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Alexey Kolodkin

Alexey Kolodkin

Research (and development) specialist

Faculty or Centre Luxembourg Centre for Systems Biomedicine
Department Bioinformatics Core
Postal Address Université du Luxembourg
6, avenue du Swing
L-4367 Belvaux
Campus Office BioTech II Ketterthill, 4.11
Email
Telephone (+352) 46 66 44 6185
Fax (+352) 46 66 44 36185

Researcher in the Bioinformatics Core group (Schneider Lab).

Last updated on: Tuesday, 12 November 2019

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2020

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See detailDevelopment and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans.
Sharma, Raju Prasad; Kumar, Vikas; Schuhmacher, Marta; Kolodkin, Alexey; Westerhoff, Hans V.

in Environmental research (2020), 182

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See detailDevelopment and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans
Sharma, Raju Prasad; Kumar, Vikas; Schuhmacher, Marta; Kolodkin, Alexey; Westerhoff, Hans Victor

in Environmental Research Journal (2020)

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See detailAdvice from a systems-biology model of the corona epidemics
Westerhoff, Hans; Kolodkin, Alexey

in NPJ Systems Biology and Applications (2020), 6(18),

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2016

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See detailSystems Biology through the Concept of Emergence
Kolodkin, Alexey

in Green, Sarah (Ed.) Philosophy of Systems Biology: Perspectives from Scientists and Philosophers (History, Philosophy and Theory of the Life Sciences) (2016)

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2014

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See detailComparison of ODE-based models for reactive oxygen species regulation system
Ignatenko, Andrew; Kolodkin, Alexey; Peters, Bernhard; Balling, Rudi

in Proceedings of ICCSA 2014 (2014, June)

See detailMechanism-based model of ROS management in health and disease
Kolodkin, Alexey; Ignatenko, Andrew; Peters, Bernhard; Matteo, Barberis; Hans, Westerhoff

Poster (2014, September)

See detailDynamic modelling of ROS management and ROS-induced mitophagy
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Glaab, Enrico; Peters, Bernhard; Price, Nathan; Brady, Nathan; Balling, Rudi

Poster (2014, June)

See detailROS-management in Parkinson’s disease: Dynamic blue-print domino-based model and design principles study. Dynamic modelling of ROS management and ROS-induced mitophagy
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Simeonidis, Vangelis; Glaab, Enrico; Peters, Bernhard; Brady, Nathan; Price, Nathan; Balling, Rudi

Poster (2014, October)

See detailROS-activated signaling network: dynamic modelling and design principles study
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Simeonidis, Vangelis; Peters, Bernhard; Sahin, Nilgun; Price, Nathan; Brady, Nathan; Balling, Rudi; Westerhoff, Hans

Poster (2014, June)

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See detailROS homeostasis in a dynamic model: How to save PD neuron?
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Simeonidis, Vangelis; Peters, Bernhard; Westerhoff, Hans; Skupin, Alexander; Yilmaz, Nilgun; Barberis, Matteo; Mondeel, Thierry; Price, Nathan; Brady, Nathan; Balling, Rudi

Poster (2014, December)

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See detailMacromolecular networks and intelligence in microorganisms
Westerhoff, Hans V.; Brooks, Aaron; Simeonidis, Vangelis; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

in Frontiers in Microbiology (2014)

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2013

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See detailFunctional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology
Ballereau, S.; Glaab, Enrico; Kolodkin, Alexey; Chaiboonchoe, A.; Biryukov, Maria; Vlassis, Nikos; Ahmed, H.; Pellet, J.; Baliga, N.; Hood, Leroy; Schneider, Reinhard; Balling, Rudi; Auffray, C.

in Prokop, Ales; Csukás, Bela (Eds.) Systems Biology: Integrative Biology and Simulation Tools (2013)

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See detailNetwork analysis for systems biology
Chaiboonchoe, A.; Jurkowski, Wiktor; Pellet, J.; Glaab, Enrico; Kolodkin, Alexey; Raussel, Antonio; Le Béchec, Antony; Meyniel, L.; Ballereau, S.; Crespo, Isaac; Ahmed, H.; Volpert, V.; Lotteau, V.; Baliga, N.; Hood, Leroy; del Sol, A.; Balling, Rudi; Auffray, C.

in Prokop, Aleš; Csukás (Eds.) Springer book in Systems Biology, Vol.1: Systems Biology:, Integrative Biology and Simulation Tools (2013)

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See detailOn different aspects of network analysis in systems biology
Chaiboonchoe, Amphun; Jurkowski, Wiktor; Pellet, Johann; Glaab, Enrico; Kolodkin, Alexey; Raussel, Antonio; Le Béchec, Antony; Ballereau, Stéphane; Meyniel, Laurene; Crespo, Isaac; Ahmed, Hassan; Volpert, Vitaly; Lotteau, Vincent; Baliga, Nitin; Hood, Leroy; Sol, Antonio del; Balling, Rudi; Auffray, Charles

in Systems Biology (2013), 1

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See detailDesign principles study of ROS management and ROS-induced mitophagy with a kinetic model
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Simeonidis, Vangelis; Peters, Bernhard; Brady, Nathan; Price, Nathan; Balling, Rudi

Poster (2013, September 27)

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See detailROS-induced regulation of mitophagy and its failure in Parkinson’s disease
Kolodkin, Alexey; Ignatenko, Andrew; Simeonidis, Vangelis; Sangar, Vineet; Choe, Charley; Peters, Bernhard; Price, Nathan; Balling, Rudi; Brady, Nathan

Poster (2013, May)

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See detailOptimization of stress response through the nuclear receptor-mediated cortisol signalling network
Kolodkin, Alexey; Sahin, Nilgun; Phillips, Anna; Hood, Steve R.; Bruggeman, Frank J.; Westerhoff, Hans V.; Plant, Nick

in Nature Communications (2013), 4

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See detailThe Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways
Ostaszewski, Marek; Fujita, Kazuhiro; Matsuoka, Yukiko; Ghosh, Samik; Glaab, Enrico; Trefois, Christophe; Crespo, Isaac; Perumal, Thanneer Malai; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kolodkin, Alexey; Kodama, Akihiko; Satagopam, Venkata; Biryukov, Maria; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

Poster (2013, March 09)

See detailModeling cellular ROS defense in mitochondrial-related diseases
Simeonidis, Vangelis; Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Balling, Rudi; Brady, Nathan

Poster (2013, July 22)

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2012

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See detailEmergence of the silicon human and network targeting drugs
Kolodkin, Alexey; Boogerda, Fred C.; Plantb, Nick; Bruggemana, Frank J.; Goncharuke, Valeri; Lunshofa, Jeantine; Moreno-Sanchezi, Rafael; Yilmaza, Nilgun; Bakkerk, Barbara M.; Snoepa, Jacky L.; Balling, Rudi; Westerhoff, Hans V.

in European Journal of Pharmaceutical Sciences (2012), 46(4), 190-197

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See detailUnderstanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.
Kolodkin, Alexey; Simeonidis, Evangelos; Balling, Rudi; Westerhoff, Hans V.

in Frontiers in Physiology (2012), 3

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See detailComputing life: Add logos to biology and bios to physics
Kolodkin, Alexey; Simeonidis, Evangelos; Westerhoff, Hans V.

in Progress in Biophysics & Molecular Biology (2012), 111(2-3), 69-74

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See detailA kinetic model and design principles study of cellular ROS defence and its failure in Parkinson’s disease
Kolodkin, Alexey; Simeonidis, Vangelis; Brady, Nathan; Balling, Rudi

Poster (2012, August)

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See detailSulfolobus Systems Biology: Cool hot design for metabolic pathways
Kouril, T.; Kolodkin, Alexey; Zaparty, M.; Steuer, R.; Ruoff, P.; Westerhoff, H. V.; Snoep, J.; Siebers, B.

in Systems Biology of Microorganisms (2012)

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2011

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See detailDesign principles of nuclear receptor signalling: How complex networking improves signal transduction
Kolodkin, Alexey; Bruggeman, Frank J.; Plant, Nick; Mone, Martijn J.; Bakker, Barbara M.; Campbell, Moray J.; van Leeuwen, Johannes P. T. M.; Carlberg, Carsten; Snoep, Jacky L.; Westerhoff, Hans V.

in Toxicology (2011), 290(2-3), 131-132

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See detailA systems biology approach towards understanding nuclear receptor interactions: Implications at the endocrine-xenobiotic signalling interface
Kolodkin, Alexey; Phillips, Anna; Hood, Steve; Bruggeman, Frank J.; Westerhoff, Hans V.; Plant, Nick

in Toxicology (2011), 290(2-3), 131-131

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2010

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See detailDesign principles of nuclear receptor signaling: how complex networking improves signal transduction.
Kolodkin, Alexey; Bruggeman, Frank J.; Plant, Nick; Mone, Martijn J.; Bakker, Barbara M.; Campbell, Moray J.; van Leeuwen, Johannes P. T. M.; Carlberg, Carsten; Snoep, Jacky L.; Westerhoff, Hans V.

in Molecular Systems Biology (2010), 6

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See detailNuclear receptors as controlling factors in chemical metabolism: Determination of regulatory signal network crucial for co-ordinating cellular response to chemicals
Kolodkin, Alexey; Phillips, Anna; Hood, Steve R.; Westerhoff, Hans V.; Bruggeman, Frank; Plant, Nick J.

in Drug Metabolism Reviews (2010), 42(1), 279-280

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2009

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See detailSystems biology towards life in silico: mathematics of the control of living cells.
Westerhoff, Hans V.; Kolodkin, Alexey; Conradie, Riaan; Wilkinson, Stephen J.; Bruggeman, Frank J.; Krab, Klaas; van Schuppen, Jan H.; Hardin, Hanna; Bakker, Barbara M.; Mone, Martijn J.; Rybakova, Katja N.; Eijken, Marco; van Leeuwen, Hans J. P.; Snoep, Jacky L.

in Journal of Mathematical Biology (2009), 58(1-2), 7-34

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