Публикации
Публикации нашей команды включают наши работы с использованием системной фармакологии, подходов системной биологии с различными методами механистического моделирования, агентного моделирования, фармакокинетического и фармакодинамического моделирования, статьи о современных программных средствах моделирования, разработанных в сотрудничестве и с нашим участием, статьи по различным областям заболеваний. В том числе, по иммунологии, онкологии, инфекционным заболеваниям, нейродегенеративным заболеваниям, респираторным заболеваниям, эндокринным заболеваниям, статьи по задачам молекулярной биологии, методологии моделирования и др.
2025
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Kulesh Victorya, Peskov Kirill, Helmlinger Gabriel and Bocharov Gennady Systematic review and quantitative meta-analysis of age-dependent human T-lymphocyte homeostasis.
Front. Immunol., 07 January 2025 Sec. T Cell Biology Volume 16 – 2025.
Read more - Victor Sokolov, Kirill Peskov, Gabriel Helmlinger. (2025) A Framework for Quantitative Systems Pharmacology Model Execution. In: Handbook of Experimental Pharmacology. Springer, Berlin, Heidelberg. Accepted on Mar 21, 2025, doi: 10.1007/164_2024_738. Read more
- Alina Volkova, Victor Sokolov, Florencia Tettamanti, Meghna Verma, Yaroslav Ugolkov, Kirill Peskov, Weifeng Tang, Holly Kimko (2025) An Integrative Mechanistic Model of Type 1 IFN-Mediated Inflammation in Systemic Lupus Erythematosus. CPT Pharmacometrics Syst Pharmacol. 2025, Accepted on 18 Apr. Read more
- Yan-ou Yang, Alina Volkova, Victor Sokolov, Xing Liu, Cristina Leon, Yuri Kosinsky, Jennifer Sheng, Xuejun Chen. Exposure‐Response Relationships for Axatilimab in Patients with Chronic Graft‐Versus‐Host Disease. Clinical Pharmacology and Therapeutics. Accepted on 14, June 2025. Read more
- Anna Mishina, Kirill Zhudenkov, Gabriel Helmlinger, Kirill Peskov. A Systematic Comparative Analysis of Tumor Size Models Based on Erlotinib Clinical Data in Advanced NSCLC. CPT: Pharmacometrics & Systems Pharmacology. Accepted on 24, July 2025. Read more
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Azarov, I. (2025). Reticular network as the lymph nodes railroad system: T cells migration modelling by the free energy minimization technique. Russian Journal of Numerical Analysis and Mathematical Modelling, 40(5), 359-378. Accepted on 26 August 2025.
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2024
- Antonina Nikitich, Gabriel Helmlinger, Kirill Peskov, Gennady Bocharov. Mathematical modeling of endogenous and exogenously administered T cell recirculation in mouse and its application to pharmacokinetic studies of cell therapies. Front. Immunol., Sec. T Cell Biology, Volume 15 – 2024. Read more
- Yaroslav Ugolkov, Antonina Nikitich, Cristina Leon, Gabriel Helmlinger, Kirill Peskov, Victor Sokolov, Alina Volkova. Mathematical modeling in autoimmune diseases: from theory to clinical application. Front. Immunol., 14 March 2024, Sec. Autoimmune and Autoinflammatory Disorders: Autoinflammatory Disorders. Read more
- Victoria Kulesh, Kirill Peskov, Gabriel Helmlinger, Gennady Bocharov. An integrative mechanistic model of thymocyte dynamics. doi: 10.3389/fimmu.2024.1321309 Read more
- Yan-ou Yang, Victor Sokolov, Alina Volkova, Xing Liu, Cristina Leon, Yuri Kosinsky, Breann Barker, Xuecheng Zhang, Peter Ordentlich, Jennifer Sheng, Xuejun Chen. Semimechanistic Population PK/PD Modeling of Axatilimab in Healthy Participants and Patients With Solid Tumors or Chronic Graft-Versus-Host Disease. Clinical Pharmacology and Therapeutics. 20 December 2024. Read more
- Nataliya Kudryashova, Boris Shulgin, Nikolai Katuninks, Victoria Kulesh, Gabriel Helmlinger, Kirill Zhudenkov, Kirill Peskov. Assessment of NSCLC disease burden: A survival model-basedmeta-analysis study. Comput Struct Biotechnol J. 2024 Sep 21:24:611-621. doi: 10.1016/j.csbj.2024.09.012 Read more
- Olga Ivanova, Michael Pratta, Ivan Azarov, Kirill Zhudenkov, Yuri Kosinsky, Kirill Peskov, Xuejun Chen, Jennifer Sheng. Evaluation of Itacitinib Impact on TNFα Levels Following Immune Effector Cell (IEC) Therapy Using PKPD Modeling and Simulation Approaches. Blood (2024) 144 (Supplement 1): 7129. doi: 10.1182/blood-2024-199649 Read more
- A. Petrov, I. Makarenko, B. Belova, A. Melikyan, V. Saparova, K. Peskov, N. Kudryashova, V. Kovalik, M. Gefen, A. Khokhlov, R. Drai. (2024) Optimization of Romiplostim Biosimilar Efficacy Trial Using In Silico Clinical Trial Approach for Patients With Immune Thrombocytopenia. Clin Pharmacol Drug Dev. Accepted on Dec 19, 2024. Read more
- N. Kudryashova, B. Shulgin, N. Katuninks, V. Kulesh, G. Helmlinger, K. Zhudenkov, K. Peskov. (2024) Assessment of NSCLC disease burden: A survival model-based meta-analysis study. Comput Struct Biotechnol J. 2024, 24:611-621. Read more
2023
- 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. Read more
- 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. Read more
- Alina Volkova, Boris Shulgin, Gabriel Helmlinger, Kirill Peskov, Victor Sokolov. Optimization of the MACE endpoint composition to increase power in studies of lipid-lowering therapies—a model-based meta-analysis. doi: 10.3389/fcvm.2023.1242845 Read more
- Volkova A, Semenyuk P. Tyrosine phosphorylation of recombinant hirudin increases affinity to thrombin and antithrombotic activity. Proteins. 2024 Mar;92(3):329-342. doi: 10.1002/prot.26616. Epub 2023 Oct 20. PMID: 37860993. Read more
- Kulesh, I. Vasyutin, A. Volkova, K. Peskov, H. Kimko, R. Alluri (2023) A tutorial for model-based evaluation and translation of cardiovascular safety in preclinical trials. CPT Pharmacometrics Syst Pharmacol. 2023; Accepted on 10th Nov. read more
- Igor Makarenko, Aleksandr Petrov, Bella Belova, Valeria Saparova, Anna Arefeva, Kirill Peskov, Nataliya Kudryashova, Alexandr Khokhlov, Roman Drai. Population Pharmacokinetic and Pharmacodynamic Modeling of Romiplostim Biosimilar GP40141 and Reference Product in Healthy Volunteers to Evaluate Biosimilarity. Clin Pharmacol Drug Dev. 2024 Apr;13(4):419-431. read more
- 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. read more
- Sokolov V, Yakovleva T, Penland RC, Boulton DW and Tang W (2023) Effectiveness of dapagliflozin as an insulin adjunct in type 1 diabetes: a semi-mechanistic exposure-response model. Front. Pharmacol. 14:1229255. doi: 10.3389/fphar.2023.1229255 Read more
2022
- 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. Read more
- 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. Read more
- Victor Sokolov, Algorithms and methodological challenges in the development and application of quantitative systems pharmacology models: a case study in type 2 diabetes. Read more
- Ivan Azarov, Gabriel Helmlinger, Yuri Kosinsky, Kirill Peskov.Elaborating on anti CTLA-4 mechanisms of action using an agent-based modeling approach. Read more
- 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. Read more
- 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. Read more
- 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. Read more
- 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. Epub 2021 Sep 28. PMID: 34309049; PMCID: PMC9292875.
- Chan, P., Peskov, K. & Song, X. Applications of Model-Based Meta-Analysis in Drug Development. Pharm Res (2022). Read more
- 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
- 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
2021
- 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 | Read more
- Leon, C. (2021). Reaction–Diffusion Model of Coexistence of Viruses in the Space of Genotypes. Smart Modelling For Engineering Systems, 265–276. Read more
- Shah,L. Stolbov, T. Yakovleva, W. Tang, V. Sokolov, R.C. Penland, D. Boulton, J. Parkinson, A model‐based approach to investigating the relationship between glucose‐insulin dynamics and dapagliflozin treatment effect in patients with type 2 diabetes, Diabetes Obesity and Metabolism, 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. Read more
2020
- 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 | Read more
- 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. Read more
- Boris Shulgin , Yuri Kosinsky, Andrey Omelchenko, Lulu Chu, Ganesh Mugundu, Sergey Aksenov, Rodrigo Pimentel, Garrett DeYulia, Geoffrey Kim, Kirill Peskov & Gabriel Helmlinger (2020) Dose dependence of treatment-related adverse events for immune checkpoint inhibitor therapies: a model-based meta-analysis, OncoImmunology, 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. Read more
- Goltsov, A.; Swat, M.; Peskov, K.; Kosinsky, Y. Cycle Network Model of Prostaglandin H Synthase-1. Pharmaceuticals 2020, 13, 265
- 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| Read more
- 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.
- 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
- 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
2019
- 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.org/10.1016/j.foodhyd.2018.11.011. 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
- 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.org/10.3389/fphar.2019.00913. Read more
- 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.org/10.1038/s41431-018-0291-3. Read more
- 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.org/10.1016/j.bmcl.2019.01.040. Read more
- 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.org/10.1007/s11030-019-09946-3. Read more
- 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.org/10.2174/1386207322666190412165316. Read more
- 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.org/10.2174/1570163816666190603095521. Read more
- 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.org/10.1007/s11094-019-01984-3. Read more
- 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.org/10.2174/1386207322666190723110539. Read more
- 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.org/10.1038/s41429-019-0211-y. Read more
- 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.org/10.2174/2211352517666181218155259. 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
- 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 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.
- 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. Read more
- 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. Read more
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
- 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.
- 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
2009
- 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.
- 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. (2009) Thermodynamic characteristization of di-, tri, and tetranucleotide microsatellite loci in D. unisexualis. Russian Journal of Genetics, 45(8), 1004 – 1008.
- 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
- 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
- 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
- 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
2008
- Shulgin, B., Stone, L., & Agur., Z (1998) Pulse vaccination strategy in the SIR epidemic model. Bulletin of Mathematical Biology, 60(6), 1123—1148. Pubmed
- 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
- 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. (2006) Uncovering the design principles of circadian clocks: mathematical analysis of flexibility and evolutionary goals. Journal of theoretical biology, 238(3), 616—635. Pubmed
- 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
- 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]
- 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
- Peskov, K., Goryanin, I., & Demin, O. (2008) Kinetic Model of Phosphofructokinase-1 from Escherichia coli. J Bioinform Comput Biol, 6(4), 843 – 67. Pubmed
