Articles

Tatiana Safronova, Anna Kravtsova, Sergei Vavilov, Cristina Leon, Anna Bragina, Victor Milyagin, Ruslan Makiev, Alexei Sumin, Kirill Peskov, Victor Sokolov, Valery Podzolkov. Model-Based Assessment of the Reference Values of CAVI in Healthy Population and Benchmarking With CAVI0. Am J Hypertens. 2024 Jan 1;37(1):77-84.

Victor Sokolov, Tatiana Yakovleva, Leonid Stolbov, Robert C. Penland, David Boulton, Joanna Parkinson, Weifeng Tang. A mechanistic modeling platform of SGLT2 inhibition: Implications for type 1 diabetes. CPT Pharmacometrics & System Pharmacology. doi: 10.1002/psp4.12956

Cristina Leon, Alexey Tokarev, Anass Bouchnita, Vitaly Volpert. Modelling of the Innate and Adaptive Immune Response to SARS Viral Infection, Cytokine Storm and Vaccination. Vaccines 2023, 11(1), 127. doi: 10.3390/vaccines11010127

Voronova V., Vislobokova A., Mutig K., Samsonov M., Peskov K., Sekacheva M., Materenchuk M., Bunyatyan N., Lebedeva S. Combination of immune checkpoint inhibitors with radiation therapy in cancer: A hammer breaking the wall of resistance. Front. Oncol., 05 December 2022. doi: 10.3389/fonc.2022.1035884

Voronova V., Sokolov V., Morias Y., Boezelman M. J., Wågberg M., Henricsson M., Hansson K., Goltsov A., Peskov K., Sundqvist M. Evaluation of therapeutic strategies targeting BCAA catabolism using a systems pharmacology model. Front. Pharmacol., 28. doi: 10.3389/fphar.2022.993422

Victor Sokolov, Algorithms and methodological challenges in the development and application of quantitative systems pharmacology models: a case study in type 2 diabetes. doi: 10.1515/rnam-2022-0025

Ivan Azarov, Gabriel Helmlinger, Yuri Kosinsky, Kirill Peskov. Elaborating on anti CTLA-4 mechanisms of action using an agent-based modeling approach. Frontiers in Applied Mathematics and Statistics, 8, 106. doi: 10.3389/fams.2022.993581

Rekić D., Azarov I., Knöchel J., Sokolov V., Nilsson C., Wernevik L., Han D., Rydén-Bergsten T., Ebrahimi A., Dota C., Carlsson B. AZD8233 Antisense Oligonucleotide targeting PCSK9 does not prolong QT interval AZD8233. British Journal of Clinical Pharmacology, 88(11), 4839-4844. doi: 10.1111/bcp.15425

Kosinsky Y, Peskov K, Stanski DR, Wetmore D, Vinetz J. Semi-Mechanistic Pharmacokinetic-Pharmacodynamic Model of Camostat Mesylate-Predicted Efficacy against SARS-CoV-2 in COVID-19. Microbiol Spectr. 2022 Apr 27;10(2):e0216721. doi: 10.1128/spectrum.02167-21

Karatza E., Yakovleva T., Adams K., Rao GG., Ait-Oudhia S., 2022. Knowledge dissemination and central indexing of resources in pharmacometrics: an ISOP education working group initiative. J Pharmacokinet Pharmacodyn. 2022 Apr 26. doi: 10.1007/s10928-022-09809-9

Victoria S. Kulesh, PharmD1,2, Roman V. Drai, MD, PhD1, Bella R. Zinnatulina, MSc1, Igor E. Makarenko, MD, PhD1, Fedor G. Pilyus, MSc2, and Alexander L. Khokhlov, MD, PhD3. Modeling of Pharmacokinetic Profiles of Insulin Aspart and Biphasic Insulin Aspart 30/70. The Journal of Clinical Pharmacology 2022, 0(0) 1–8, 2022, The American College of Clinical Pharmacology. doi: 10.1002/jcph.2049

Leon, C., Tokarev, A. A., & Volpert, V. A. (2022). Modelling of cytokine storm in respiratory viral infections. Computer Research and Modeling, 14(3), 619–645. doi: 10.1007/s10928-022-09809-9

Leon, C., Kutsenko, I., & Volpert, V. (2022). Existence of solutions for a nonlocal reaction-diffusion equation in biomedical applications. Israel Journal of Mathematics, 248(1), 67–93. doi: 10.1007/s11856-022-2294-6

Voronova V, Cullberg M, Delff P, Parkinson J, Dota C, Schiavon G, Maroj B, Rekić D, Cheung SYA. Concentration-QT modelling shows no evidence of clinically significant QT interval prolongation with capivasertib at expected therapeutic concentrations. Br J Clin Pharmacol. 2022 Feb;88(2):858-864. doi: 10.1111/bcp.15006

Chan, P., Peskov, K. & Song, X. Applications of Model-Based Meta-Analysis in Drug Development. Pharm Res (2022). doi: 10.1007/s11095-022-03201-5

Zhudenkov K, Gavrilov S, Sofronova A, et al. A workflow for the joint modeling of longitudinal and event data in the development of therapeutics: Tools, statistical methods, and diagnostics. CPT Pharmacometrics Syst Pharmacol. 2022;00:1-13. doi: 10.1002/psp4.12763

Kirill Zhudenkov, Robert Palmér, Alexandra Jauhiainen, Gabriel Helmlinger, Oleg Stepanov, Kirill Peskov, Ulf G Eriksson, Ulrika Wählby Hamrén. Longitudinal FEV1 and Exacerbation Risk in COPD: Quantifying the Association Using Joint Modelling. International Journal of Chronic Obstructive Pulmonary Disease 16 (2021): 101. doi: 10.2147/COPD.S284720

Genovese MC, Durez P, Fleischmann R, Tanaka Y, Furst D,  Yamanaka H, Korneva E, Vasyutin I, Takeuchi T. Long-term safety and efficacy of olokizumab in patients with rheumatoid arthritis and inadequate response to tumor necrosis factor inhibitor therapy in phase II studies. Eur J Rheumatol. 2021 Jul;8(3):120-129. doi: 10.5152/eurjrheum.2021.19207

Vasyutin I, Butnaru D, Lyundup A, et al. Frontiers in urethra regeneration: current state and future perspective. Biomed Mater. 2021 Mar 9;16(4). doi: 10.1088/1748-605X/ab99d2

Voronova Veronika, Peskov Kirill, Kosinsky Yuri, Helmlinger Gabriel, Chu Lulu, Borodovsky Alexandra, Woessner Richard, Sachsenmeier Kris, Shao Wenlin, Kumar Rakesh, Pouliot Gayle, Merchant Melinda, Kimko Holly, Mugundu Ganesh. Evaluation of Combination Strategies for the A2AR Inhibitor AZD4635 Across Tumor Microenvironment Conditions via a Systems Pharmacology Model. Front. Immunol., 02 March 2021. doi: 10.3389/fimmu.2021.617316

Leon, C. (2021). Reaction–Diffusion Model of Coexistence of Viruses in the Space of Genotypes. Smart Modelling For Engineering Systems, 265–276. doi: 10.1007/978-981-33-4709-0_22

Shah M., Stolbov L., Yakovleva T., Tang W., Penland RC., Sokolov V., Boulton DW., Parkinson J., 2021. A model-based approach to investigating the relationship between glucose-insulin dynamics and dapagliflozin treatment effect in patients with type 2 diabetes. Diabetes Obes Metab. 2021 Jan 10. doi: 10.1111/dom.14305

Sergey Gavrilov, Kirill Zhudenkov, Gabriel Helmlinger, James Dunyak, Kirill Peskov, Sergey Aksenov. Longitudinal Tumor Size and Neutrophil-to-Lymphocyte Ratio Are Prognostic Biomarkers for Overall Survival in Patients With Advanced Non-Small Cell Lung Cancer Treated With Durvalumab. CPT: Pharmacometrics & Systems Pharmacology. 2020. doi: 10.1002/psp4.12578

Veronika Voronova, Svetlana Lebedeva, Marina Sekacheva, Gabriel Helmlinger and Kirill Peskov. Quantification of Scheduling Impact on Safety and Efficacy Outcomes of Brain Metastasis Radio- and Immuno-Therapies: A Systematic Review and Meta-Analysis. Front. Oncol., 02 September 2020. doi: 10.3389/fonc.2020.01609

L. Stolbov, D. Druzhilovskiy, A. Rudik, D. Filimonov, V. Poroikov, M. Nicklaus. AntiHIV-Pred: Web-resource for in silico prediction of anti-HIV/AIDS activity. Bioinformatics, Volume 36, Issue 3, 1 February 2020, Pages 978–979. doi: 10.1093/bioinformatics/btz638

Boris Shulgin , Yuri Kosinsky, Andrey Omelchenko, Lulu Chu, Ganesh Mugundu, Sergey Aksenov, Rodrigo Pimentel, Garrett DeYulia, Geoffrey Kim, Kirill Peskov & Gabriel Helmlinger. Dose dependence of treatment-related adverse events for immune checkpoint inhibitor therapies: a model-based meta-analysis, OncoImmunology, 2020 May 21;9(1):1748982, doi: 10.1080/2162402X.2020.1748982

L. Stolbov, D. Druzhilovskiy, D. Filimonov, M. Nicklaus and V. Poroikov. (Q)SAR models of HIV-1 proteins inhibition by drug-like compounds. Molecules. 2020 Jan; 25(1): 87. doi: 10.3390/molecules25010087

Goltsov, A.; Swat, M.; Peskov, K.; Kosinsky, Y. Cycle Network Model of Prostaglandin H Synthase-1. Pharmaceuticals 2020, 13, 265. doi: 10.3390/ph13100265

V.Voronova, P. Glybochko, A. Svistunov, V. Fomin, P. Kopylov, P. Tzarkov, A. Egorov, E. Gitel, A. Ragimov, A. Boroda, E. Poddubskaya and M. Sekacheva. Diagnostic Value of Combinatorial Markers in Colorectal Carcinoma. Front. Oncol., 22 May 2020, volume 10. doi: 10.3389/fonc.2020.00832

Goltsov A, Sokolovski SG, Sidorov VV, Rafailov E. Editorial: Advanced non-invasive photonic methods for functional monitoring of haemodynamics and vasomotor regulation in health and diseases. Frontiers in Physiology. April 2020. V 11, Article 325. doi: 10.3389/fphys.2020.00325

Victor Sokolov, Tatiana Yakovleva, Lulu Chu, Weifeng Tang, Peter J. Greasley, Susanne Johansson, Kirill Peskov, Gabriel Helmlinger, David W. Boulton, Robert C. Penland. 2020. Differentiating the Sodium‐Glucose Cotransporter 1 Inhibition Capacity of Canagliflozin vs. Dapagliflozin and Empagliflozin Using Quantitative Systems Pharmacology Modeling, CPT Pharmacometrics Syst Pharmacol. 2020 Feb 16. doi: 10.1002/psp4.12498

Voronova V, Sokolov V, Al-Khaifi A, Straniero S, Kumar C, Peskov K, Helmlinger G, Rudling M, Angelin B. A physiology-based model of bile acid distribution and metabolism under healthy and pathological conditions in humans. Cell Mol Gastroenterol Hepatol. Volume 10, Issue 1, 2020, Pages 149-170. doi: 10.1016/j.jcmgh.2020.02.005

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

Sofronova, A., Semenyuk, P., and Muronetz, V. (2019). The influence of β-casein glycation on its interaction with natural and synthetic polyelectrolytes. Food Hydrocoll. 89, 425–433. doi: 10.1016/j.foodhyd.2018.11.011

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

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

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

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. doi: 10.1111/bcp.13981

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

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. doi: 10.1111/dom.13586 

Ivanenkov, Y.A., Zhavoronkov, A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Veselov, M.S., Ayginin, A.A., Kartsev, V.G., Skvortsov, D.A., Chemeris, A.V., Baimiev, A.Kh., Sofronova, A.A., Malyshev, A.S., et al. (2019). Identification of Novel Antibacterials Using Machine Learning Techniques. Front. Pharmacol. 10, 913. doi: 10.3389/fphar.2019.00913

BIOS consortium, GoNL consortium, Shvetsova, E., Sofronova, A., Monajemi, R., Gagalova, K., Draisma, H.H.M., White, S.J., Santen, G.W.E., Chuva de Sousa Lopes, S.M., et al. (2019). Skewed X-inactivation is common in the general female population. Eur. J. Hum. Genet. 27, 455–465. doi: 10.1038/s41431-018-0291-3

Ivanenkov, Y.A., Machulkin, A.E., Garanina, A.S., Skvortsov, D.A., Uspenskaya, A.A., Deyneka, E.V., Trofimenko, A.V., Beloglazkina, E.K., Zyk, N.V., Koteliansky, V.E., Bezrukov, D.S., Aladinskaya, A.V., Vorobyeva, N.S., Puchinina, M.M., Riabykh, G.K., Sofronova, A.A., Malyshev, A.S., Majouga, A.G. (2019). Synthesis and biological evaluation of Doxorubicin-containing conjugate targeting PSMA. Bioorg. Med. Chem. Lett. 29, 1246–1255. doi: 10.1016/j.bmcl.2019.01.040

Veselov, M.S., Ivanenkov, Y.A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Ayginin, A.A., Skvortsov, D.A., Komarova, K.S., Chemeris, A.V., Baimiev, A.K., Sofronova, A.A., et al. (2019). Identification of pyrrolo-pyridine derivatives as novel class of antibacterials. Mol. Divers. doi: 10.1007/s11030-019-09946-3

Ivanenkov, Y.A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Veselov, M.S., Ayginin, A.A., Skvortsov, D.A., Sofronova, A.A., et al. (2019). Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform. Comb. Chem. High Throughput Screen. 22, 346–354. doi: 10.2174/1386207322666190412165316

Ivanenkov, Y.A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Veselov, M.S., Ayginin, A.A., Skvortsov, D.A., Sofronova, A.A., et al. (2019). Large-scale high-throughput screening revealed 5’-(carbonylamino)-2,3’-bithiophene-4’-carboxylate as novel template for antibacterial agents. Curr. Drug Discov. Technol. 16. doi: 10.2174/1570163816666190603095521

Ivanenkov, Y.A., Komarova, E.S., Osterman, I.A., Sergiev, P.V., Yamidanov, R.S., Deineka, E.V., Terent’ev, V.A., Fil’kov, G.I., Sofronova, A.A., Mazhuga, A.G., et al. (2019). N-Pyridyl-Substituted Carboxypiperidine Amides: A New Class of Prokaryote Translation Inhibitors. Pharm. Chem. J. 53, 225–229. doi: 10.1007/s11094-019-01984-3

Ivanenkov, Y.A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Ayginin, A.A., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Veselov, M.S., Skvortsov, D.A., Sofronova, A.A., et al. (2019). Substituted Furanocoumarins as Novel Class of Antibacterial Translation Inhibitors. Comb. Chem. High Throughput Screen. 22, 400–410. doi: 10.2174/1386207322666190723110539

Ivanenkov, Y.A., Yamidanov, R.S., Osterman, I.A., Sergiev, P.V., Aladinskiy, V.A., Aladinskaya, A.V., Terentiev, V.A., Veselov, M.S., Ayginin, A.A., Skvortsov, D.A., Sofronova, A.A., et al. (2019). 2-Pyrazol-1-yl-thiazole derivatives as novel highly potent antibacterials. J. Antibiot. (Tokyo). doi: 10.1038/s41429-019-0211-y 

Ivanenkov, Y.A., Osterman, I.A., Komarova, E.S., Bogdanov, A.A., Sergiev, P.V., Dontsova, O.A., Sofronova, A.A., Terentiev, V.A., Filkov, G.I., Yamidanov, R.S., et al. (2019). Tetrahydrocarbazoles as Novel Class of DNA Biosynthesis Inhibitors in Bacteria. Anti-Infect. Agents 17. doi: 10.2174/2211352517666181218155259 

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. doi: 10.1111/joim.12811

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. 

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. 

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. 

Petrov, R.A., Maklakova, S.Y., Ivanenkov, Y.A., Petrov, S.A., Sergeeva, O.V., Yamansarov, E.Y., Saltykova, I.V., Kireev, I.I., Alieva, I.B., Deyneka, E.V., Sofronova, A.A., et al. (2018). Synthesis and biological evaluation of novel mono- and bivalent ASGP-R-targeted drug-conjugates. Bioorg. Med. Chem. Lett. 28, 382–387. doi.org/10.1016/j.bmcl.2017.12.032.

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. 

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.

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.

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. 

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. 

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.

Sofronova, A.A., Evstafyeva, D.B., Izumrudov, V.A., Muronetz, V.I., and Semenyuk, P.I. (2017). Protein-polyelectrolyte complexes: Molecular dynamics simulations and experimental study. Polymer 113, 39–45. doi.org/10.1016/j.polymer.2017.02.047. 

Sofronova, A.A., Izumrudov, V.A., Muronetz, V.I., and Semenyuk, P.I. (2017). Similarly charged polyelectrolyte can be the most efficient suppressor of the protein aggregation. Polymer 108, 281–287. doi.org/10.1016/j.polymer.2016.11.073. 

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. 

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. 

Shulgin, B., Helmlinger, G., & Kosinsky, Yu. (2016). A Generic Mechanism for Enhanced Cytokine Signaling via Cytokine-Neutralizing Antibodies. PLoS One, 11(2), e0149154. 

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.

Rozova, S., & Bratus, A. S. (2016). Therapy strategy in tumour cells and immune system interaction mathematical model. Applicable Analysis, 95, 1548–1559. 

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. 

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. 

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.

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. 

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.

Veshchunov, M. S., & Azarov, I. B. (2015). Condensation rate of light vapour molecules in the transition regime. Journal of Aerosol Science, 86, 13—23.

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. 

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.

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. 

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.

Peskov, K.V. (2013) Mathematical modeling in drug development. Vestnik Roszdravnadzora (Bulletin of Federal Service on Surveillance in Healthcare), 1, 57–60.

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.

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. 

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. 

Omelchenko, A. V. (2013) Molecular characteristic of dinucleotide microsatellite loci of genome of D. unisexualis. Moscow. “Prometey” MSPU PRESS.

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.

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.

Peskov, K., Mogilevskaya, E., & Demin, O. (2012) Kinetic modelling of central carbon metabolism in Escherichia coli. FEBS Journal, 279, 3374–3385. 

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. 

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».

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.

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. doi: 10.1186/1752-0509-4-109

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. doi: 10.1134/S1810232810030033

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. 

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. 

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. 

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. 

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.