Brett G. Olivier

发表

COMBINE archive: One File To Share Them All pdf

Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath, 2014, ArXiv.

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

Dagmar Waltemath, Sven Sahle, Jonathan Cooper, 2015, J. Integr. Bioinform..

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

Chris J. Myers, Claudine Chaouiya, Matthias König, 2018, J. Integr. Bioinform..

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

Chris J. Myers, Dagmar Waltemath, Michael Hucka, 2018, J. Integr. Bioinform..

MEMOTE for standardized genome-scale metabolic model testing

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2020, Nature Biotechnology.

Harmonizing semantic annotations for computational models in biology

Chris J. Myers, Olaf Wolkenhauer, Jacky L. Snoep, 2018, bioRxiv.

SBML Level 3 Package Proposal: Flux

Frank Bergmann, Brett G. Olivier, 2010 .

One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project

David P. Nickerson, Stian Soiland-Reyes, Dagmar Waltemath, 2014, 1407.4992.

Progress report: SBML Level 3 package FBA

Frank Bergmann, Brett G. Olivier, 2010 .

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2018, bioRxiv.

SBML Level 3 Package: Flux Balance Constraints ('fbc')

Frank Bergmann, Frank T. Bergmann, Brett G. Olivier, 2013 .

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

Chris J. Myers, Nicolas Le Novère, Dagmar Waltemath, 2015, J. Integr. Bioinform..

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

Frank T. Bergmann, Brett G. Olivier, 2015, Journal of integrative bioinformatics.

SBML Level 3 Package: Flux Balance Constraints version 2

Frank T. Bergmann, Brett G. Olivier, B. Olivier, 2018, J. Integr. Bioinform..

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

Timo R. Maarleveld, Frank J. Bruggeman, Bas Teusink, 2015, PLoS Comput. Biol..

Fast Flux Module Detection Using Matroid Theory

Leen Stougie, Frank J. Bruggeman, Brett G. Olivier, 2014, RECOMB.

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

Leen Stougie, Frank J. Bruggeman, Brett G. Olivier, 2012, Scientific Reports.

Modelling cellular systems with PySCeS

Jan-Hendrik S. Hofmeyr, Johann M. Rohwer, Brett G. Olivier, 2005, Bioinform..

Fast Flux Module Detection Using Matroid Theory

Leen Stougie, Frank J. Bruggeman, Brett G. Olivier, 2014, RECOMB.

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

Chris J. Myers, Carole Goble, Dagmar Waltemath, 2011, Standards in Genomic Sciences.

A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools

Bas Teusink, Brett G. Olivier, Douwe Molenaar, 2019 .

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

Nicolas Le Novère, David P. Nickerson, Stian Soiland-Reyes, 2014, BMC Bioinformatics.

FAME, the Flux Analysis and Modeling Environment

Joost Boele, Bas Teusink, Brett G. Olivier, 2012, BMC Systems Biology.

Web-based kinetic modelling using JWS Online

Jacky L. Snoep, Brett G. Olivier, J. Snoep, 2004, Bioinform..

Modelling? Using Standards Can Help You

Bas Teusink, Brett G. Olivier, 2016, ERCIM News.

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

Brett G. Olivier, 2011 .

CBMPy release 0.8.2

Brett G. Olivier, Willi Gottstein, B. Olivier, 2021 .

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

Frank J. Bruggeman, Bas Teusink, Brett G. Olivier, 2015, Front. Microbiol..

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

Jan-Hendrik S. Hofmeyr, Johann M. Rohwer, Brett G. Olivier, 2000 .

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

Frank J. Bruggeman, Bas Teusink, Brett G. Olivier, 2017, PloS one.

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

Ursula Kummer, Bas Teusink, Brett G. Olivier, 2014, Applied and Environmental Microbiology.

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

Ursula Kummer, Ruedi Aebersold, Brett G. Olivier, 2017 .

Top 10 metrics for life science software good practices

Rafael C. Jimenez, Pedro L. Fernandes, Manuel Corpas, 2016, F1000Research.

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

Timo R. Maarleveld, Frank J. Bruggeman, Brett G. Olivier, 2013, PloS one.