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SIMEONIDIS Vangelis

Main Referenced Co-authors
KOLODKIN, Alexey  (10)
BALLING, Rudolf  (9)
Brady, Nathan (7)
Sangar, Vineet (7)
IGNATENKO, Andrew  (6)
Main Referenced Keywords
flux balance analysis (3); Systems biology (3); Glycolysis (2); systems biology (2); Algorithms (1);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) (11)
Manchester Centre for Integrative Systems Biology (2)
Luxembourg Centre for Systems Biomedicine (1)
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) (1)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (17)
Biochemistry, biophysics & molecular biology (3)
Engineering, computing & technology: Multidisciplinary, general & others (1)
Mathematics (1)

Publications (total 21)

The most downloaded
394 downloads
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 https://hdl.handle.net/10993/1595

The most cited

798 citations (OpenCitations)

Thiele, I.* , Swainston, N.* , Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., ... Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419-425. doi:10.1038/nbt.2488 https://hdl.handle.net/10993/422

Basler, G., & Simeonidis, V. (03 February 2015). Integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems. Frontiers in Genetics, 6, 20. doi:10.3389/fgene.2015.00020
Peer Reviewed verified by ORBi

Simeonidis, V., & Price, N. (13 January 2015). Genome-scale modeling for metabolic engineering. Journal of Industrial Microbiology and Biotechnology, 42 (3), 327–338. doi:10.1007/s10295-014-1576-3
Peer Reviewed verified by ORBi

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.

Richards, M. A., Cassen, V., Heavner, B. D., Ajami, N. E., HerrMann, A., Simeonidis, V., & Price, N. D. (06 August 2014). MediaDB: A Database of Microbial Growth Conditions in Defined Media. PLoS ONE, 9 (8), 103548. doi:10.1371/journal.pone.0103548
Peer Reviewed verified by ORBi

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.

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., 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.

Smallbone, K.* , Messiha, H. L.* , Carroll, K. M.* , Winder, C. L.* , Malys, N.* , Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P., Simeonidis, V., Spasic, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., ... Mendes, P. (02 September 2013). A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, 587 (17), 2832-2841. doi:10.1016/j.febslet.2013.06.043
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

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.

Simeonidis, E., Chandrasekaran, S., & Price, N. D. (2013). A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism). Methods in Molecular Biology, 985, 103-112. doi:10.1007/978-1-62703-299-5_6
Peer reviewed

Thiele, I.* , Swainston, N.* , Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., ... Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419-425. doi:10.1038/nbt.2488
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

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

Sangar, V., Eddy, J. A., Simeonidis, E., & Price, N. D. (2012). Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in Physiology, 3, 404. doi:10.3389/fphys.2012.00404
Peer Reviewed verified by ORBi

Simeonidis, V., Roach, J., Brunkow, M., Glusman, G., Reynolds, S., Balling, R., Hood, L., Galas, D. J., Wichmann, H.-E., Grimm, S., & Gelinas, R. (July 2011). Candidate mutations for early-onset lung cancer by family genome sequencing [Poster presentation]. ISMB/ECCB 2011 - 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria.

Simeonidis, V., Murabito, E., Smallbone, K., Dunn, W., Winder, C., Swainston, N., Mendes, P., & Westerhoff, H. V. (26 June 2011). Chasing the flux: selecting target pathways through flux analysis of carbon metabolism [Poster presentation]. 1st Conference on Constraint-based Reconstruction and Analysis, Reykjavik, Iceland.

Smallbone, K., Malys, N., Messiha, H. L., Wishart, J. A., & Simeonidis, E. (2011). Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae. Methods in Enzymology, 500, 355-70. doi:10.1016/B978-0-12-385118-5.00018-9
Peer Reviewed verified by ORBi

Simeonidis, V., Dartnell, L., Bogle, I. D. L., & Papageorgiou, L. G. (2005). Analysis of biochemical networks using linear programming. In Proceedings of the 7th World Congress of Chemical Engineering on CD-ROM. Institution of Chemical Engineers (IChemE).
Peer reviewed

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