson, U., Hamrén, B., Lambert, C., Masson, E., Tomkinson, H., & Stanski, D. (2017) Drug-disease modeling in the pharmaceutical industry – where mechanistic systems pharmacology and statistical pharmacometrics meet. European Journal of Pharmaceutical Sciences, Volume 109 (S), Pages S39-S46. Read more
  • Panov, A., Kochkina, J., Yartsev, E., Eremin, D., Yakovleva, T., & Kedik, S. (2017) Modification of the antitumor effect of cytotoxic drugs by copolymers of N-vinylpyrrolidone and 2-methyl-5-vinylpyridine. Pharmaceutical Chemistry Journal, 51(7), 3—7.
  • Voronova, V., Zhudenkov, K.,  Helmlinger, G., & Peskov, K. (2017). Interpretation of metabolic memory phenomenon using a physiological systems model: What drives oxidative stress following glucose normalization? PLoS ONE,12(2), e0171781. PubMed
  • Zhikrivetskaya, S. O., Snezhkina, A. V., Zaretsky, A. R., Alekseev, B. Y., Pokrovsky, A. V., Golovyuk, A. L., Melnikova, N. V.,  Stepanov, O. A., Kalinin, D. V., Moskalev, A. A., Krasnov, G. S., Dmitriev, A. A., & Kudryavtseva, A. V. (2017). Molecular markers of paragangliomas/pheochromocytomas. Oncotarget, 8, 25756. Paper
  • Potapov, A. M., Goncharov, A. A., Semenina, E. E., Korotkevich, A. Yu., Tsurikov, S. M., Rozanova, O. L., Anichkin, A. E., Zuev, A. G., Samoylova, E. S., Semenyuk, I. I., Yevdokimov, I. V., & Tiunov, A. V. (2017) Arthropods in the subsoil: Abundance and vertical distribution as related to soil organic matter, microbial biomass. European Journal of Soil Biology, 82, 88—97.
  • Ryskov, A. P., Osipov, F. A., Omelchenko, A. V., Semyenova, S. K., Girnyk, A. E., Korchagin, V. I., Vergun, A. A., & Murphy, R. W. (2017) The origin of multiple clones in D. rostombekowi. PLoS ONE, 12(9), e018516.
  • Chernikova, D., Pázsit, I., Favalli, A., & Croft, S. (2017) The Inclusion of Photofission, Photonuclear, (n, xn), (n, n′xγ), and (n, xγ) Reactions in the Neutron-Gamma Feynman-Alpha Variance-to-Mean Formalism. Nuclear Science and Engineering, 185, 206—216.
  • Girnyk, A. E., Vergun, A. A., Omelchenko, A. V., Petrosyan, V. G., Korchagin, V. I., & Ryskov, A. P. (2017) Molecular and genetic characterization of the allelic variants of Du215, Du281, Du323, and Du47G microsatellite loci in D. armeniaca. Russian Journal of Genetics, 53(4), 472–482.

2016

  • Domijan, M., Brown, P.E., Shulgin, B. V., & Rand, D. A. (2016). PeTTSy: a computational tool for perturbation analysis of complex systems biology models. BMC bioinformatics, 17(1), 124. PubMed
  • Karelina, T., Voronova, V., Demin, O., Colice, G., & Agoram, B. M. (2016). A Mathematical Modelling Approach to Understanding the Effect of Anti-Interleukin Therapy on Eosinophils. CPT Pharmacometrics Syst. Pharmacol, 5(11), 608. PubMed
  • Shulgin, B., Helmlinger, G., & Kosinsky, Yu. (2016). A Generic Mechanism for Enhanced Cytokine Signaling via Cytokine-Neutralizing Antibodies. PLoS One, 11(2), e0149154. PubMed
  • Shashkova, T., Popenko A., Tyakht A., Peskov K., Kosinsky Y., Bogolubsky L., Raigorodskii A., Ischenko D., Alexeev D., & Govorun V. (2016). Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations. PLoS One, 11(2), e0148386. PubMed
  • Rozova, S., & Bratus, A. S. (2016). Therapy strategy in tumour cells and immune system interaction mathematical model. Applicable Analysis, 95, 1548–1559. Paper
  • Snezhkina, A. V., Krasnov, G. S., Lipatova, A. V., Sadritdinova, A. F., Kardymon, O. L., Fedorova, M. S., Melnikova, N. V., Stepanov, A., Zaretsky, A. R., Kaprin, A. D., Alekseev, B. Y., Dmitriev, A. A., & Kudryavtseva, A.V. (2016). The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection. OMCL, 2353560. Paper 
  • Neroev V., Malyugin, B. E., Trubilin, V. N., Zhudenkov, V., & Orlova, O. M. (2016). Clinical and social burden of cataract in Russia. Cataract and Refractive Surgery, 16(1), 4–14.
  • Noren, D. P., Long, B. L., Norel, R., Rrhissorrakrai, K., Hess, K., Hu, C. W., Bisberg, A. J., Schultz, A., Engquist, E., Liu, L., Lin, X., Chen, G. M., Xie, H., Hunter, G. A. M., Boutros, P. C., Stepanov, , DREAM 9 AML-OPC Consortium, Norman, T., Friend, S. H., Stolovitzky, G., Kornblau, S., & Qutub, A.A. (2016) A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML (Acute Myeloid Leukemia) Prognosis. PLOS Computational Biology, 1004890. Paper
  • Omelchenko, A. V., Girnyk, А. Е., Osipov, А., Petrosyan, V. G., Vergun, А. А., & Ryskov, А. P. (2016) Detection of genotypic changes in D. armeniaca. Russian Journal of Biological Invasions, 7(3), 275–282.
  • Omelchenko, A. V., Girnyk, A. E., Osipov, F. A., Vergun, A. A., Petrosyan, V. G., Danielyan, F. D., Arakelyan, M. S., & Ryskov, A. P. (2016) Genetic Differentiation among Natural Populations of the D. raddei as Inferred from Genome Microsatellite Marking. Russian Journal of Genetics, 52(2), 231–235.
  • Polovnikov, P. V., Azarov, I. B., & Veshchunov, M. S. (2016). Advancement of the kinetic approach to Brownian coagulation on the base of the Langevin theory. Journal of Aerosol Science, 96, 14-23.

2015

  • Vinogradova, S. V., Zhudenkov, K. V., Benson, N., Van Der Graaf, P. H., Demin, O.V., & Karelina, T. A. (2015) Prediction of long-term treatment outcome in HCV following 24 day PEG-IFN alpha-2b therapy using population pharmacokinetic-pharmacodynamic mixture modeling and classification analysis. J Theor Biol., 8, 382, 91–98. PubMed
  • Goncharov, A. A., Zalewski, M., Dudek, D., Godeau, J. F., Sienkiewicz, P., Ulrich, W., & Tiunov, A. V. (2015) Sex-related variation in δ15N. Pedobiologia, 58, 147–151.
  • Tsurikov, S. M., Goncharov, A. A. & Tiunov, A. V. (2015) Intrabody variation and ontogenetic changes in the isotopic composition (13C/12C and 15N/14N). Zoologicheskii Zhurnal, 94(3), 336 – 344.
  • Veshchunov, M. S., & Azarov, I. B. (2015). Condensation rate of light vapour molecules in the transition regime. Journal of Aerosol Science, 86, 13—23.

2014

  • Demin, O. Jr, Yakovleva, T., Kolobkov, D., & Demin, O. (2014) Analysis of the efficacy of SGLT2 inhibitors using semi-mechanistic model. Front Pharmacol, 5, 218, 1–10. PubMed
  • Smirnov, S., Metelkin, E., Gizzatkulov, N., Stepanov, O., & Demin, O. (2014) Towards Modeling of Metabolic Syndrome: Tissue Crosstalk in Lipid Spillover. In M. Oresic, A. Vidal-Puig (Eds.) “A Systems Biology Approach to Study Metabolic Syndrome”. Springer, 341—366. Springer
  • Sadritdinova, A. F., Dmitriev, A. A., Snezhkina, A. V., Belenikin, M. S., Krasnov, G. S., Manylov, O. G., Kudryavtsev, A. A., Melnikova, N. V., Speranskaya, A. S., Darii, M. V., Lakunina, V.A., Uroshlev, L. A., Smurov, A. O., Stepanov O. A., & Kudryavtseva, A.V. (2014) A new reliable reference gene UBA52 for quantitative real-time polymerase chain reaction studies in pyloric cecal tissues. Genetics and Molecular Research, 13(2), 3972–3980. Paper
  • Vergun, A. A, Martirosyan, I. A., Semyenova, S. K., Omelchenko, A. V., Petrosyan, V. G., et al. (2014) Clonal Diversity and Clone Formation in D. dahli. PLoS ONE 9(3), e91674. doi:10.1371/journal.pone.0091674
  • Azarov, I. B. & Veshchunov, M. S. (2014) On the Theory of Point Defect Recombination in Crystals. Journal of Experimental and Theoretical Physics, 119(3), 473–478.

2013

  • Peskov, K.V. (2013) Mathematical modeling in drug development. Vestnik Roszdravnadzora (Bulletin of Federal Service on Surveillance in Healthcare), 1, 57–60. [in Russian]
  • Demin, O. O., Smirnov, S. V., Sokolov, V. V., Cucurull-Sanchez, L., Pichardo-Almarza, C., Flores, M. V., Benson, N., & Demin, O. V. (2013) Modeling of celiac disease immune response and the therapeutic effect of potential drugs. BMC System Biology, 7, 56, 1–10. PubMed
  • Oparina, N. Yu., Snezhkina, A. V., Sadritdinova, A. F., Veselovskii, V. A., Dmitriev, A. A., Senchenko, V. N., Mel’nikova, N. V., Speranskaya, A. S., Darii, M. V., Stepanov, O., Barkhatov, I. M., & Kudryavtseva, A. V. (2013) Differential expression of genes that encode glycolysis enzymes in kidney and lung cancer in humans. Russian Journal of Genetics, 49(7), 707—716. PubMed
  • Sadritdinova, A. F., Snezhkina, A. V., Dmitriev, A. A., Krasnov, G. S., Astakhova, L. N., Kudryavtsev, A. A., Mel’nikova, N. V., Speranskaya, A. S., Darii, M. V., Lakunina, V. A., Uroshlev, L. A., Smurov, A. O., Stepanov, O. A., & Kudryavtseva, A. V. (2013) A new reference gene, Ef1A, for quantitative real-time PCR assay of the starfish Asterias rubens pyloric ceca. Dokl Biol Sci., 452, 310-2. PubMed
  • Omelchenko, A. V. (2013) Molecular characteristic of dinucleotide microsatellite loci of genome of D. unisexualis. Moscow. “Prometey” MSPU PRESS. [in Russian]
  • McIntosh, J. R., O’Toole, E., Zhudenkov, K., Morphew, M., Schwartz, C., Ataullakhanov, F. I., & Grishchuk, E. L. (2013) Conserved and divergent features of kinetochores and spindle microtubule ends from five species. J Cell Biol, 200(4), 459–74. PubMed

2012

  • Karelina, T. A., Zhudenkov, K. V., Demin, O. O., Svetlichny, D. V., Agoram, B., Fairman, D., & Demin, O. V. (2012) Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach. BMC System Biology, 6 (141), 1—14. PubMed
  • Peskov, K., Mogilevskaya, E., & Demin, O. (2012) Kinetic modelling of central carbon metabolism in Escherichia coli. FEBS Journal, 279, 3374–3385. PubMed
  • Ostapchenko, V. G., Gasparian, M. E., Kosinsky, Yu. A., Efremov, R. G., Dolgikh, D. A., & Kirpichnikov, M. P. (2012) Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit. Biomol. Struct. & Dyn, 30(1), 62–73. PubMed
  • Petrosyan, V. G., Bessonov, S. A., & Omelchenko, A. V. (2012) Mathematical modeling of population dynamics and the demographic parameters for populations of moose (Alces alces) on the basis of long-term monitoring data. In E.V. Budilova (Ed.), “Mathematics and Reality: the Confrontation of Rigor and Complexity” (pp. 458-472). Moscow, M: Edition «Soliton». [in Russian]
  • Petrosyan, V. G, Dergunova, N. N., Bessonov, S. A., & Omelchenko, A. V. (2012) Modeling the Dynamics of Population, Evaluation and Comparative Analysis of the Demographic Parameters of Moose in Russia and Finland Using Long-Term Monitoring Data. Mathematical Biology and Bioinformatics. 7(1), 244–256.
  • Veshchunov, M. S., & Azarov, I. B. (2012) Next approximation of the random walk theory for Brownian coagulation. Journal of Aerosol Science, 47, 70–77.

2010

  • Gizzatkulov, N. M., Goryanin, I. I., Metelkin, E. A., Mogilevskaya, E. A., Peskov, K. V., & Demin, O. V. (2010) DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Systems Biology, 4, 109. PubMed
  • Azarov, I. B. & Veshchunov, M. S. (2010). Development of the new approach to the Brownian coagulation theory: transition regime. Journal of Engineering Thermophysics, 19(3), 128—137.

2009

  • Mogilevskaya, E., Peskov, K., Metelkin, E., Plyusnina, T., Lebedeva, G., Goryanin, I., & Demin, O. (2009) Kinetic modeling of E. coli enzymes: integration of in vitro data. In S. Y. Lee (Ed.) “Systems Biology and Biotechnology of Esherichia coli”. Springer, 177 – 207. Springer
  • Goltsov, A., Maryashkin, A., Swat, M., Kosinsky, Y., Humphery-Smith, I., Demin, O., Goryanin I., & Lebedeva G. (2009) Kinetic modelling of NSAID action on COX-1: focus on in vitro/in vivoaspects and drug combinations. J. Pharmac. Sciences, 36, 122—136. PubMed
  • Lesovoy, D. M., Bocharov, E. V., Lyukmanova, E. N., Kosinsky, Yu. A., Shulepko, M. A., Dolgikh, D. A., Kirpichnikov, M. P., Efremov, R. G., & Arseniev, A. S. (2009) Specific membrane binding of neurotoxin II can facilitate its delivery to acetylcholine receptor. J., 97(7), 2089–2097. PubMed
  • Mogilevskaya, E., Bagrova, N., Plyusnina, T., Gizzatkulov, N., Metelkin, E., Goryacheva, E., Smirnov, S., Kosinsky, Y., Dorodnov, A., Peskov, K., Karelina, T., Lebedeva, G., Goryanin, I., & Demin O. (2009) Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods Mol Biol, 563, 197 – 218. PubMed
  • Omelchenko, A. V., & Korchagin, V. I. (2009) Thermodynamic characteristization of di-, tri, and tetranucleotide microsatellite loci in D. unisexualis. Russian Journal of Genetics, 45(8), 1004 – 1008.
  • Petrosyan, V. G., Dergunova, N. N., Bessonov, S. A., Nazarova, K. A., & Omelchenko, A. V. (2009) Estimation of population dynamics and population’s age-sex structure of a moose ( alces L.) in Russia by means simulation model and the data of multi-years monitoring. Journal of Samara Science Centre of the Russian Academy of Sciences, 11(7), 1566–1574.
  • Omelchenko, A. V., Korchagin, V. I., Sevast’yanova, G. A., Ryskov, A. P., Tokarskaya, O. N. (2009) Molecular genetic characteristic of dinucleotide microsatellite loci in D. unisexualis. Russian Journal of Genetics. 45(2), 203 – 210.

Before 2009

  • Peskov, K., Goryanin, I., & Demin, O. (2008) Kinetic Model of Phosphofructokinase-1 from Escherichia coli. J Bioinform Comput Biol, 6(4), 843 – 67. PubMed
  • Peskov, K., Goryanin, I., Prank, K., Tobin, F., & Demin, O. (2008) Kinetic Modeling of ace operon genetic regulation in Escherichia coli. J Bioinform Comput Biol, 6(5), 933–959. PubMed
  • Omelchenko, A. V. (2008) Mathematical modeling of genetic population processes on the basis of polymorphism of microsatellite DNA in D. unisexualis. Current trends of natural Sciences. The Articles. (pp. 163-168). “Prometey” MSPU PRESS. [in Russian]
  • McIntosh, J., Grishchuk, E., Morphew, M., Efremov, A., Zhudenkov, K., Volkov, V., Cheeseman, I., Desai, A., Mastronarde, D., & Ataullakhanov, F. (2008) Fibrils Connect Microtubule Tips with Kinetochores: A Mechanism to Couple Tubulin Dynamics to Chromosome Motion. Cell, 135(2), 322–333. PubMed
  • Rand, D. A., Shulgin, B. V., Salazar, J. D., & Millar, A. J. (2006) Uncovering the design principles of circadian clocks: mathematical analysis of flexibility and evolutionary goals. Journal of theoretical biology, 238(3), 616—635. PubMed
  • Korchagin, V. I., Martirosyan, I. A., Omelchenko, A. V. (2004) Study of allelic polymorphism of (GATA)n-containing loci in D. unisexualis. Russian Journal of Genetics, 40(10), 1095 – 1101.
  • Rand, D. A., Shulgin, B. V., Salazar, J. D., & Millar, A. J. (2004) Design principles underlying circadian clocks, Journal of The Royal Society Interface 1 (1), 119-130. PubMed
  • Shulgin, B., Stone, L., & Agur., Z (1998) Pulse vaccination strategy in the SIR epidemic model. Bulletin of Mathematical Biology, 60(6), 1123—1148. PubMed