Vangelis Simeonidis

Research Scientist / Program Manager

Systems Biologist & Chemical Engineer

 

Update: After almost 8 great years at the Institute for Systems Biology, in September 2018 I moved on to a new job as Program Manager at Lumen Bioscience, Inc.

My research focuses on the development of mathematical models for the analysis of biological networks. These range from fully parametrized, kinetic models of pathways to genome-scale models of either kinetic or purely stoichiometric nature. The analysis and control of metabolic flux is also among my main interests. The techniques I use for the modelling of these systems vary from kinetic and ODE-based modelling, to stroichiometric and optimization-based approaches (Flux Balance Analysis being a prime example). At the same time, I develop novel and hybrid approaches for the characterization of metabolic behavior.

At the ISB, I work in the Hood-Price lab, which has years of expertise in genome-scale metabolic modeling and the integration of regulatory information, metabolic networks and expression profiles to accurately model molecular processes in living organisms. The focal points of our research are disease network analysis, molecular signatures of diseases, metabolomics and neurodegenerative diseases.

Since January 2016, I have taken on the duties of Project Manager for the Hood-Price lab. In this role, I manage our federal and foundation funded research projects, making sure of delivering project timelines on schedule and within budget and scope. I am a strong advocate of collaborative work, and always emphasize a dialogue-based approach, in order to ensure well-established goals exist and that project contributors are all on the same page. I have conducted these duties at scales from in-group projects to international collaborations, and have been involved in projects from the proposal and grant-writing phase to late-stage project maintenance activities.

PhD, Department of Chemical Engineering, University College London, UK

MSc, Department of Chemical Engineering, Imperial College London, UK

Diploma, Department of Chemical Engineering, Aristoteleion University of Thessaloniki, Greece

For a comprehensive publication list with downloadable pdf files, please visit my profile on ResearchGate ResearchGate.

Below you will find the research papers I have published during my time at the Institute for Systems Biology:

Smallbone, Kieran, Naglis Malys, Hanan L. Messiha, Jill A. Wishart, and Evangelos Simeonidis. 2011. “Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces Cerevisiae.” Methods in Enzymology 500: 355–70. https://doi.org/10.1016/B978-0-12-385118-5.00018-9. Cite
Kolodkin, Alexey, Evangelos Simeonidis, Rudi Balling, and Hans V. Westerhoff. 2012. “Understanding Complexity in Neurodegenerative Diseases: In Silico Reconstruction  of Emergence.” Frontiers in Physiology 3. https://doi.org/10.3389/fphys.2012.00291. Cite
Sangar, Vineet, James A. Eddy, Evangelos Simeonidis, and Nathan D. Price. 2012. “Mechanistic Modeling of Aberrant Energy Metabolism in Human Disease.” Frontiers in Physiology 3. https://doi.org/10.3389/fphys.2012.00404. Cite
Simeonidis, Evangelos, Sriram Chandrasekaran, and Nathan D. Price. 2013. “A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism).” Methods in Molecular Biology (Clifton, N.J.) 985: 103–12. https://doi.org/10.1007/978-1-62703-299-5_6. Cite
Kolodkin, Alexey, Evangelos Simeonidis, and Hans V. Westerhoff. 2013. “Computing Life: Add Logos to Biology and Bios to Physics.” Progress in Biophysics and Molecular Biology 111 (2–3). https://doi.org/10.1016/j.pbiomolbio.2012.10.003. Cite
Thiele, Ines, Neil Swainston, Ronan M. T. Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K. Aurich, Hulda Haraldsdottir, et al. 2013. “A Community-Driven Global Reconstruction of Human Metabolism.” Nature Biotechnology 31 (5): 419–25. https://doi.org/10.1038/nbt.2488. Cite
Smallbone, Kieran, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, et al. 2013. “A Model of Yeast Glycolysis Based on a Consistent Kinetic Characterisation of All Its Enzymes.” FEBS Letters 587 (17): 2832–41. https://doi.org/10.1016/j.febslet.2013.06.043. Cite
Westerhoff, Hans V., Aaron N. Brooks, Evangelos Simeonidis, Rodolfo Garcia-Contreras, Fei He, Fred C. Boogerd, Victoria J. Jackson, Valeri Goncharuk, and Alexey Kolodkin. 2014. “Macromolecular Networks and Intelligence in Microorganisms.” Frontiers in Microbiology 5. https://doi.org/10.3389/fmicb.2014.00379. Cite
Richards, Matthew A., Victor Cassen, Benjamin D. Heavner, Nassim E. Ajami, Andrea Herrmann, Evangelos Simeonidis, and Nathan D. Price. 2014. “MediaDB: A Database of Microbial Growth Conditions in Defined Media.” PloS One 9 (8): e103548. https://doi.org/10.1371/journal.pone.0103548. Cite
Basler, Georg, and Evangelos Simeonidis. 2015. “Integrating Food Webs with Metabolic Networks: Modeling Contaminant Degradation in Marine Ecosystems.” Frontiers in Genetics 6. https://doi.org/10.3389/fgene.2015.00020. Cite
Simeonidis, Evangelos, and Nathan D. Price. 2015. “Genome-Scale Modeling for Metabolic Engineering.” Journal of Industrial Microbiology & Biotechnology 42 (3): 327–38. https://doi.org/10.1007/s10295-014-1576-3. Cite
King, Brendan, Terry Farrah, Matthew A. Richards, Michael Mundy, Evangelos Simeonidis, and Nathan D. Price. 2017. “ProbAnnoWeb and ProbAnnoPy: Probabilistic Annotation and Gap-Filling of Metabolic Reconstructions.” Bioinformatics (Oxford, England). https://doi.org/10.1093/bioinformatics/btx796. Cite
Wang, Zhuo, Samuel A. Danziger, Benjamin D. Heavner, Shuyi Ma, Jennifer J. Smith, Song Li, Thurston Herricks, et al. 2017. “Combining Inferred Regulatory and Reconstructed Metabolic Networks Enhances Phenotype Prediction in Yeast.” PLoS Computational Biology 13 (5): e1005489. https://doi.org/10.1371/journal.pcbi.1005489. Cite

You can access live versions of my résumé on re.vu and on linkedin.com.

For a more traditional version, a short 2-page CV plus publication list is available for download here:

file-pdf-o_666666_22CV Simeonidis (236KB pdf)

 Postal address

Institute for Systems Biology
401 Terry Avenue North
Seattle, WA 98109
USA

 

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