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Items: 1 to 20 of 32


Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2018 Nov 21. doi: 10.1093/bib/bby087. [Epub ahead of print]


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

Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E.

Stand Genomic Sci. 2018 Aug 9;13:17. doi: 10.1186/s40793-018-0320-4. eCollection 2018.


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

Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Smith L, Waltemath D.

J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0086/jib-2017-0086.xml. doi: 10.1515/jib-2017-0086.


SBML Level 3 Package: Flux Balance Constraints version 2.

Olivier BG, Bergmann FT.

J Integr Bioinform. 2018 Mar 9;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0082/jib-2017-0082.xml. doi: 10.1515/jib-2017-0082.


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

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2018 Mar 9;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0081/jib-2017-0081.xml. doi: 10.1515/jib-2017-0081.


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

Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P.

Appl Environ Microbiol. 2017 Aug 25. pii: AEM.01528-17. doi: 10.1128/AEM.01528-17. [Epub ahead of print]


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

Hanemaaijer M, Olivier BG, Röling WF, Bruggeman FJ, Teusink B.

PLoS One. 2017 Mar 9;12(3):e0173183. doi: 10.1371/journal.pone.0173183. eCollection 2017.


Top 10 metrics for life science software good practices.

Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D.

F1000Res. 2016 Aug 16;5. pii: ELIXIR-2000. doi: 10.12688/f1000research.9206.1. eCollection 2016.


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 KW, Hering S, Veith N, Olivier BG, Klett L, Hugenholtz J, Teusink B, Kreikemeyer B, Kummer U.

J Biotechnol. 2016 Aug 20;232:25-37. doi: 10.1016/j.jbiotec.2016.01.035. Epub 2016 Mar 10.


Constraint-based stoichiometric modelling from single organisms to microbial communities.

Gottstein W, Olivier BG, Bruggeman FJ, Teusink B.

J R Soc Interface. 2016 Nov;13(124). pii: 20160627. doi: 10.1098/rsif.2016.0627. Review.


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

Olivier BG, Swat MJ, Moné MJ.

Methods Mol Biol. 2016;1386:441-63. doi: 10.1007/978-1-4939-3283-2_19. Review.


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

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.


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

Olivier BG, Bergmann FT.

J Integr Bioinform. 2015 Sep 4;12(2):269. doi: 10.2390/biecoll-jib-2015-269.


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

Hanemaaijer M, Röling WF, Olivier BG, Khandelwal RA, Teusink B, Bruggeman FJ.

Front Microbiol. 2015 Mar 19;6:213. doi: 10.3389/fmicb.2015.00213. eCollection 2015.


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

Maarleveld TR, Wortel MT, Olivier BG, Teusink B, Bruggeman FJ.

PLoS Comput Biol. 2015 Apr 7;11(4):e1004166. doi: 10.1371/journal.pcbi.1004166. eCollection 2015 Apr.


Fast flux module detection using matroid theory.

Reimers AC, Bruggeman FJ, Olivier BG, Stougie L.

J Comput Biol. 2015 May;22(5):414-24. doi: 10.1089/cmb.2014.0141. Epub 2015 Jan 7.


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 KW, Olivier BG, Levering J, Grosseholz R, Hugenholtz J, Holo H, Nes I, Teusink B, Kummer U.

Appl Environ Microbiol. 2015 Mar;81(5):1622-33. doi: 10.1128/AEM.03279-14. Epub 2014 Dec 19.


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

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.

BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.


StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes.

Maarleveld TR, Olivier BG, Bruggeman FJ.

PLoS One. 2013 Nov 18;8(11):e79345. doi: 10.1371/journal.pone.0079345. eCollection 2013.


Basic concepts and principles of stoichiometric modeling of metabolic networks.

Maarleveld TR, Khandelwal RA, Olivier BG, Teusink B, Bruggeman FJ.

Biotechnol J. 2013 Sep;8(9):997-1008. doi: 10.1002/biot.201200291. Epub 2013 Jul 29. Review.

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