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  1. Article › Research › Peer-reviewed

  2. A bird's-eye overview of molecular mechanisms regulating feed intake in chickens—with mammalian comparisons

    Volyanskaya, A. R., Akberdin, I. R., Kulyashov, M. A., Yevshin, I. S., Romanov, M. N., Shagimardanova, E. I., Gusev, O. A. & Kolpakov, F. A., 1 Jun 2024, In: Animal Nutrition. 17, p. 61-74

    Research output: Contribution to journal › Article › peer-review

  3. A genome-scale metabolic model of 2,3-butanediol production by thermophilic bacteria geobacillus icigianus

    Kulyashov, M., Peltek, S. E. & Akberdin, I. R., 1 Jul 2020, In: Microorganisms. 8, 7, p. 1-13 13 p., 1002.

    Research output: Contribution to journal › Article › peer-review

  4. A mathematical model linking Ca2+-dependent signaling pathway and gene expression regulation in Human Skeletal Muscle

    Akberdin, I. R., Vertyshev, A. Y., Pintus, S. S., Popov, D. V. & Kolpakov, F. A., 1 Jan 2020, In: Mathematical Biology and Bioinformatics. 15, 1, p. 20-39 20 p.

    Research output: Contribution to journal › Article › peer-review

  5. A modular mathematical model of exercise-induced changes in metabolism, signaling, and gene expression in human skeletal muscle

    Akberdin, I. R., Kiselev, I. N., Pintus, S. S., Sharipov, R. N., Vertyshev, A. Y., Vinogradova, O. L., Popov, D. V. & Kolpakov, F. A., 1 Oct 2021, In: International Journal of Molecular Sciences. 22, 19, 10353.

    Research output: Contribution to journal › Article › peer-review

  6. A modular visual model of energy metabolism in human skeletal muscle

    Kiselev, I. N., Akberdin, I. R., Vertyshev, A. Y., D.V., P. & Kolpakov, F. A., 1 Jan 2019, In: Mathematical Biology and Bioinformatics. 14, 2, p. 373-392 20 p.

    Research output: Contribution to journal › Article › peer-review

  7. BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

    Kolpakov, F., Akberdin, I., Kashapov, T., Kiselev, L., Kolmykov, S., Kondrakhin, Y., Kutumova, E., Mandrik, N., Pintus, S., Ryabova, A., Sharipov, R., Yevshin, I. & Kel, A., 1 Jul 2019, In: Nucleic Acids Research. 47, W1, p. W225-W233 9 p.

    Research output: Contribution to journal › Article › peer-review

  8. BioUML—towards a universal research platform

    Колпаков, Ф., Акбердин, И. Р., Киселев, И., Колмыков, С. К., Кондрахин, Ю., Куляшов, М. А., Кутумова, Е., Пинтус, С. С., Рябова, А., Шарипов, Р. Н., Евшин, И., Жатченко, С. & Кель, А., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W124-W131 8 p.

    Research output: Contribution to journal › Article › peer-review

  9. Delay-differential SEIR modeling for improved modelling of infection dynamics

    Киселев, И., Акбердин, И. Р. & Колпаков, Ф., 18 Aug 2023, In: Scientific Reports. 13, 1, 15 p., 13439.

    Research output: Contribution to journal › Article › peer-review

  10. Genome-wide atlas of promoter expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy of skeletal muscle

    Pintus, S. S., Akberdin, I. R., Yevshin, I., Makhnovskii, P., Tyapkina, O., Nigmetzyanov, I., Nurullin, L., Devyatiyarov, R., Shagimardanova, E., Popov, D., Kolpakov, F. A., Gusev, O. & Gazizova, G. R., Jun 2021, In: Biology. 10, 6, 557.

    Research output: Contribution to journal › Article › peer-review

  11. Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli

    Akberdin, I. R., Kozlov, K. N., Kazantsev, F. V., Fadeev, S. I., Likhoshvai, V. A. & Khlebodarova, T. M., 2 Mar 2023, In: International Journal of Molecular Sciences. 24, 5, 4806.

    Research output: Contribution to journal › Article › peer-review

  12. MAMMOTh: A new database for curated mathematical models of biomolecular systems

    Kazantsev, F., Akberdin, I., Lashin, S., Ree, N., Timonov, V., Ratushny, A., Khlebodarova, T. & Likhoshvai, V., 1 Feb 2018, In: Journal of Bioinformatics and Computational Biology. 16, 1, 16 p., 1740010.

    Research output: Contribution to journal › Article › peer-review

  13. Methane utilization in Methylomicrobium alcaliphilum 20ZR: A systems approach

    Akberdin, I. R., Thompson, M., Hamilton, R., Desai, N., Alexander, D., Henard, C. A., Guarnieri, M. T. & Kalyuzhnaya, M. G., 6 Feb 2018, In: Scientific Reports. 8, 1, p. 2512 13 p., 2512.

    Research output: Contribution to journal › Article › peer-review

  14. Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example

    Kutumova, E., Akberdin, I., Kiselev, I., Sharipov, R. & Kolpakov, F., 1 Apr 2022, In: Mathematics. 10, 7, 20 p., 1176.

    Research output: Contribution to journal › Article › peer-review

  15. Multicompartmental Mathematical Model of SARS-CoV-2 Distribution in Human Organs and Their Treatment

    Afonyushkin, V. N., Акбердин, И. Р., Kozlova, Y., Щукин, И. А., Mironova, T., Bobikova, A., Cherepushkina, V., Donchenko, N., Poletaeva, Y. E. & Колпаков, Ф., 1 Jun 2022, In: Mathematics. 10, 11, 1925.

    Research output: Contribution to journal › Article › peer-review

  16. Physiologically based pharmacokinetic model for predicting the biodistribution of albumin nanoparticles after induction and recovery from acute lung injury

    Акбердин, И. Р., 8 May 2024, In: Heliyon.

    Research output: Contribution to journal › Article › peer-review

  17. Pluripotency gene network dynamics: System views from parametric analysis

    Akberdin, I. R., Omelyanchuk, N. A., Fadeev, S. I., Leskova, N. E., Oschepkova, E. A., Kazantsev, F. V., Matushkin, Y. G., Afonnikov, D. A. & Kolchanov, N. A., 29 Mar 2018, In: PLoS ONE. 13, 3, p. e0194464 24 p., 0194464.

    Research output: Contribution to journal › Article › peer-review

  18. Rare Earth Elements alter redox balance in methylomicrobium alcaliphilum 20ZR

    Akberdin, I. R., Collins, D. A., Hamilton, R., Oshchepkov, D. Y., Shukla, A. K., Nicora, C. D., Nakayasu, E. S., Adkins, J. N. & Kalyuzhnaya, M. G., 27 Nov 2018, In: Frontiers in Microbiology. 9, NOV, p. 2735 12 p., 2735.

    Research output: Contribution to journal › Article › peer-review

  19. The phylogeny of class b flavoprotein monooxygenases and the origin of the yucca protein family

    Turnaev, I. I., Gunbin, K. V., Suslov, V. V., Akberdin, I. R., Kolchanov, N. A. & Afonnikov, D. A., 1 Sept 2020, In: Plants. 9, 9, p. 1-22 22 p., 1092.

    Research output: Contribution to journal › Article › peer-review

  20. Comment/debate › Research › Peer-reviewed

  21. Correction: Methane utilization in Methylomicrobium alcaliphilum 20ZR: A systems approach (Scientific Reports (2017) DOI: 10.1038/s41598-018-20574-z): a systems approach (vol 8, 2017)

    Akberdin, I. R., Thompson, M., Hamilton, R., Desai, N., Alexander, D., Henard, C. A., Guarnieri, M. T. & Kalyuzhnaya, M. G., 14 Mar 2018, In: Scientific Reports. 8, 1, p. 4753 1 p., 4753.

    Research output: Contribution to journal › Comment/debate › peer-review

  22. Review article › Research › Peer-reviewed

  23. Numerous Trigger-like Interactions of Kinases/Protein Phosphatases in Human Skeletal Muscles Can Underlie Transient Processes in Activation of Signaling Pathways during Exercise

    Vertyshev, A. Y., Akberdin, I. R. & Kolpakov, F. A., 7 Jul 2023, In: International Journal of Molecular Sciences. 24, 13, 11223.

    Research output: Contribution to journal › Review article › peer-review

  24. Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools

    Кутумова, Е. О., Акбердин, И. Р., Киселев, И. Н., Шарипов, Р. Н., Егорова, В. С., Сырочева, А. О., Parodi, A., Замятнин, А. А. & Колпаков, Ф. А., 19 Oct 2022, In: International Journal of Molecular Sciences. 23, 20, 22 p., 12560.

    Research output: Contribution to journal › Review article › peer-review

  25. State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs

    Куляшов, М. А., Колмыков, С. К., Хлебодарова, Т. М. & Акбердин, И. Р., 14 Dec 2023, In: Microorganisms. 11, 12, 22 p., 2987.

    Research output: Contribution to journal › Review article › peer-review

ID: 3432692