Dagmar Waltemath
TitleCited byYear
Controlled vocabularies and semantics in systems biology
M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ...
Molecular systems biology 7 (1), 2011
2182011
Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language
D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ...
BMC systems biology 5 (1), 198, 2011
1862011
Minimum information about a simulation experiment (MIASE)
D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ...
PLoS computational biology 7 (4), 2011
1142011
SED-ML–An XML Format for the Implementation of the MIASE Guidelines
D Köhn, N Le Novère
International Conference on Computational Methods in Systems Biology, 176-190, 2008
642008
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ...
BMC bioinformatics 15 (1), 369, 2014
622014
A call for virtual experiments: accelerating the scientific process
J Cooper, JO Vik, D Waltemath
Progress in biophysics and molecular biology 117 (1), 99-106, 2015
442015
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ...
Frontiers in bioengineering and biotechnology 3, 19, 2015
412015
Toward community standards and software for whole-cell modeling
D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ...
IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016
362016
Ranked retrieval of computational biology models
R Henkel, L Endler, A Peters, N Le Novère, D Waltemath
BMC bioinformatics 11 (1), 423, 2010
352010
How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine
D Waltemath, O Wolkenhauer
IEEE Transactions on Biomedical Engineering 63 (10), 1999-2006, 2016
342016
Improving the reuse of computational models through version control
D Waltemath, R Henkel, R Hälke, M Scharm, O Wolkenhauer
Bioinformatics 29 (6), 742-748, 2013
322013
Combining computational models, semantic annotations and simulation experiments in a graph database
R Henkel, O Wolkenhauer, D Waltemath
Database 2015, 2015
302015
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
D Waltemath, FT Bergmann, C Chaouiya, T Czauderna, P Gleeson, ...
Standards in genomic sciences 9 (3), 1285-1301, 2014
212014
An algorithm to detect and communicate the differences in computational models describing biological systems
M Scharm, O Wolkenhauer, D Waltemath
Bioinformatics 32 (4), 563-570, 2016
182016
The Systems Biology Markup Language (SBML): language specification for level 3 version 2 core
M Hucka, FT Bergmann, A Dräger, S Hoops, SM Keating, N Le Novère, ...
Journal of integrative bioinformatics 15 (1), 2018
162018
Simulation experiment description markup language (SED-ML) Level 1 Version 2
FT Bergmann, J Cooper, N Le Novere, D Nickerson, D Waltemath
Journal of integrative bioinformatics 12 (2), 119-212, 2015
152015
Annotation-based feature extraction from sets of SBML models
R Alm, D Waltemath, M Wolfien, O Wolkenhauer, R Henkel
Journal of biomedical semantics 6 (1), 20, 2015
142015
Harmonizing semantic annotations for computational models in biology
ML Neal, M König, D Nickerson, G Mısırlı, R Kalbasi, A Dräger, K Atalag, ...
Briefings in bioinformatics 20 (2), 540-550, 2019
132019
Specifications of standards in systems and synthetic biology
F Schreiber, GD Bader, M Golebiewski, M Hucka, B Kormeier, ...
Journal of integrative bioinformatics 12 (2), 1-3, 2015
132015
The CombineArchiveWeb application–A web based tool to handle files associated with modelling results
M Scharm, F Wendland, M Peters, M Wolfien, T Theile, D Waltemath
PeerJ PrePrints, 2014
122014
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Articles 1–20