Dagmar Waltemath

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Michael HuckaCalifornia Institute of TechnologyVerified email at caltech.edu
David Phillip NickersonAuckland Bioengineering Institute, University of AucklandVerified email at auckland.ac.nz
Frank T. BergmannBioQUANT/COS, Heidelberg University, Heidelberg, GermanyVerified email at caltech.edu
Ron HenkelHeidelberg Institute for Theoretical StudiesVerified email at uni-rostock.de
Martin GolebiewskiHITS gGmbH, Heidelberg (Germany)Verified email at h-its.org
Chris MyersUniversity of UtahVerified email at ece.utah.edu
Martin ScharmHead of IT @ Dept. of Systems Biology and BioinformaticsVerified email at binfalse.de
Brett G. OlivierVU AmsterdamVerified email at vu.nl
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Jonathan CooperUniversity College LondonVerified email at ucl.ac.uk
Stefan HoopsResearch Associate Professor, Biocomplexity Institute & Initiative, University of VirginiaVerified email at virginia.edu
Darren WilkinsonProfessor of Statistics, Durham University, U.K.Verified email at durham.ac.uk
Herbert M SauroUniversity of WashingtonVerified email at u.washington.edu
Padraig GleesonDepartment of Neuroscience, Physiology and Pharmacology, University College LondonVerified email at ucl.ac.uk
Andreas DrägerJuniorprofessor for Computational Systems Biology of Infection and Antimicrobial-ResistanceVerified email at uni-tuebingen.de
Nicolas RodriguezSenior Software Systems and Database Architect, Babraham InstituteVerified email at babraham.ac.uk
Snoep JLStellenbosch University; Manchester University; Vrije Universiteit AmsterdamVerified email at sun.ac.za
Gary BaderProfessor of Molecular Genetics and Computer Science, The Donnelly Centre, University of TorontoVerified email at utoronto.ca
Claudine ChaouiyaI2M UMR 7373, Aix Marseille University (France)Verified email at univ-amu.fr
Bjorn SommerPhD, Royal College of Art (Innovation Design Engineering), LondonVerified email at CELLmicrocosmos.org

Dagmar Waltemath

Professor of Medical Informatics

Verified email at uni-greifswald.de - Homepage

biomedical research data management data integration


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Controlled vocabularies and semantics in systems biology M Courtot, N Juty, C Knupfer, D Waltemath, A Zhukova, A Drager, ... Molecular Systems Biology 7 (543), 2011	299	2011
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), 1-10, 2011	263	2011
Minimum information about a simulation experiment (MIASE) D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ... PLoS computational biology 7 (4), e1001122, 2011	146	2011
SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020	126	2020
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), 1-9, 2014	126	2014
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	73	2015
SED-ML-An XML format for the implementation of the MIASE guidelines. D Köhn, N Le Novère CMSB, 176-190, 2008	73	2008
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	66	2018
The systems biology markup language (SBML): language specification for level 3 version 2 core release 2 M Hucka, FT Bergmann, C Chaouiya, A Dräger, S Hoops, SM Keating, ... Journal of integrative bioinformatics 16 (2), 20190021, 2019	60	2019
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	59	2016
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	55	2015
Combining computational models, semantic annotations and simulation experiments in a graph database R Henkel, O Wolkenhauer, D Waltemath Database 2015, 2015	54	2015
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	50	2016
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	48	2019
Ranked retrieval of computational biology models R Henkel, L Endler, A Peters, N Le Novère, D Waltemath BMC bioinformatics 11, 1-12, 2010	38	2010
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	33	2013
Specifications of standards in systems and synthetic biology: status and developments in 2020 F Schreiber, B Sommer, T Czauderna, M Golebiewski, TE Gorochowski, ... Journal of integrative bioinformatics 17 (2-3), 2020	31	2020
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	29	2014
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	26	2016
The JWS online simulation database M Peters, JJ Eicher, DD Van Niekerk, D Waltemath, JL Snoep Bioinformatics 33 (10), 1589-1590, 2017	25	2017

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