Brett G. Olivier / Postdoctoral Researcher


Brett G. Olivier

Vrije Universiteit Amsterdam
Systems Bioinformatics
O2 building, room 01E51
De Boelelaan 1085
1081 HV, Amsterdam
The Netherlands

Tel: +31 20 59 87248
Fax: +31 20 59 87229
Email: b.g.olivier@vu.dot.nl

Current interests
Biochemist and Software Developer specializing in Systems Biology with experience in both fundamental theoretical research (metabolic regulation analysis, control analysis, constraint based modelling) and software design and development.

My current research includes developing and applying constraint based modelling techniques to the analysis of microbial communities and multiple environments. This involves both the development of theory (going from one to many organisms) but also software tools for large scale optimization. I am also actively involved in the development of standards in Systems Biology

Skill areas
biochemistry, modeling, metabolic control analysis, Python, software development, systems biology, standards, interoperability

Contact details
For a more detailed list of activities and CV please see my personal website and blog or contact me on Twitter (@Brett_Olivier).

Publications
See the PubMed listing at the end of this page or search Google Scholar and PubMed directly.

Standards Development
I am actively involved in the development of standards in systems biology and currently serve as an elected editor on the editorial boards of two community standards, the Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML). I also co-ordinate the development of the SBML Level 3 Flux Balance Constraints Package (FBC) and working group responsible for developing a standard encoding format for genome-scale, constraint-based models.

Software Projects
Software projects that I am (or have been) involved with include: CBMPy (lead developer 2010-present), FAME (co-developer 2012-present), MEMESA Tools (co-developer 2012-present), StochPy, PySundials, PySCeS (lead developer 2001-present), JWS Online (lead developer 2001-2005).

PySCeS is now ranked on depsy.org:

Social Profiles
Here are a collection of some web 2.0 profiles (apparently all me):

 


PubMed publications

  1. Hanemaaijer, M, Olivier, BG, Röling, WF, Bruggeman, FJ, Teusink, B. Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS ONE. 2017;12 (3):e0173183. doi: 10.1371/journal.pone.0173183. PubMed PMID:28278266 PubMed Central PMC5344373.
  2. Artaza, H, Chue Hong, N, Corpas, M, Corpuz, A, Hooft, R, Jimenez, RC et al.. Top 10 metrics for life science software good practices. F1000Res. 2016;5 :. doi: 10.12688/f1000research.9206.1. PubMed PMID:27635232 PubMed Central PMC5007752.
  3. Levering, J, Fiedler, T, Sieg, A, van Grinsven, KW, Hering, S, Veith, N et al.. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets. J. Biotechnol. 2016;232 :25-37. doi: 10.1016/j.jbiotec.2016.01.035. PubMed PMID:26970054 .
  4. Gottstein, W, Olivier, BG, Bruggeman, FJ, Teusink, B. Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface. 2016;13 (124):. doi: 10.1098/rsif.2016.0627. PubMed PMID:28334697 PubMed Central PMC5134014.
  5. Olivier, BG, Swat, MJ, Moné, MJ. Modeling and Simulation Tools: From Systems Biology to Systems Medicine. Methods Mol. Biol. 2016;1386 :441-63. doi: 10.1007/978-1-4939-3283-2_19. PubMed PMID:26677194 .
  6. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform. 2015;12 (2):271. doi: 10.2390/biecoll-jib-2015-271. PubMed PMID:26528569 PubMed Central PMC5457286.
  7. Olivier, BG, Bergmann, FT. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J Integr Bioinform. 2015;12 (2):269. doi: 10.2390/biecoll-jib-2015-269. PubMed PMID:26528567 .
  8. Hanemaaijer, M, Röling, WF, Olivier, BG, Khandelwal, RA, Teusink, B, Bruggeman, FJ et al.. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol. 2015;6 :213. doi: 10.3389/fmicb.2015.00213. PubMed PMID:25852671 PubMed Central PMC4365725.
  9. Maarleveld, TR, Wortel, MT, Olivier, BG, Teusink, B, Bruggeman, FJ. Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models. PLoS Comput. Biol. 2015;11 (4):e1004166. doi: 10.1371/journal.pcbi.1004166. PubMed PMID:25849486 PubMed Central PMC4388735.
  10. Reimers, AC, Bruggeman, FJ, Olivier, BG, Stougie, L. Fast flux module detection using matroid theory. J. Comput. Biol. 2015;22 (5):414-24. doi: 10.1089/cmb.2014.0141. PubMed PMID:25565150 .
  11. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  12. Bergmann, FT, Adams, R, Moodie, S, Cooper, J, Glont, M, Golebiewski, M et al.. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15 :369. doi: 10.1186/s12859-014-0369-z. PubMed PMID:25494900 PubMed Central PMC4272562.
  13. Maarleveld, TR, Olivier, BG, Bruggeman, FJ. StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS ONE. 2013;8 (11):e79345. doi: 10.1371/journal.pone.0079345. PubMed PMID:24260203 PubMed Central PMC3832486.
  14. Maarleveld, TR, Khandelwal, RA, Olivier, BG, Teusink, B, Bruggeman, FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J. 2013;8 (9):997-1008. doi: 10.1002/biot.201200291. PubMed PMID:23893965 PubMed Central PMC4671265.
  15. Khandelwal, RA, Olivier, BG, Röling, WF, Teusink, B, Bruggeman, FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS ONE. 2013;8 (5):e64567. doi: 10.1371/journal.pone.0064567. PubMed PMID:23741341 PubMed Central PMC3669319.
  16. Kelk, SM, Olivier, BG, Stougie, L, Bruggeman, FJ. Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep. 2012;2 :580. doi: 10.1038/srep00580. PubMed PMID:22896812 PubMed Central PMC3419370.
  17. Boele, J, Olivier, BG, Teusink, B. FAME, the Flux Analysis and Modeling Environment. BMC Syst Biol. 2012;6 :8. doi: 10.1186/1752-0509-6-8. PubMed PMID:22289213 PubMed Central PMC3317868.
  18. Pillay, CS, Hofmeyr, JH, Olivier, BG, Snoep, JL, Rohwer, JM. Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context. Biochem. J. 2009;417 (1):269-75. doi: 10.1042/BJ20080690. PubMed PMID:18694397 .
  19. Olivier, BG, Rohwer, JM, Snoep, JL, Hofmeyr, JH. Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms. Syst Biol (Stevenage). 2006;153 (5):335-7. . PubMed PMID:16986311 .
  20. Snoep, JL, Bruggeman, F, Olivier, BG, Westerhoff, HV. Towards building the silicon cell: a modular approach. BioSystems. ;83 (2-3):207-16. doi: 10.1016/j.biosystems.2005.07.006. PubMed PMID:16242236 .
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Supervision and related

NameCo-supervisor(s)TitleTypeYear
Thomas BraamBas TeusinkAccounting for enzyme costs in FBAMSc project2016
Nicolas HuberBas TeusinkVisualising genome scale networksMSc project2016-2017
Carl ChristensenDevelopment of an Integrated Metabolic Analysis ToolboxPhD thesis (examiner)2016
Marnette CoetzeeFeedforward activation in metabolic systemsMSc thesis (examiner)2016
Timo MaarleveldFrank Bruggeman
Bas Teusink
Fluxes and Feedback in Biochemical modelsPhD2015
Maarten ReitsemaBas TeusinkComparison of Gap Filling AlgorithmsMSc literature2015
Hanneke LaanBas TeusinkThe integration of the macromolecular synthesis machinery with genome-scale metabolic modelsMSc literature2015
Johannes HettlingViable Models of Energy MetabolismPhD thesis (committee)2013

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