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KOLODKIN Alexey

University of Luxembourg

Main Referenced Co-authors
BALLING, Rudolf  (16)
Westerhoff, Hans V. (11)
SIMEONIDIS, Vangelis  (10)
IGNATENKO, Andrew  (9)
PETERS, Bernhard  (9)
Main Referenced Keywords
systems biology (6); nuclear receptors (5); Emergence (2); kinetic modelling (2); Parkinson’s disease (2);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) (10)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (2)
Luxembourg Centre for Systems Biomedicine (1)
Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) (1)
Luxembourg Centre for Systems Biomedicine (LCSB): Chemical Biology (Crawford Group) (1)
Main Referenced Disciplines
Biochemistry, biophysics & molecular biology (15)
Life sciences: Multidisciplinary, general & others (13)
Human health sciences: Multidisciplinary, general & others (2)
Computer science (1)
Neurology (1)

Publications (total 32)

The most downloaded
4382 downloads
Ballereau, S., Glaab, E., Kolodkin, A., Chaiboonchoe, A., Biryukov, M., Vlassis, N., Ahmed, H., Pellet, J., Baliga, N., Hood, L., Schneider, R., Balling, R., & Auffray, C. (2013). Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology. In A. Prokop & B. Csukás (Eds.), Systems Biology: Integrative Biology and Simulation Tools. Springer. doi:10.1007/978-94-007-6803-1_1 https://hdl.handle.net/10993/1247

The most cited

67 citations (Scopus®)

Westerhoff, H. V., Kolodkin, A., Conradie, R., Wilkinson, S. J., Bruggeman, F. J., Krab, K., van Schuppen, J. H., Hardin, H., Bakker, B. M., Mone, M. J., Rybakova, K. N., Eijken, M., van Leeuwen, H. J. P., & Snoep, J. L. (2009). Systems biology towards life in silico: mathematics of the control of living cells. Journal of Mathematical Biology, 58 (1-2), 7-34. doi:10.1007/s00285-008-0160-8 https://hdl.handle.net/10993/1594

Sosero, Y. L., Bandres-Ciga, S., Ferwerda, B., Tocino, M. T. P., Belloso, D. R., Gómez-Garre, P., Faouzi, J., Taba, P., PAVELKA, L., Marques, T. M., GOMES, C., KOLODKIN, A., MAY, P., Milanowski, L. M., Wszolek, Z. K., Uitti, R. J., Heutink, P., van Hilten, J. J., Simon, D. K., ... Gan-Or, Z. (2023). Dopamine pathway and Parkinson's risk variants are associated with levodopa-induced dyskinesia. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/57440. doi:10.1101/2023.08.28.23294610

Kolodkin, A., Colangelo, A., Ignatenko, A., Martorana, F., Jennen, D., Briedé, J., Brady, N., Barberis, M., Mondeel, T., Papa, M., Kumar, V., Peters, B., Skupin, A., Alberghina, L., Balling, R., & Westerhoff, H. (2020). ROS networks: designs, aging, Parkinson's disease and precision therapies. NPJ Systems Biology and Applications. doi:10.1038/s41540-020-00150-w
Peer Reviewed verified by ORBi

Westerhoff, H., & Kolodkin, A. (12 June 2020). Advice from a systems-biology model of the corona epidemics. NPJ Systems Biology and Applications, 6 (18). doi:10.1038/s41540-020-0138-8
Peer Reviewed verified by ORBi

Sharma, R. P., Kumar, V., Schuhmacher, M., Kolodkin, A., & Westerhoff, H. V. (2020). Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans. Environmental Research Journal. doi:10.1016/j.envres.2019.108948
Peer reviewed

Sharma, R. P., Kumar, V., Schuhmacher, M., Kolodkin, A., & Westerhoff, H. V. (2020). Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans. Environmental Research, 182, 108948. doi:10.1016/j.envres.2019.108948
Peer Reviewed verified by ORBi

Kolodkin, A. (2016). Systems Biology through the Concept of Emergence. In S. Green, Philosophy of Systems Biology: Perspectives from Scientists and Philosophers (History, Philosophy and Theory of the Life Sciences) (1st, pp. 175-189). Springer Nature.
Peer reviewed

Kolodkin, A., Ignatenko, A., Sangar, V., Simeonidis, V., Peters, B., Westerhoff, H., Skupin, A., Yilmaz, N., Barberis, M., Mondeel, T., Price, N., Brady, N., & Balling, R. (December 2014). ROS homeostasis in a dynamic model: How to save PD neuron? [Poster presentation]. Benelux Bioinformatics conference, Luxembourg, Luxembourg.

Kolodkin, A., Ignatenko, A., Sangar, V., Simeonidis, V., Glaab, E., Peters, B., Brady, N., Price, N., & Balling, R. (October 2014). ROS-management in Parkinson’s disease: Dynamic blue-print domino-based model and design principles study. Dynamic modelling of ROS management and ROS-induced mitophagy [Poster presentation]. GFG Neurogenetics Conference & PD Symposium, Munsbach, Luxembourg.

Kolodkin, A., Ignatenko, A., Peters, B., Matteo, B., & Hans, W. (September 2014). Mechanism-based model of ROS management in health and disease [Poster presentation]. Systems Biology-Systems Medicine School, Como, Italy.

Westerhoff, H. V.* , Brooks, A.* , Simeonidis, V.* , García-Contreras, R.* , He, F., Boogerd, F. C., Jackson, V. J., Goncharuk, V., & Kolodkin, A. (2014). Macromolecular networks and intelligence in microorganisms. Frontiers in Microbiology. doi:10.3389/fmicb.2014.00379
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

Ignatenko, A., Kolodkin, A., Peters, B., & Balling, R. (2014). Comparison of ODE-based models for reactive oxygen species regulation system. Proceedings of ICCSA 2014, 199-203.
Peer reviewed

Kolodkin, A., Ignatenko, A., Sangar, V., Simeonidis, V., Peters, B., Sahin, N., Price, N., Brady, N., Balling, R., & Westerhoff, H. (June 2014). ROS-activated signaling network: dynamic modelling and design principles study [Poster presentation]. Interdisciplinary Signalling Workshop, Vizegrad, Hungary.

Kolodkin, A., Ignatenko, A., Sangar, V., Glaab, E., Peters, B., Price, N., Brady, N., & Balling, R. (June 2014). Dynamic modelling of ROS management and ROS-induced mitophagy [Poster presentation]. Gordon workshop on Cell Death Mechanisms, West Dover, United States.

Kolodkin, A., Ignatenko, A., Sangar, V., Simeonidis, V., Peters, B., Brady, N., Price, N., & Balling, R. (27 September 2013). Design principles study of ROS management and ROS-induced mitophagy with a kinetic model [Poster presentation]. 2013 BMES Annual Meeting, Seattle, United States.

Simeonidis, V., Kolodkin, A., Ignatenko, A., Sangar, V., Balling, R., & Brady, N. (22 July 2013). Modeling cellular ROS defense in mitochondrial-related diseases [Poster presentation]. 21st Annual International Conference on Intelligent Systemsfor Molecular Biology and 12th European Conference on Computational Biology, Berlin, Germany.

Kolodkin, A., Ignatenko, A., Simeonidis, V., Sangar, V., Choe, C., Peters, B., Price, N., Balling, R., & Brady, N. (May 2013). ROS-induced regulation of mitophagy and its failure in Parkinson’s disease [Poster presentation]. Mitochondria: from Signaling to Disease, Lisbon, Portugal.

Kolodkin, A.* , Sahin, N.* , Phillips, A., Hood, S. R., Bruggeman, F. J., Westerhoff, H. V., & Plant, N. (30 April 2013). Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications, 4. doi:10.1038/ncomms2799
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

Ostaszewski, M., Fujita, K., Matsuoka, Y., Ghosh, S., Glaab, E., Trefois, C., Crespo, I., Perumal, T. M., Jurkowski, W., Antony, P., Diederich, N., Buttini, M., Kolodkin, A., Kodama, A., Satagopam, V., Biryukov, M., Eifes, S., del Sol Mesa, A., Schneider, R., ... Balling, R. (09 March 2013). The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways [Poster presentation]. The 11th International Conference on Alzheimer's & Parkinson's Diseases, Florence, Italy.

Chaiboonchoe, A., Jurkowski, W., Pellet, J., Glaab, E., Kolodkin, A., Raussel, A., Le Béchec, A., Ballereau, S., Meyniel, L., Crespo, I., Ahmed, H., Volpert, V., Lotteau, V., Baliga, N., Hood, L., Sol, A. D., Balling, R., & Auffray, C. (2013). On different aspects of network analysis in systems biology. Systems Biology, 1, 181-207. doi:10.1007/978-94-007-6803-1_6
Peer reviewed

Ballereau, S., Glaab, E., Kolodkin, A., Chaiboonchoe, A., Biryukov, M., Vlassis, N., Ahmed, H., Pellet, J., Baliga, N., Hood, L., Schneider, R., Balling, R., & Auffray, C. (2013). Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology. In A. Prokop & B. Csukás (Eds.), Systems Biology: Integrative Biology and Simulation Tools. Springer. doi:10.1007/978-94-007-6803-1_1
Peer reviewed

Chaiboonchoe, A., Jurkowski, W., Pellet, J., Glaab, E., Kolodkin, A., Raussel, A., Le Béchec, A., Meyniel, L., Ballereau, S., Crespo, I., Ahmed, H., Volpert, V., Lotteau, V., Baliga, N., Hood, L., del Sol, A., Balling, R., & Auffray, C. (2013). Network analysis for systems biology. In A. Prokop & Csukás (Eds.), Springer book in Systems Biology, Vol.1: Systems Biology:, Integrative Biology and Simulation Tools (Springer book in Systems Biology, Vol.1). Springer. doi:10.1007/978-94-007-6803-1
Peer reviewed

Kolodkin, A., Simeonidis, E., & Westerhoff, H. V. (October 2012). Computing life: Add logos to biology and bios to physics. Progress in Biophysics and Molecular Biology, 111 (2-3), 69-74. doi:10.1016/j.pbiomolbio.2012.10.003
Peer Reviewed verified by ORBi

Kolodkin, A., Simeonidis, V., Brady, N., & Balling, R. (August 2012). A kinetic model and design principles study of cellular ROS defence and its failure in Parkinson’s disease [Poster presentation]. ICSB 2013 - 13th International Conference on Systems Biology, Toronto, Canada.

Kolodkin, A., Simeonidis, E., Balling, R., & Westerhoff, H. V. (2012). Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. Frontiers in Physiology, 3, 291. doi:10.3389/fphys.2012.00291
Peer Reviewed verified by ORBi

Kolodkin, A., Boogerda, F. C., Plantb, N., Bruggemana, F. J., Goncharuke, V., Lunshofa, J., Moreno-Sanchezi, R., Yilmaza, N., Bakkerk, B. M., Snoepa, J. L., Balling, R., & Westerhoff, H. V. (2012). Emergence of the silicon human and network targeting drugs. European Journal of Pharmaceutical Sciences, 46 (4), 190-197. doi:10.1016/j.ejps.2011.06.006
Peer reviewed

Kouril, T., Kolodkin, A., Zaparty, M., Steuer, R., Ruoff, P., Westerhoff, H. V., Snoep, J., & Siebers, B. (2012). Sulfolobus Systems Biology: Cool hot design for metabolic pathways. In Systems Biology of Microorganisms. Norwich, UK, Horizon Scientific Press and Caister Academic Press.
Peer reviewed

Yilmaz, N., Kolodkin, A., Plant, N., & Westerhoff, H. (2012). Low stress weekends promote adaptation to stressful weeks: The design principles of the biological response to stress [Poster presentation]. 15th ECB.

Kolodkin, A., Bruggeman, F. J., Plant, N., Mone, M. J., Bakker, B. M., Campbell, M. J., van Leeuwen, J. P. T. M., Carlberg, C., Snoep, J. L., & Westerhoff, H. V. (2011). Design principles of nuclear receptor signalling: How complex networking improves signal transduction. Toxicology, 290 (2-3), 131-132. doi:10.1016/j.tox.2011.09.055
Peer Reviewed verified by ORBi

Kolodkin, A., Phillips, A., Hood, S., Bruggeman, F. J., Westerhoff, H. V., & Plant, N. (2011). A systems biology approach towards understanding nuclear receptor interactions: Implications at the endocrine-xenobiotic signalling interface. Toxicology, 290 (2-3), 131-131. doi:10.1016/j.tox.2011.09.054
Peer Reviewed verified by ORBi

Kolodkin, A., Phillips, A., Hood, S. R., Westerhoff, H. V., Bruggeman, F., & Plant, N. J. (2010). Nuclear receptors as controlling factors in chemical metabolism: Determination of regulatory signal network crucial for co-ordinating cellular response to chemicals. Drug Metabolism Reviews, 42 (1), 279-280.
Peer Reviewed verified by ORBi

Kolodkin, A., Bruggeman, F. J., Plant, N., Mone, M. J., Bakker, B. M., Campbell, M. J., van Leeuwen, J. P. T. M., Carlberg, C., Snoep, J. L., & Westerhoff, H. V. (2010). Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Molecular Systems Biology, 6, 446. doi:10.1038/msb.2010.102
Peer Reviewed verified by ORBi

Westerhoff, H. V., Kolodkin, A., Conradie, R., Wilkinson, S. J., Bruggeman, F. J., Krab, K., van Schuppen, J. H., Hardin, H., Bakker, B. M., Mone, M. J., Rybakova, K. N., Eijken, M., van Leeuwen, H. J. P., & Snoep, J. L. (2009). Systems biology towards life in silico: mathematics of the control of living cells. Journal of Mathematical Biology, 58 (1-2), 7-34. doi:10.1007/s00285-008-0160-8
Peer reviewed

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