Ranked retrieval of Computational Biology models. - Ron Henkel; Lukas Endler; André Peters; Nicolas Le Novère; Dagmar Waltemath (BMC Bioinform., 2010)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - Dagmar Waltemath; Richard R. Adams; Frank T. Bergmann; Michael Hucka; Fedor A. Kolpakov; Andrew K. Miller; Ion I. Moraru; David P. Nickerson; Sven Sahle; Jacky L. Snoep; Nicolas Le Novère (BMC Syst. Biol., 2011)

Das Sombi-Framework zum Ermitteln geeigneter Suchfunktionen für biologische Modelldatenbasen. - Dagmar Waltemath; Ron Henkel; Holger Meyer 001; Andreas Heuer 001 (Datenbank-Spektrum, 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Annotation-based storage and retrieval of models and simulation descriptions in computational biology - Dagmar Waltemath (2011)

Considerations of graph-based concepts to manage of computational biology models and associated simulations. - Ron Henkel; Nicolas Le Novère; Olaf Wolkenhauer; Dagmar Waltemath (GI-Jahrestagung, 2012)

Improving the reuse of computational models through version control. - Dagmar Waltemath; Ron Henkel; Robert Hälke; Martin Scharm; Olaf Wolkenhauer (Bioinform., 2013)

Information Retrieval in Life Sciences: A Programmatic Survey. - Matthias Lange 001; Ron Henkel; Wolfgang Müller 001; Dagmar Waltemath; Stephan Weise (Approaches in Integrative Bioinformatics, 2014)

Annotation-Based Feature Extraction from Sets of SBML Models. - Rebekka Alm; Dagmar Waltemath; Olaf Wolkenhauer; Ron Henkel (DILS, 2014)

MaSyMoS: Finding Hidden Treasures in Model Repositories. - Ron Henkel; Dagmar Waltemath (SWAT4LS, 2014)

How Can Semantic Annotations Support the Identification of Network Similarities? - Christian Rosenke; Dagmar Waltemath (SWAT4LS, 2014)

The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results. - Martin Scharm; Florian Wendland; Martin Peters; Markus Wolfien; Tom Theile; Dagmar Waltemath (SWAT4LS, 2014)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T. Bergmann; Richard R. Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (BMC Bioinform., 2014)

COMBINE archive: One File To Share Them All. - Frank T. Bergmann; Richard Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (CoRR, 2014)

Simulation Experiment Description Markup Language (SED-ML). - Dagmar Waltemath; Nicolas Le Novère (Encyclopedia of Computational Neuroscience, 2014)

Extracting reproducible simulation studies from model repositories using the combinearchive toolkit. - Martin Scharm; Dagmar Waltemath (BTW Workshops, 2015)

Combining computational models, semantic annotations and simulation experiments in a graph database. - Ron Henkel; Olaf Wolkenhauer; Dagmar Waltemath (Database J. Biol. Databases Curation, 2015)

Annotation-based feature extraction from sets of SBML models. - Rebekka Alm; Dagmar Waltemath; Markus Wolfien; Olaf Wolkenhauer; Ron Henkel (J. Biomed. Semant., 2015)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. - Frank T. Bergmann; Jonathan Cooper; Nicolas Le Novère; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2015)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2015)

Specifications of Standards in Systems and Synthetic Biology. - Falk Schreiber; Gary D. Bader; Martin Golebiewski; Michael Hucka; Benjamin Kormeier; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Stephan Weise (J. Integr. Bioinform., 2015)

Finding pattern in biochemical reaction networks - a sub-graph mining approach. - Ron Henkel; Fabienne Lambusch; Dagmar Waltemath (PeerJ Prepr., 2015)

Challenges and opportunities for system biology standards and tools in medical research. - Matthias König 003; Anika Oellrich; Dagmar Waltemath; Richard J. B. Dobson; Tim J. P. Hubbard; Olaf Wolkenhauer (ODLS, 2016)

An algorithm to detect and communicate the differences in computational models describing biological systems. - Martin Scharm; Olaf Wolkenhauer; Dagmar Waltemath (Bioinform., 2016)

COMODI: an ontology to characterise differences in versions of computational models in biology. - Martin Scharm; Dagmar Waltemath; Pedro Mendes 001; Olaf Wolkenhauer (J. Biomed. Semant., 2016)

STON: exploring biological pathways using the SBGN standard and graph databases. - Vasundra Touré; Alexander Mazein; Dagmar Waltemath; Irina Balaur; Mansoor A. S. Saqi; Ron Henkel; Johann Pellet; Charles Auffray (BMC Bioinform., 2016)

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. - Martin Scharm; Dagmar Waltemath (F1000Research, 2016)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2016)

Finding patterns in biochemical reaction networks. - Ron Henkel; Fabienne Lambusch; Olaf Wolkenhauer; Kurt Sandkuhl; Christian Rosenke; Dagmar Waltemath (PeerJ Prepr., 2016)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. - Dagmar Waltemath; Olaf Wolkenhauer (IEEE Trans. Biomed. Eng., 2016)

A brief history of COMBINE. - Chris J. Myers; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; David P. Nickerson; Falk Schreiber; Dagmar Waltemath (WSC, 2017)

Notions of similarity for systems biology models. - Ron Henkel; Robert Hoehndorf; Tim Kacprowski; Christian Knüpfer; Wolfram Liebermeister; Dagmar Waltemath (Briefings Bioinform., 2017)

SED-ML web tools: generate, modify and export standard-compliant simulation studies. - Frank T. Bergmann; David P. Nickerson; Dagmar Waltemath; Martin Scharm (Bioinform., 2017)

The JWS online simulation database. - Martin Peters; Johann J. Eicher; David D. van Niekerk; Dagmar Waltemath; Jacky L. Snoep (Bioinform., 2017)

Identifying frequent patterns in biochemical reaction networks: a workflow. - Fabienne Lambusch; Dagmar Waltemath; Olaf Wolkenhauer; Kurt Sandkuhl; Christian Rosenke; Ron Henkel (Database J. Biol. Databases Curation, 2018)

Evolution of computational models in BioModels Database and the Physiome Model Repository. - Martin Scharm; Tom Gebhardt; Vasundra Touré; Andrea Bagnacani; Ali Salehzadeh-Yazdi; Olaf Wolkenhauer; Dagmar Waltemath (BMC Syst. Biol., 2018)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. - Falk Schreiber; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2018)

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. - Vasundra Touré; Nicolas Le Novère; Dagmar Waltemath; Olaf Wolkenhauer (PLoS Comput. Biol., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. - Falk Schreiber; Björn Sommer 001; Gary D. Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2019)

Towards standardization guidelines for in silico approaches in personalized medicine. - Søren Brunak; Catherine Bjerre Collin; Katharina Eva Ó Cathaoir; Martin Golebiewski; Marc Kirschner; Ingrid Kockum; Heike Moser; Dagmar Waltemath (J. Integr. Bioinform., 2020)

Open modeling and exchange (OMEX) metadata specification version 1.0. - Maxwell Lewis Neal; John H. Gennari; Dagmar Waltemath; David P. Nickerson; Matthias König 003 (J. Integr. Bioinform., 2020)

Specifications of standards in systems and synthetic biology: status and developments in 2020. - Falk Schreiber; Björn Sommer 001; Tobias Czauderna; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2020)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). - Dagmar Waltemath; Martin Golebiewski; Michael L. Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M. Keating; Matthias König 003; Olga Krebs; Rahuman S. Malik-Sheriff; David P. Nickerson; et al. (J. Integr. Bioinform., 2020)

Investigating the FAIR Equivalency in National Guidance in Health in Kenya. - Esther Thea Inau; Reginald Nalugala; William Muhadi Nandwa; Fredrick Obwanda; Antony Wachira; Dagmar Waltemath; Antonio Cartaxo; Atinkut Zeleke (EFMI-STC, 2021)

Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies. - Carsten Oliver Schmidt; Johannes Darms; Aliaksandra Shutsko; Matthias Löbe; Rajini Nagrani; Bastian Seifert; Birte Lindstädt; Martin Golebiewski; Sofiya Koleva; Theresa Bender; Christian Robert Bauer; Ulrich Sax; et al. (MIE, 2021)

COVIDGraph: Connecting Biomedical COVID-19 Resources and Computational Biology Models. - Martin Preusse; Alexander Jarasch; Tim Bleimehl; Sebastian Müller; Jamie Munro; Lea Gütebier; Ron Henkel; Dagmar Waltemath (SEA-Data@VLDB, 2021)

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. - Adrien Rougny; Vasundra Touré; John Albanese; Dagmar Waltemath; Denis Shirshov; Anatoly A. Sorokin; Gary D. Bader; Michael L. Blinov; Alexander Mazein (Briefings Bioinform., 2021)

OMEX metadata specification (version 1.2). - John H. Gennari; Matthias König 003; Goksel Misirli; Maxwell Lewis Neal; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2021)

Specifications of standards in systems and synthetic biology: status and developments in 2021. - Falk Schreiber; Padraig Gleeson; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath (J. Integr. Bioinform., 2021)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2021)

CovidGraph: Integrating COVID-19 Data. - Ron Henkel; Lea Gütebier; Dagmar Waltemath (MIE, 2022)

Disparities in Regional Publication Trends on the Topic of Artificial Intelligence in Biomedical Science Over the Last Five Years: A Bibliometric Analysis. - Kirubel Biruk Shiferaw; Dagmar Waltemath; Atinkut Zeleke (MIE, 2022)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

CovidGraph: a graph to fight COVID-19. - Lea Gütebier; Tim Bleimehl; Ron Henkel; Jamie Munro; Sebastian Müller; Axel Morgner; Jakob Laenge; Anke Pachauer; Alexander Erdl; Jens Weimar; Kirsten Walther Langendorf; Vincent Vialard; et al. (Bioinform., 2022)

Building the Next Generation of Data Savvy Biomedical Researchers. - Jens Dierkes; Birte Lindstädt; Ulrich Sax; Canan Hastik; Julia Fürst; Tanja Hörner; Sebastian Klammt; Ines Perrar; Iris Pigeot; Katja Restel; Carsten Oliver Schmidt; Aliaksandra Shutsko; et al. (CoRDI, 2023)

A Survey on the Current Status of Research Data Management in Mecklenburg-Vorpommern Preliminary Results for a Questionnaire Study Among Researchers. - Max Schröder; Sascha Genehr; Rüdiger Köhling; Stefan Schmidt; Ralf Schneider; Sascha Spors; Gero Szepannek; Dagmar Waltemath; Frank Krüger 001 (CoRDI, 2023)

Experiences From FAIRifying Community Data and FAIR Infrastructure in Biomedical Research Domains. - Dagmar Waltemath; Esther Thea Inau; Lea Michaelis; Venkata P. Satagopam; Irina Balaur (CoRDI, 2023)

Herding Cats in Pandemic Times - Towards Technological and Organizational Convergence of Heterogeneous Solutions for Investigating and Mastering the Pandemic in University Medical Centers. - Dagmar Krefting; Nico T. Mutters; Rüdiger Pryss; Martin Sedlmayr; Martin Boeker; Christoph Dieterich; Carolin Koll; Martina Mueller; Anna Slagman; Dagmar Waltemath; Antje Wulff; Sven Zenker (MedInfo, 2023)

Identifying Relevant FHIR Elements for Data Quality Assessment in the German Core Data Set. - Christian Draeger; Erik Tute; Carsten Oliver Schmidt; Dagmar Waltemath; Martin Boeker; Alfred Winter; Matthias Löbe (MIE, 2023)

Exploring Use Cases for CovidGraph. - Lea Gütebier; Ron Henkel; Christian Niklas; Dagmar Waltemath (MIE, 2023)

Harvesting the Low Hanging Fruits From the FAIRtree. - Esther Thea Inau; Atinkut Zeleke; Dagmar Waltemath (MIE, 2023)

Exploring New Possibilities for Research Data Exploration Using the Example of the German Core Data Set. - Felix Menzel; Dagmar Waltemath; Ron Henkel (MIE, 2023)

Insights into the FAIRness of the German Network University Medicine: A Survey. - Lea Michaelis; Rasim Atakan Poyraz; Michael Rusongoza Muzoora; Kerstin Gierend; Alexander Bartschke; Christoph Dieterich; Tim Johann; Dagmar Krefting; Dagmar Waltemath; Sylvia Thun (MIE, 2023)

Assessing the FAIRness of Deep Learning Models in Cardiovascular Disease Using Computed Tomography Images: Data and Code Perspective. - Kirubel Biruk Shiferaw; Atinkut Zeleke; Dagmar Waltemath (MIE, 2023)

Representing Sex and Gender Information in Biomedical Research. - Dagmar Waltemath; Hilke Beelich; Philipp Töpfer; Corinna Bergelt; Agnes Flöel; Elpiniki Katsari; Elke Krüger; Stine Lutze; Michael Schöner; Sebastian Paschen; Moritz Roloff; Hanne Roth; et al. (MIE, 2023)

Contributions to the reuse and reproducibility of computational biology models. - Ron Henkel; Dagmar Waltemath (SWAT4HCLS, 2023)

First Steps Towards the FAIRification of the DZD CORE DATASET at the German Center for Diabetes Research. - Esther Thea Inau; Angela Dedie; Ivona Anastasova; Andreas Birkenfeld; Brigitte Fröhlich; Martin Hrabe de Angelis; Michael Roden; Renate Schick; Yaroslav Zdravomyslov; Atinkut Zeleke; Dagmar Waltemath; Martin Preusse (SWAT4HCLS, 2023)

Experiences from compiling a FAIR survey in the German Network University Medicine. - Lea Michaelis; Rasim Atakan Poyraz; Michael Rusongoza Muzoora; Kerstin Gierend; Alexander Bartschke; Dagmar Waltemath; Sylvia Thun (SWAT4HCLS, 2023)

MeDaX project plan: How to sustainably improve biomedical (research) data management. - Judith A. H. Wodke; Ron Henkel; Dagmar Waltemath (SWAT4HCLS, 2023)

TAPP: Defining standard provenance information for clinical research data and workflows - Obstacles and opportunities. - Kerstin Gierend; Judith A. H. Wodke; Sascha Genehr; Robert Gött; Ron Henkel; Frank Krüger 001; Markus Mandalka; Lea Michaelis; Alexander Scheuerlein; Max Schröder; Atinkut Zeleke; Dagmar Waltemath (WWW (Companion Volume), 2023)

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. - Matthias König 003; Padraig Gleeson; Martin Golebiewski; Thomas E. Gorochowski; Michael Hucka; Sarah M. Keating; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Falk Schreiber (J. Integr. Bioinform., 2023)

Towards FAIR Data Workflows for Multidisciplinary Science: Ongoing Endeavors and Future Perspectives in Plasma Technology. - Robert Wagner; Dagmar Waltemath; Kristina Yordanova; Markus M. Becker (DATA, 2024)

MeDaX: A Knowledge Graph on FHIR. - Ilya Mazein; Tom Gebhardt; Lea Michaelis; Dagmar Waltemath; Ron Henkel (MIE, 2024)

MeDaX Prototype v0.2. - Ilya Mazein; Sarah Braun; Tom Gebhardt; Ron Henkel; Lea Michaelis; Dagmar Waltemath; Judith A. H. Wodke (SWAT4HCLS, 2024)

Applying the RDA Data Maturity Model on the Core Dataset of the German Medical Informatics Initiative. - Lea Michaelis; Esther Thea Inau; Michael Rusongoza Muzoora; Judith A. H. Wodke; Thomas Ganslandt; Sylvia Thun; Dagmar Waltemath (SWAT4HCLS, 2024)

Graph databases in systems biology: a systematic review. - Ilya Mazein; Adrien Rougny; Alexander Mazein; Ron Henkel; Lea Gütebier; Lea Michaelis; Marek Ostaszewski; Reinhard Schneider 002; Venkata P. Satagopam; Lars Juhl Jensen; Dagmar Waltemath; Judith A. H. Wodke; et al. (Briefings Bioinform., 2024)

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. - Martin Golebiewski; Gary D. Bader; Padraig Gleeson; Thomas E. Gorochowski; Sarah M. Keating; Matthias König 003; Chris J. Myers; David P. Nickerson; Björn Sommer 001; Dagmar Waltemath; Falk Schreiber (J. Integr. Bioinform., 2024)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2024)

Making Epidemiological and Clinical Studies FAIR Using the Example of COVID-19. - Iris Pigeot; Wolfgang Ahrens; Johannes Darms; Juliane Fluck; Martin Golebiewski; Horst K. Hahn; Xiaoming Hu; Timm Intemann; Elisa Kasbohm; Toralf Kirsten; Sebastian Klammt; Sophie Anne Ines Klopfenstein; et al. (Datenbank-Spektrum, 2024)