| 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 | 252 | 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, 1-9, 2014 | 165 | 2014 |
| 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 | 75 | 2019 |
| The cardiac electrophysiology web lab J Cooper, M Scharm, GR Mirams Biophysical journal 110 (2), 292-300, 2016 | 70 | 2016 |
| 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 | 65 | 2016 |
| 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 | 36 | 2013 |
| 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 | 30 | 2016 |
| SED-ML web tools: generate, modify and export standard-compliant simulation studies FT Bergmann, D Nickerson, D Waltemath, M Scharm Bioinformatics 33 (8), 1253-1254, 2017 | 17 | 2017 |
| Exploring the metabolic heterogeneity of cancers: A benchmark study of context-specific models M Jalili, M Scharm, O Wolkenhauer, M Damaghi, A Salehzadeh-Yazdi Journal of Personalized Medicine 11 (6), 496, 2021 | 16 | 2021 |
| COMODI: an ontology to characterise differences in versions of computational models in biology M Scharm, D Waltemath, P Mendes, O Wolkenhauer Journal of biomedical semantics 7, 1-8, 2016 | 14 | 2016 |
| 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 | 13 | 2014 |
| A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos M Scharm, D Waltemath F1000Research 5, 2016 | 11 | 2016 |
| Data management in computational systems biology: exploring standards, tools, databases, and packaging best practices NJ Stanford, M Scharm, PD Dobson, M Golebiewski, M Hucka, ... Yeast Systems Biology: Methods and Protocols, 285-314, 2019 | 8 | 2019 |
| Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit M Scharm, D Waltemath PeerJ PrePrints, 2015 | 7 | 2015 |
| Evolution of computational models in BioModels Database and the Physiome Model Repository M Scharm, T Gebhardt, V Touré, A Bagnacani, A Salehzadeh-Yazdi, ... BMC Systems Biology 12, 1-10, 2018 | 6 | 2018 |
| The CombineArchive Toolkit-facilitating the transfer of research results M Scharm, F Wendland, M Peters, M Wolfien, T Theile, D Waltemath PeerJ PrePrints 2, e514v1, 2014 | 4 | 2014 |
| Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models M Jalili, M Scharm, O Wolkenhauer, A Salehzadeh-Yazdi NPJ Systems Biology and Applications 9 (1), 15, 2023 | 3 | 2023 |
| Improving reproducibility and reuse of modelling results in the life sciences M Scharm Dissertation, Rostock, Universität Rostock, 2018, 2018 | 3 | 2018 |
| Exploring the evolution of biochemical models at the network level T Gebhardt, V Touré, D Waltemath, O Wolkenhauer, M Scharm Plos one 17 (3), e0265735, 2022 | 1 | 2022 |
| GEMtractor: extracting views into genome-scale metabolic models M Scharm, O Wolkenhauer, M Jalili, A Salehzadeh-Yazdi Bioinformatics 36 (10), 3281-3282, 2020 | 1 | 2020 |
