Shared documents for downloading may be helpful for those who are interested in ISB research.
Journal articles
2017
Karelina T., Demin O., Nicholas T., Lu Y., Duvvuri S., Barton HA. A translational systems pharmacology model for Aβ kinetics in mouse, monkey, and human. CPT: Pharmacometrics & Systems Pharmacology. 2017. doi: 10.1002/psp4.122116, PubMed, DOI.
Shalgunov V, Zaytseva-Zotova D, Zinchenko A, Levada T, Shilov Y, Andreyev D, Dzhumashev D, Metelkin E, Urusova A, Demin O, McDonnell K, Troiano G, Zale S, Safarovа E. Comprehensive study of the drug delivery properties of poly(l-lactide)-poly(ethylene glycol) nanoparticles in rats and tumor-bearing mice. J Control Release. S0168-3659(17)30646-6, PubMed, DOI.
2016
Karelina T., Voronova V., Demin O., Colice G., Agoram BM. A Mathematical Modeling Approach to Understanding the Effect of Anti-Interleukin Therapy on Eosinophils. CPT: Pharmacometrics & Systems Pharmacology. 2016. v.5(6), p.608-616, PubMed, DOI.
Noren DP., Long BL., Norel R., Rrhissorrakrai K., Hess K., Hu CW., Bisberg AJ., Schultz A., Engquist E., Liu L., Lin X., Chen GM., Xie H., Hunter GAM., Boutros PC., Stepanov O. A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. PLOS Computational Bioology. 2016. v.12(6), e1004890, PubMed, DOI.
2015
Vinogradova S., Zhudenkov K., Benson N., Van Der Graaf P., Demin O., Karelina T. 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. Journal of theoretical biology. 2015. v.382, p.91-98, PubMed, DOI, download.
Kolobkov D., Demin O., Metelkin E. Comparison of Asymptotic Confidence Sets for Regression in Small Samples. J Biopharm Stat. 2015 Jun 22. (Epub ahead of print), PubMed, DOI, download.
2014
Demin Jr O, Yakovleva T, Kolobkov D and Demin O. Analysis of efficacy of SGLT2 inhibitors using semi-mechanistic model. 2014 Front. Pharmacol. 5, 218, PubMed, DOI
Benson N, Metelkin E, Demin O, Li GL, Nichols D, van der Graaf PH. A systems pharmacology perspective on the clinical development of Fatty Acid amide hydrolase inhibitors for pain. 2014 CPT Pharmacometrics Syst Pharmacol. 3, e91, PubMed, DOI
2013
Smirnov S., Metelkin E., Gizzatkulov N., Stepanov O., Demin O. "Towards Modeling of Metabolic Syndrome: Tissue Crosstalk in Lipid Spillover" in "A Systems Biology Approach to Study Metabolic Syndrome" Springer 2014 p.341, DOI.
Demin O, Karelina T, Svetlichniy D, Metelkin E, Speshilov G, Demin O Jr, Fairman D, van der Graaf PH, Agoram BM. Systems pharmacology models can be used to understand complex pharmacokinetic-pharmacodynamic behavior: an example using 5-lipoxygenase inhibitors. 2013 CPT Pharmacometrics Syst Pharmacol. 2, e74. PubMed, DOI.
Benson N., Matsuura T., Smirnov S., Demin O., Jones HM., Dua P., van der Graaf PH. Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets using sensitivity analysis and the integration of physiology and pharmacology. 2013 Interface Focus 3: 20120071. DOI .
Demin OO, Smirnov SV, Sokolov VV, Cucurull-Sanchez L, Pichardo-Almarza C, Flores MV, Benson N, Demin OV. Modeling of celiac disease immune response and the therapeutic effect of potential drugs. 2013 BMC Syst Biol. 56. PubMed, DOI.
2012
Karelina TA, Zhudenkov KV, Demin OO, Svetlichny DV, Agoram B, Fairman D, Demin OV. Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach. BMC Syst Biol. 2012 Nov 12;6(1):141. PubMed.
Peskov K, Mogilevskaya E, Demin O. Kinetic modelling of central carbon metabolism in Escherichia?coli. FEBS J. 2012 Sep;279(18):3374-85. PubMed.
Benson N, Cucurull-Sanchez L, Demin O, Smirnov S, van der Graaf P. Reducing systems biology to practice in pharmaceutical company research; selected case studies. Adv Exp Med Biol. 2012;736:607-15. PubMed.
Nicholas, T., Barton, H., Lu, Y., Duvvuri, S., Karelina, T., Demin, O., Zhudenkov K., Sergey Belykh, Demin, O, Jr. Beta-amyloid aggregation human systems pharmacology modeling: Development and application to pharmacological targets in Alzheimer's disease. Alzheimer's & Dementia. 2012; 8(4), P192-P193. DOI.
2011
Agoram BM, Demin O. Integration not isolation: arguing the case for quantitative and systems pharmacology in drug discovery and development. Drug Discov Today. 2011 Dec;16(23-24):1031-6. PubMed.
T. A. Karelina, H. Ma, I. Goryanin, and O. V. Demin. EI of the Phosphotransferase System of Escherichia coli: Mathematical Modeling Approach to Analysis of Its Kinetic Properties. J Biophys. 2011;2011:579402. PubMed, Download.
Chinopoulos C, Konrad C, Kiss G, et al. Modulation of F(0) F(1) -ATP synthase activity by cyclophilin D regulates matrix adenine nucleotide levels. The FEBS journal. 2011. 278(7): 1112-1125. PubMed, Download.
2010
Nail M Gizzatkulov, Igor I Goryanin, Eugeny A Metelkin, Ekaterina A Mogilevskaya, Kirill V Peskov and Oleg V Demin. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Systems Biology, 2010, 4 (109): 1-11. PubMed, Download.
Peskov K., Demin O., (on Russian) Кинетическая модель фосфофруктокиназы-2 из клеток Escherichia coli. Вопросы биологической, медицинской и фармацевтической химии. (2010) №5, 11-22.
2009
Metelkin EA, Lebedeva GV, Gorianin II, Demin OV. [A kinetic model of beta-galactosidase of Escherichia coli]. Biofizika. 2009; 54(2):226-34. PubMed, Download. (RU) Метелкин Е, Лебедева Г, Горянин И, Демин О. Кинетическая модель beta-галактозидазы Escherichia coli. Биофизика. 2009; 54(2).
Mogilevskaya E, Bagrova N, Plyusnina T, et al. Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods in molecular biology (Clifton, N.J.). 2009; 563:197-218. PubMed, Download.
Metelkin E, Demin O, Kovacs Z, Chinopoulos C. Modeling of ATP-ADP steady-state exchange rate mediated by the adenine nucleotide translocase in isolated mitochondria. The FEBS journal. 2009; 276(23):6942-55. PubMed, Download.
Goltsov A, Maryashkin A, Swat M, Kosinsky Y, Humphery-Smith I, Demin O, Goryanin I, Lebedeva G. Kinetic modelling of NSAID action on COX-1: focus on in vitro/in vivo aspects and drug combinations. Eur J Pharm Sci. 2009;36(1):122-136. PubMed.
Smirnov S, Belashov A, Demin O. Optimization of antimicrobial drug gramicidin S dosing regime using biosimulations. Eur J Pharm Sci. 2009;36(1):105-109. PubMed.
etc
Metelkin E, Goryanin I, Demin OV. Mathematical modeling of mitochondrial adenine nucleotide translocase. Biophysical journal. 2006; 90(2):423-32. PubMed, Download.
Goryanin II, Lebedeva GV, Mogilevskaya EA, Metelkin EA, Demin OV. Cellular kinetic modeling of the microbial metabolism. Methods of biochemical analysis. 2006; 49:437-88. PubMed.
Demin OV, Goryanin II, Dronov S, Lebedeva GV. Kinetic model of imidazologlycerol-phosphate synthetase from Escherichia coli. Biochemistry (Mosc). 2004; 69(12):1324-1335. PubMed.
Peskov K, Goryanin I, Prank K, Tobin F, Demin O. Kinetic modeling of ace operon genetic regulation in Escherichia coli. J Bioinform Comput Biol. 2008, 5:933-959. PubMed.
Peskov K, Goryanin I, Demin O. Kinetic model of phosphofructokinase-1 from Escherichia coli. J Bioinform Comput Biol. 2008, 4:843-67. PubMed.
Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I. The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol. 2007;3:135. PubMed.
Mogilevskaia EA, Lebedeva GV, Gorianin II, Demin OV. A kinetic model of functioning and regulation of Escherichia coli isocitrate dehydrogenase. Biofizika. 2007;52(1):30-39. Springer.
Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN. Signal processing at the Ras circuit: what shapes Ras activation patterns? Syst Biol (Stevenage). 2004;1(1):104-113. PubMed, Download.
Mogilevskaya E, Demin O, Goryanin I. Kinetic model of mitochondrial Krebs cycle: unraveling the mechanism of salicylate hepatotoxic effects. J Biol Phys. 2006;32(3-4):245-271. PubMed.
Goryanin II, Lebedeva GV, Mogilevskaya EA, Metelkin EA, Demin OV. Cellular kinetic modeling of the microbial metabolism. Methods Biochem Anal. 2006;49:437-488. PubMed, No PDF
Noble M, Sinha Y, Kolupaev A, Demin O, Earnshaw D, Tobin F, West J, Martin JD, Qiu C, Liu WS, DeWolf WE Jr, Tew D, Goryanin II. The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening. Biotechnol Bioeng. 2006;95(4):560-573. PubMed.
Sorokin, A.; Paliy, K.; Selkov, A.; Demin, O. V.; Dronov, S.; Ghazal, P.; Goryanin, I. The Pathway Editor: A tool for managing complex biological networks. 2006; 50(6): 561 - 573. DOI.
Mogilevskaja E., Lebedeva G., Demin O. (on Russian) Кинетическая модель функционирования 2-кетоглутаратдегидрогеназы Escherichia coli. 2006; 7:442 - 449. Medline.
Mogilevskaja E., Demin O. (on Russian) Исследование влияния салицилата на цикл Кребса митохондрии с помощью кинетической модели. Труды VII международной конференции «Идентификация систем и задачи управления». Институт проблем управления им. В.А.Трапезникова РАН. (2008) с. 1235-1245.
