A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

by Scharm, Martin, Waltemath, Dagmar
Published in F1000Res (2016)

Combining computational models, semantic annotations and simulation experiments in a graph database

by Henkel, Ron, Wolkenhauer, Olaf, Waltemath, Dagmar
Published in Database (Oxford) (2015)

An algorithm to detect and communicate the differences in computational models describing biological systems

by Scharm, Martin, Wolkenhauer, Olaf, Waltemath, Dagmar
Published in Bioinformatics (2016)

COMODI: an ontology to characterise differences in versions of computational models in biology

by Scharm, Martin, Waltemath, Dagmar, Mendes, Pedro, Wolkenhauer, Olaf
Published in J Biomed Semantics (2016)

SED-ML web tools: generate, modify and export standard-compliant simulation studies

by Bergmann, Frank T, Nickerson, David, Waltemath, Dagmar, Scharm, Martin
Published in Bioinformatics (2017)

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

by Touré, Vasundra, Le Novère, Nicolas, Waltemath, Dagmar, Wolkenhauer, Olaf
Published in PLoS Comput Biol (2018)

Annotation-based feature extraction from sets of SBML models

by Alm, Rebekka, Waltemath, Dagmar, Wolfien, Markus, Wolkenhauer, Olaf, Henkel, Ron
Published in J Biomed Semantics (2015)

Initiatives, Concepts, and Implementation Practices of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles in Health Data Stewardship Practice: Protocol for a...

by Inau, Esther Thea, Sack, Jean, Waltemath, Dagmar, Zeleke, Atinkut Alamirrew
Published in JMIR Res Protoc (2021)

Ranked retrieval of Computational Biology models

by Henkel, Ron, Endler, Lukas, Peters, Andre, Le Novère, Nicolas, Waltemath, Dagmar
Published 2010

Notions of similarity for systems biology models

by Henkel, Ron, Hoehndorf, Robert, Kacprowski, Tim, Knüpfer, Christian, Liebermeister, Wolfram, Waltemath, Dagmar
Published in Brief Bioinform (2016)

Notions of similarity for systems biology models

by Henkel, Ron, Hoehndorf, Robert, Kacprowski, Tim, Knüpfer, Christian, Liebermeister, Wolfram, Waltemath, Dagmar
Published in Brief Bioinform (2017)

Identifying frequent patterns in biochemical reaction networks: a workflow

by Lambusch, Fabienne, Waltemath, Dagmar, Wolkenhauer, Olaf, Sandkuhl, Kurt, Rosenke, Christian, Henkel, Ron
Published in Database (Oxford) (2018)

Open modeling and exchange (OMEX) metadata specification version 1.0

by Neal, Maxwell L., Gennari, John H., Waltemath, Dagmar, Nickerson, David P., König, Matthias
Published in J Integr Bioinform (2020)

Evolution of computational models in BioModels Database and the Physiome Model Repository

by Scharm, Martin, Gebhardt, Tom, Touré, Vasundra, Bagnacani, Andrea, Salehzadeh-Yazdi, Ali, Wolkenhauer, Olaf, Waltemath, Dagmar
Published in BMC Syst Biol (2018)

STON: exploring biological pathways using the SBGN standard and graph databases

by Touré, Vasundra, Mazein, Alexander, Waltemath, Dagmar, Balaur, Irina, Saqi, Mansoor, Henkel, Ron, Pellet, Johann, Auffray, Charles
Published in BMC Bioinformatics (2016)

Towards standardization guidelines for in silico approaches in personalized medicine

by Brunak, Søren, Bjerre Collin, Catherine, Eva Ó Cathaoir, Katharina, Golebiewski, Martin, Kirschner, Marc, Kockum, Ingrid, Moser, Heike, Waltemath, Dagmar
Published in J Integr Bioinform (2020)

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

by Bergmann, Frank T., Cooper, Jonathan, König, Matthias, Moraru, Ion, Nickerson, David, Le Novère, Nicolas, Olivier, Brett G., Sahle, Sven, Smith, Lucian, Waltemath, Dagmar
Published in J Integr Bioinform (2018)

Specifications of Standards in Systems and Synthetic Biology

by Schreiber, Falk, Bader, Gary D., Golebiewski, Martin, Hucka, Michael, Kormeier, Benjamin, Le Novère, Nicolas, Myers, Chris, Nickerson, David, Sommer, Björn, Waltemath, Dagmar, Weise, Stephan
Published in J Integr Bioinform (2015)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

by Schreiber, Falk, Sommer, Björn, Bader, Gary D., Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Keating, Sarah M., König, Matthias, Myers, Chris, Nickerson, David, Waltemath, Dagmar
Published in J Integr Bioinform (2019)

Specifications of standards in systems and synthetic biology: status and developments in 2020

by Schreiber, Falk, Sommer, Björn, Czauderna, Tobias, Golebiewski, Martin, Gorochowski, Thomas E., Hucka, Michael, Keating, Sarah M., König, Matthias, Myers, Chris, Nickerson, David, Waltemath, Dagmar
Published in J Integr Bioinform (2020)