20022020

Research output per year

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Research Output

  • 37 Article
  • 1 Comment / Letter to the editor
  • 1 Letter
  • 1 Review article
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Article
2019
Open Access

Harmonizing semantic annotations for computational models in biology

Neal, M. L., König, M., Nickerson, D., Misirli, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., Crook, S., De Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., Myers, C. & 8 others, Olivier, B. G., Sauro, H. M., Scharm, M., Snoep, J. L., Touré, V., Wipat, A., Wolkenhauer, O. & Waltemath, D., 22 Mar 2019, In : Briefings in bioinformatics. 20, 2, p. 540-550 11 p.

Research output: Contribution to JournalArticle

Open Access

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N. L., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J. & Zhang, F., 20 Jun 2019, In : Journal of Integrative Bioinformatics. 16, 2, p. 1-183 183 p.

Research output: Contribution to JournalArticle

Open Access
2018

Alignment of microbial fitness with engineered product formation: Obligatory coupling between acetate production and photoautotrophic growth

Du, W., Jongbloets, J. A., van Boxtel, C., Hernández, H. P., Lips, D., Olivier, B. G., Hellingwerf, K. J. & dos Santos, F. B., 13 Feb 2018, In : Biotechnology for Biofuels. 11, 38, p. 1-13 13 p., 38.

Research output: Contribution to JournalArticle

Open Access

SBML Level 3 Package: Flux Balance Constraints version 2

Olivier, B. G. & Bergmann, F. T., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-39 39 p.

Research output: Contribution to JournalArticle

Open Access

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L. & Waltemath, D., 19 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-98 98 p.

Research output: Contribution to JournalArticle

Open Access

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-182 182 p.

Research output: Contribution to JournalArticle

Open Access

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 19 Jun 2018, In : Journal of Integrative Bioinformatics. 15, 1

Research output: Contribution to JournalArticle

2017

Model-based quantification of metabolic interactions from dynamic microbial-community data

Hanemaaijer, M., Olivier, B. G., Röling, W. F. M., Bruggeman, F. J. & Teusink, B., 1 Mar 2017, In : PLoS ONE. 12, 3, e0173183.

Research output: Contribution to JournalArticle

Open Access

Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough

dos Santos, F. B., Olivier, B. G., Boele, J., Krumpochova, P., Klau, G. W., Giera, M. & Teusink, B., 1 Nov 2017, In : Applied and Environmental Microbiology. 83, 21

Research output: Contribution to JournalArticle

Open Access
2016
Open Access

Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets.

Levering, J., Fiedler, T., Sieg, A., van Grinsven, K. W., Hering, S., Veith, N., Olivier, B. G., Klett, L., Hugenholtz, J., Teusink, B., Kreikemeyer, B. & Kummer, U., 2016, In : Journal of Biotechnology. 232, p. 25-37

Research output: Contribution to JournalArticle

Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Grosseholz, R., Ching-Chiek, K., Veith, N., Fiedler, T., Strauss, M., Olivier, B. G., Collins, B. C., Schubert, O. T., Bergmann, F., Kreikemeyer, B., Aebersold, R. & Kummer, U., 2016, In : NPJ systems biology and applications. 16017.

Research output: Contribution to JournalArticle

Open Access

Modeling and simulation tools: from systems biology to systems medicine

Olivier, B. G., Swat, M. J. & Mone, M. J., 2016, In : Methods in Molecular Biology. 1386, p. 441-463

Research output: Contribution to JournalArticle

Modelling? Using standards can help you.

Olivier, B. G. & Teusink, B., 2016, In : ERCIM NEWS. 104, p. 34-38

Research output: Contribution to JournalArticle

Top 10 metrics for life science software good practices.

Artaza, H., Chue Hong, N., Corpas, M., Corpuz, A., Hooft, R., Jimenez, R. C., Leskosek, B., Olivier, B. G., Stourac, J., Svobodova Varekova, R., van Parys, T. & Vaughan, D., 2016, In : F1000Research. 5, ELIXIR-2000.

Research output: Contribution to JournalArticle

Open Access
2015

Fast flux module detection using matroid theory.

Reimers, A. C., Bruggeman, F. J., Olivier, B. G. & Stougie, L., 2015, In : Journal of Computational Biology. 22, p. 414-424 5.

Research output: Contribution to JournalArticle

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models.

Maarleveld, T. R., Wortel, M. T., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2015, In : PLoS Computational Biology. 7, 11, 4.

Research output: Contribution to JournalArticle

Open Access

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 2015, In : Journal of Integrative Bioinformatics. 12, p. 271 2.

Research output: Contribution to JournalArticle

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Hanemaaijer, M. J., Roling, W. F. M., Olivier, B. G., Khandelwal, R. A., Teusink, B. & Bruggeman, F. J., 2015, In : Frontiers in Microbiology. 6, 213.

Research output: Contribution to JournalArticle

Open Access

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

Olivier, B. G. & Bergmann, F. T., 2015, In : Journal of Integrative Bioinformatics. 12, p. 269 2.

Research output: Contribution to JournalArticle

Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism

Veith, N., Solheim, M., van Grinsven, K. W. A., Olivier, B. G., Levering, J., Grosseholz, R., Hugenholtz, J., Holo, H., Nes, I., Teusink, B. & Kummer, U., Mar 2015, In : Applied and Environmental Microbiology. 81, 5, p. 1622-1633 12 p.

Research output: Contribution to JournalArticle

2014

COMBINE archive and OMEX format: One file to share all information to reproduce a modeling project

Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., Olivier, B. G., Rodriguez, N., Sauro, H. M., Scharm, M., Soiland-Reyes, S., Waltemath, D., Yvon, F. & Le Novere, N., 14 Dec 2014, In : BMC Bioinformatics. 15, p. 1-9 9 p., 326.

Research output: Contribution to JournalArticle

Open Access

Meeting report from the fourth meeting of computational modeling in biology network (COMBINE).

Waltemath, D., Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C. A., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., Le Novere, N., Mi, H., Moraru, I. I., Myers, C. J., Nickerson, D., Olivier, B. G., Rodriguez, N., Schreiber, F., Smith, L., Zhang, F. & 1 others, Bonnet, E., 2014, In : Standards in Genomic Sciences. 2014, 9, p. 1285-1301 5279417.

Research output: Contribution to JournalArticle

Open Access
2013

Basic concepts and principles of stoichiometric modeling of metabolic networks.

Maarleveld, T. R., Khandelwal, R. A., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2013, In : Biotechnology Journal. 8, 9, p. 997-1008

Research output: Contribution to JournalArticle

Open Access

Community flux balance analysis for microbial consortia at balanced growth

Khandelwal, R. A., Olivier, B. G., Roling, W. F. M., Teusink, B. & Bruggeman, F. J., 2013, In : PLoS ONE. 8, 5

Research output: Contribution to JournalArticle

Open Access

StochPy: a comprehensive, userfriendly tool for simulating stochastic biological processes

Maarleveld, T. M., Olivier, B. G. & Bruggeman, F. J., 2013, In : PLoS ONE. 8, 11

Research output: Contribution to JournalArticle

Open Access
2012

FAME, the flux analysis and modelling environment

Boele, J., Olivier, B. G. & Teusink, B., 2012, In : BMC Systems Biology. 6, 8.

Research output: Contribution to JournalArticle

Open Access
File
Open Access
File
2011

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.

Swat, M., Kielbasa, S. M., Polak, S., Olivier, B. G., Bruggeman, F. J., Quinton Tulloch, M., Snoep, J. L., Verhoeven, A. J. & Westerhoff, H. V., 2011, In : Interfaces. 1, p. 16-23

Research output: Contribution to JournalArticle

2009

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

Pillay, C. S., Hofmeyr, J. H. S., Olivier, B. G., Snoep, J. L. & Rohwer, J. M., 1 Jan 2009, In : Biochemical Journal. 417, 1, p. 269-275 7 p.

Research output: Contribution to JournalArticle

2006

Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms

Olivier, B. G., Rohwer, J. M., Snoep, J. L. & Hofmeyr, J. H. S., Sep 2006, In : Systems Biology. 153, 5, p. 335-337 3 p.

Research output: Contribution to JournalArticle

Towards building the silicon cell: A modular approach

Snoep, J. L., Bruggeman, F., Olivier, B. G. & Westerhoff, H. V., Feb 2006, In : BioSystems. 83, 2-3 SPEC. ISS., p. 207-216 10 p.

Research output: Contribution to JournalArticle

2005

Modelling cellular systems with PySCeS

Olivier, B. G., Rohwer, J. M. & Hofmeyr, J. H. S., 15 Feb 2005, In : Bioinformatics. 21, 4, p. 560-561 2 p.

Research output: Contribution to JournalArticle

2003

JWS online cellular systems modelling and microbiology

Snoep, J. L. & Olivier, B. G., Nov 2003, In : Microbiology. 149, 11, p. 3045-3047 3 p.

Research output: Contribution to JournalArticle

2002

Modelling cellular processes with Python and Scipy

Olivier, B. G., Rohwer, J. M. & Hofmeyr, J. H. S., 2002, In : Molecular Biology Reports. 29, 1-2, p. 249-254 6 p.

Research output: Contribution to JournalArticle

The regulatory design of an allosteric feedback loop: the effect of saturation by pathway substrate.

Hofmeyr, J. H. S. & Olivier, B. G., Apr 2002, In : Biochemical Society Transactions. 30, 2, p. 19-25 7 p.

Research output: Contribution to JournalArticle