All Stories

  1. BioSimulators: a central registry of simulation engines and services for recommending specific tools

    Article • Nucleic Acids Research, May 2022, Oxford University Press (OUP)

    Matúš Kalaš, Brett G Olivier

  2. Inspecting the Solution Space of Genome-Scale Metabolic Models

    Article • Metabolites, January 2022, MDPI AG

    Brett G Olivier

  3. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers

    Article • Communications Biology, May 2021, Springer Science + Business Media

    Brett G Olivier

  4. Protein cost allocation explains metabolic strategies in Escherichia coli

    Article • Journal of Biotechnology, February 2021, Elsevier

    Brett G Olivier

  5. SBML Level 3: an extensible format for the exchange and reuse of biological models

    Article • Molecular Systems Biology, August 2020, EMBO

    Jun.-Prof. Dr. Andreas Dräger, Brett G Olivier, Professor Chris Evelo

  6. MEMOTE for standardized genome-scale metabolic model testing

    Article • Nature Biotechnology, March 2020, Springer Science + Business Media

    Dr.-Ing. Birgitta Elisabeth Ebert, Jun.-Prof. Dr. Andreas Dräger, Brett G Olivier

  7. A systematic assessment of current genome-scale metabolic reconstruction tools

    Article • Genome Biology, August 2019, Springer Science + Business Media

    Brett G Olivier

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

    Article • Journal of Integrative Bioinformatics, June 2019, De Gruyter

    Jun.-Prof. Dr. Andreas Dräger, Brett G Olivier

  9. A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Brett G Olivier

  10. Harmonizing semantic annotations for computational models in biology

    Article • Briefings in Bioinformatics, November 2018, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger, Brett G Olivier

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

    Article • Journal of Integrative Bioinformatics, April 2018, De Gruyter

    Brett G Olivier, Jun.-Prof. Dr. Andreas Dräger

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

    Article • Journal of Integrative Bioinformatics, March 2018, De Gruyter

    Brett G Olivier, David P Nickerson

  13. SBML Level 3 Package: Flux Balance Constraints version 2

    Article • Journal of Integrative Bioinformatics, March 2018, De Gruyter

    Brett G Olivier

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

    Article • Journal of Integrative Bioinformatics, March 2018, De Gruyter

    Brett G Olivier, Jun.-Prof. Dr. Andreas Dräger

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

    Article • Biotechnology for Biofuels, February 2018, Springer Science + Business Media

    Brett G Olivier

  16. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough

    Article • Applied and Environmental Microbiology, August 2017, ASM Journals

    Bas Teusink, Brett G Olivier

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

    Article • PLOS One, March 2017, PLOS

    Brett G Olivier

  18. Using modelling to understand microbial communities

    Article • Journal of The Royal Society Interface, November 2016, Royal Society Publishing

    Brett G Olivier

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

    Article • npj Systems Biology and Applications, September 2016, Nature

    Brett G Olivier

  20. How to measure whether software is produced "professionally"

    Article • F1000Research, August 2016, Faculty of 1000, Ltd.

    Ms Haydee H Artaza, Mr Neil P Chue Hong, Rob Hooft, Brett G Olivier, Mr Rafael C Jimenez

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

    Article • Journal of Biotechnology, August 2016, Elsevier

    Brett G Olivier

  22. Modeling and Simulation Tools: From Systems Biology to Systems Medicine

    Article • January 2016, Springer Science + Business Media

    Brett G Olivier

  23. Fast Flux Module Detection Using Matroid Theory

    Article • Journal of Computational Biology, May 2015, Mary Ann Liebert Inc

    Brett G Olivier

  24. Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models

    Article • PLoS Computational Biology, April 2015, PLOS

    Brett G Olivier

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

    Article • Frontiers in Microbiology, March 2015, Frontiers

    Brett G Olivier

  26. Using a Genome-Scale Metabolic Model of Enterococcus faecalis V583 To Assess Amino Acid Uptake and Its Impact on Central Metabolism

    Article • Applied and Environmental Microbiology, December 2014, ASM Journals

    Brett G Olivier

  27. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

    Article • BMC Bioinformatics, December 2014, Springer Science + Business Media

    Brett G Olivier, David P Nickerson

  28. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    Article • Standards in Genomic Sciences, March 2014, Springer Science + Business Media

    Brett G Olivier, David P Nickerson

  29. Fast Flux Module Detection Using Matroid Theory

    Article • January 2014, Springer Science + Business Media

    Brett G Olivier

  30. StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes

    Article • PLOS One, November 2013, PLOS

    Brett G Olivier

  31. Basic concepts and principles of stoichiometric modeling of metabolic networks

    Article • Biotechnology Journal, July 2013, Wiley

    Brett G Olivier

  32. Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

    Article • PLOS One, May 2013, PLOS

    Brett G Olivier

  33. Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

    Article • Scientific Reports, August 2012, Nature

    Brett G Olivier

  34. FAME, the Flux Analysis and Modeling Environment

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Brett G Olivier

  35. Updates to the SBML Level 3 Flux Balance Constraints (FBC) package

    Article • Nature Reports Climate Change, September 2011, Nature

    Brett G Olivier

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

    Article • Interface Focus, December 2010, Royal Society Publishing

    Brett G Olivier

  37. Progress report: SBML Level 3 package FBA

    Article • Nature Reports Climate Change, October 2010, Nature

    Brett G Olivier

  38. SBML Level 3 Package Proposal: Flux

    Article • Nature Reports Climate Change, February 2010, Nature

    Brett G Olivier

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

    Article • Biochemical Journal, January 2009, Portland Press Ltd.

    Brett G Olivier

  40. Towards building the silicon cell: A modular approach

    Article • Biosystems, February 2006, Elsevier

    Brett G Olivier

  41. Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms

    Article • Systems Biology, January 2006, the Institution of Engineering and Technology (the IET)

    Brett G Olivier

  42. Modelling cellular systems with PySCeS

    Article • Bioinformatics, September 2004, Oxford University Press (OUP)

    Brett G Olivier

  43. Web-based kinetic modelling using JWS Online

    Article • Bioinformatics, April 2004, Oxford University Press (OUP)

    Brett G Olivier

  44. JWS Online Cellular Systems Modelling and Microbiology

    Article • Microbiology, November 2003, Society for General Microbiology

    Brett G Olivier

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

    Article • Biochemical Society Transactions, April 2002, Portland Press Ltd.

    Brett G Olivier

  46. Article • Molecular Biology Reports, January 2002, Springer Science + Business Media

    Brett G Olivier

  47. Article • Molecular Biology Reports, January 2002, Springer Science + Business Media

    Brett G Olivier

  48. Moiety Conservation and Flux Enhancement

    Article • January 2000, Springer Science + Business Media

    Brett G Olivier

  49. Putting the Cart before the Horse: Designing a Metabolic System in order to Understand it

    Article • January 2000, Springer Science + Business Media

    Brett G Olivier