Brett G. Olivier / Data Steward / Research Software Engineer

Computational Systems Biologist and Data Steward @ VU Amsterdam
Technical Program Manager @ Holomicrobiome Innovation Institute

Specialized in FAIR Data Stewardship, Systems Biology Software and Open Data Standards (SBML)

For more information about me, my software, current projects: https://www.brettolivier.nl/
or LinkedIn: https://www.linkedin.com/in/brettolivier/

PubMed publications (last 20)

1. Sauro, HM, Agmon, E, Blinov, ML, Gennari, JH, Hellerstein, JL, Heydarabadipour, A et al.. From FAIR to CURE: guidelines for computational models of biological systems. NPJ Syst Biol Appl. 2026;12 (1):. doi: 10.1038/s41540-026-00651-0. PubMed PMID:41888157 PubMed Central PMC13230930.
2. Sauro, HM, Agmon, E, Blinov, ML, Gennari, JH, Hellerstein, J, Heydarabadipour, A et al.. From FAIR to CURE: Guidelines for Computational Models of Biological Systems. ArXiv. 2025; :. . PubMed PMID:40034129 PubMed Central PMC11875277.
3. Shaikh, B, Smith, LP, Vasilescu, D, Marupilla, G, Wilson, M, Agmon, E et al.. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 2022;50 (W1):W108-W114. doi: 10.1093/nar/gkac331. PubMed PMID:35524558 PubMed Central PMC9252793.
4. Loghmani, SB, Veith, N, Sahle, S, Bergmann, FT, Olivier, BG, Kummer, U et al.. Inspecting the Solution Space of Genome-Scale Metabolic Models. Metabolites. 2022;12 (1):. doi: 10.3390/metabo12010043. PubMed PMID:35050165 PubMed Central PMC8779308.
5. Grigaitis, P, Olivier, BG, Fiedler, T, Teusink, B, Kummer, U, Veith, N et al.. Protein cost allocation explains metabolic strategies in Escherichia coli. J Biotechnol. 2021;327 :54-63. doi: 10.1016/j.jbiotec.2020.11.003. PubMed PMID:33309962 .
6. Keating, SM, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C et al.. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol. 2020;16 (8):e9110. doi: 10.15252/msb.20199110. PubMed PMID:32845085 PubMed Central PMC8411907.
7. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (4):504. doi: 10.1038/s41587-020-0477-4. PubMed PMID:32265554 PubMed Central PMC7138757.
8. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (3):272-276. doi: 10.1038/s41587-020-0446-y. PubMed PMID:32123384 PubMed Central PMC7082222.
9. Mendoza, SN, Olivier, BG, Molenaar, D, Teusink, B. A systematic assessment of current genome-scale metabolic reconstruction tools. Genome Biol. 2019;20 (1):158. doi: 10.1186/s13059-019-1769-1. PubMed PMID:31391098 PubMed Central PMC6685185.
10. Hucka, M, Bergmann, FT, Chaouiya, C, Dräger, A, Hoops, S, Keating, SM et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform. 2019;16 (2):. doi: 10.1515/jib-2019-0021. PubMed PMID:31219795 PubMed Central PMC6798823.
11. Neal, ML, König, M, Nickerson, D, Mısırlı, G, Kalbasi, R, Dräger, A et al.. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 2019;20 (2):540-550. doi: 10.1093/bib/bby087. PubMed PMID:30462164 PubMed Central PMC6433895.
12. Waltemath, D, Bergmann, FT, Chaouiya, C, Czauderna, T, Gleeson, P, Goble, C et al.. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2018;13 :17. doi: 10.1186/s40793-018-0320-4. PubMed PMID:30117501 PubMed Central PMC6083578.
13. Bergmann, FT, Cooper, J, König, M, Moraru, I, Nickerson, D, Le Novère, N et al.. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0086. PubMed PMID:29550789 PubMed Central PMC6167040.
14. Olivier, BG, Bergmann, FT. SBML Level 3 Package: Flux Balance Constraints version 2. J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0082. PubMed PMID:29522419 PubMed Central PMC6167036.
15. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0081. PubMed PMID:29522418 PubMed Central PMC6167032.
16. Branco Dos Santos, F, Olivier, BG, Boele, J, Smessaert, V, De Rop, P, Krumpochova, P et al.. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough. Appl Environ Microbiol. 2017;83 (21):. doi: 10.1128/AEM.01528-17. PubMed PMID:28842544 PubMed Central PMC5648915.
17. 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.
18. 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.
19. 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 .
20. 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.

Supervision and related

Back to top.