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Dagmar Waltemath

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affiliation: University of Rostock, Germany

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2020 – today

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2024
[j45]
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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, Bianca Lassen-Schmidt, Manuela Peters, Ulrich Sax, Dagmar Waltemath, Carsten Oliver Schmidt:
Making Epidemiological and Clinical Studies FAIR Using the Example of COVID-19. Datenbank-Spektrum 24(2): 117-128 (2024)
[j44]
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Martin Golebiewski, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. 21(1) (2024)
[j43]
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Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21(1) (2024)
[c31]
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Robert Wagner, Dagmar Waltemath, Kristina Yordanova, Markus M. Becker:
Towards FAIR Data Workflows for Multidisciplinary Science: Ongoing Endeavors and Future Perspectives in Plasma Technology. DATA 2024: 471-477
[c30]
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Ilya Mazein, Tom Gebhardt, Lea Michaelis, Dagmar Waltemath, Ron Henkel:
MeDaX: A Knowledge Graph on FHIR. MIE 2024: 367-371
2023
[j42]
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Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J. Integr. Bioinform. 20(1) (2023)
[c29]
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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, Dagmar Waltemath, Atinkut Zeleke:
Building the Next Generation of Data Savvy Biomedical Researchers. CoRDI 2023
[c28]
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Max Schröder, Sascha Genehr, Rüdiger Köhling, Stefan Schmidt, Ralf Schneider, Sascha Spors, Gero Szepannek, Dagmar Waltemath, Frank Krüger:
A Survey on the Current Status of Research Data Management in Mecklenburg-Vorpommern Preliminary Results for a Questionnaire Study Among Researchers. CoRDI 2023
[c27]
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Dagmar Waltemath, Esther Thea Inau, Lea Michaelis, Venkata P. Satagopam, Irina Balaur:
Experiences From FAIRifying Community Data and FAIR Infrastructure in Biomedical Research Domains. CoRDI 2023
[c26]
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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:
Herding Cats in Pandemic Times - Towards Technological and Organizational Convergence of Heterogeneous Solutions for Investigating and Mastering the Pandemic in University Medical Centers. MedInfo 2023: 1271-1275
[c25]
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Kirubel Biruk Shiferaw, Atinkut Zeleke, Dagmar Waltemath:
Assessing the FAIRness of Deep Learning Models in Cardiovascular Disease Using Computed Tomography Images: Data and Code Perspective. MIE 2023: 63-67
[c24]
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Christian Draeger, Erik Tute, Carsten Oliver Schmidt, Dagmar Waltemath, Martin Boeker, Alfred Winter, Matthias Löbe:
Identifying Relevant FHIR Elements for Data Quality Assessment in the German Core Data Set. MIE 2023: 272-276
[c23]
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Esther Thea Inau, Atinkut Zeleke, Dagmar Waltemath:
Harvesting the Low Hanging Fruits From the FAIRtree. MIE 2023: 390-391
[c22]
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Lea Michaelis, Rasim Atakan Poyraz, Michael Rusongoza Muzoora, Kerstin Gierend, Alexander Bartschke, Christoph Dieterich, Tim Johann, Dagmar Krefting, Dagmar Waltemath, Sylvia Thun:
Insights into the FAIRness of the German Network University Medicine: A Survey. MIE 2023: 741-742
[c21]
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Lea Gütebier, Ron Henkel, Christian Niklas, Dagmar Waltemath:
Exploring Use Cases for CovidGraph. MIE 2023: 747-748
[c20]
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Felix Menzel, Dagmar Waltemath, Ron Henkel:
Exploring New Possibilities for Research Data Exploration Using the Example of the German Core Data Set. MIE 2023: 749-750
[c19]
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Dagmar Waltemath, Hilke Beelich, Philipp Töpfer, Corinna Bergelt, Agnes Flöel, Elpiniki Katsari, Elke Krüger, Stine Lutze, Michael Schöner, Sebastian Paschen, Moritz Roloff, Hanne Roth, Sylvia Stracke:
Representing Sex and Gender Information in Biomedical Research. MIE 2023: 757-758
[c18]
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Ron Henkel, Dagmar Waltemath:
Contributions to the reuse and reproducibility of computational biology models. SWAT4HCLS 2023: 122-123
[c17]
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Judith A. H. Wodke, Ron Henkel, Dagmar Waltemath:
MeDaX project plan: How to sustainably improve biomedical (research) data management. SWAT4HCLS 2023: 133-134
[c16]
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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:
First Steps Towards the FAIRification of the DZD CORE DATASET at the German Center for Diabetes Research. SWAT4HCLS 2023: 139-140
[c15]
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Lea Michaelis, Rasim Atakan Poyraz, Michael Rusongoza Muzoora, Kerstin Gierend, Alexander Bartschke, Dagmar Waltemath, Sylvia Thun:
Experiences from compiling a FAIR survey in the German Network University Medicine. SWAT4HCLS 2023: 157-158
[c14]
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Kerstin Gierend, Judith A. H. Wodke, Sascha Genehr, Robert Gött, Ron Henkel, Frank Krüger, Markus Mandalka, Lea Michaelis, Alexander Scheuerlein, Max Schröder, Atinkut Zeleke, Dagmar Waltemath:
TAPP: Defining standard provenance information for clinical research data and workflows - Obstacles and opportunities. WWW (Companion Volume) 2023: 1551-1554
2022
[j41]
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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, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022)
[j40]
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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, Thorsten Liebig, Martin Preusse, Dagmar Waltemath, Alexander Jarasch:
CovidGraph: a graph to fight COVID-19. Bioinform. 38(20): 4843-4845 (2022)
[c13]
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Kirubel Biruk Shiferaw, Dagmar Waltemath, Atinkut Zeleke:
Disparities in Regional Publication Trends on the Topic of Artificial Intelligence in Biomedical Science Over the Last Five Years: A Bibliometric Analysis. MIE 2022: 609-613
[c12]
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Ron Henkel, Lea Gütebier, Dagmar Waltemath:
CovidGraph: Integrating COVID-19 Data. MIE 2022: 711-712
2021
[j39]
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Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly A. Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein:
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings Bioinform. 22(5) (2021)
[j38]
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John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath:
OMEX metadata specification (version 1.2). J. Integr. Bioinform. 18(3) (2021)
[j37]
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Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2021. J. Integr. Bioinform. 18(3) (2021)
[j36]
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Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18(3) (2021)
[c11]
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Esther Thea Inau, Reginald Nalugala, William Muhadi Nandwa, Fredrick Obwanda, Antony Wachira, Dagmar Waltemath, Antonio Cartaxo, Atinkut Zeleke:
Investigating the FAIR Equivalency in National Guidance in Health in Kenya. EFMI-STC 2021: 59-60
[c10]
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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, Xiaoming Hu, Michael Lieser, Vivien Junker, Sophie Klopfenstein, Atinkut Zeleke, Dagmar Waltemath, Iris Pigeot, Juliane Fluck:
Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies. MIE 2021: 794-798
[c9]
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Martin Preusse, Alexander Jarasch, Tim Bleimehl, Sebastian Muller, Jamie Munro, Lea Gütebier, Ron Henkel, Dagmar Waltemath:
COVIDGraph: Connecting Biomedical COVID-19 Resources and Computational Biology Models. SEA-Data@VLDB 2021: 34-37
2020
[j35]
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Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath:
Towards standardization guidelines for in silico approaches in personalized medicine. J. Integr. Bioinform. 17(2-3) (2020)
[j34]
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Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König:
Open modeling and exchange (OMEX) metadata specification version 1.0. J. Integr. Bioinform. 17(2-3) (2020)
[j33]
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Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2020. J. Integr. Bioinform. 17(2-3) (2020)
[j32]
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Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers:
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17(2-3) (2020)

2010 – 2019

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2019
[j31]
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Maxwell Lewis Neal, Matthias König, 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, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019)
[j30]
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Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019)
[j29]
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Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16(2) (2019)
2018
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Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 19(1): 77-88 (2018)
[j27]
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Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks: a workflow. Database J. Biol. Databases Curation 2018: bay051 (2018)
[j26]
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Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath:
Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Syst. Biol. 12(1): 53:1-53:10 (2018)
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Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J. Integr. Bioinform. 15(1) (2018)
[j24]
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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, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018)
[j23]
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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, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018)
[j22]
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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, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15(1) (2018)
[j21]
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Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer:
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput. Biol. 14(2) (2018)
[i6]
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Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 6: e1479 (2018)
2017
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Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath:
Notions of similarity for systems biology models. Briefings Bioinform. 18(5): 902 (2017)
[j19]
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Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm:
SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinform. 33(8): 1253-1254 (2017)
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Martin Peters, Johann J. Eicher, David D. van Niekerk, Dagmar Waltemath, Jacky L. Snoep:
The JWS online simulation database. Bioinform. 33(10): 1589-1590 (2017)
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Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath:
A brief history of COMBINE. WSC 2017: 884-895
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Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks - a workflow. PeerJ Prepr. 5: e1479 (2017)
2016
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Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath:
An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinform. 32(4): 563-570 (2016)
[j16]
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Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer:
COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. 7: 46 (2016)
[j15]
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Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor A. S. Saqi, Ron Henkel, Johann Pellet, Charles Auffray:
STON: exploring biological pathways using the SBGN standard and graph databases. BMC Bioinform. 17: 494:1-494:9 (2016)
[j14]
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Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13(3) (2016)
[j13]
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Dagmar Waltemath, Olaf Wolkenhauer:
How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans. Biomed. Eng. 63(10): 1999-2006 (2016)
[j12]
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Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber:
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63(10): 2007-2014 (2016)
[c7]
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Matthias König, Anika Oellrich, Dagmar Waltemath, Richard J. B. Dobson, Tim J. P. Hubbard, Olaf Wolkenhauer:
Challenges and opportunities for system biology standards and tools in medical research. ODLS 2016: 1-6
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Martin Scharm, Dagmar Waltemath:
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5: 2421 (2016)
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Ron Henkel, Fabienne Lambusch, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Dagmar Waltemath:
Finding patterns in biochemical reaction networks. PeerJ Prepr. 4: e1479 (2016)
2015
[j11]
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Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath:
Combining computational models, semantic annotations and simulation experiments in a graph database. Database J. Biol. Databases Curation 2015 (2015)
[j10]
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Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer, Ron Henkel:
Annotation-based feature extraction from sets of SBML models. J. Biomed. Semant. 6: 20 (2015)
[j9]
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Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. J. Integr. Bioinform. 12(2) (2015)
[j8]
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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, Darren J. Wilkinson:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015)
[j7]
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Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Stephan Weise:
Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. 12(2) (2015)
[c6]
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Martin Scharm, Dagmar Waltemath:
Extracting reproducible simulation studies from model repositories using the combinearchive toolkit. BTW Workshops 2015: 137-142
[i2]
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Ron Henkel, Fabienne Lambusch, Dagmar Waltemath:
Finding pattern in biochemical reaction networks - a sub-graph mining approach. PeerJ Prepr. 3: e1479 (2015)
2014
[j6]
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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, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15: 369 (2014)
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Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel:
Annotation-Based Feature Extraction from Sets of SBML Models. DILS 2014: 81-95
[c4]
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Ron Henkel, Dagmar Waltemath:
MaSyMoS: Finding Hidden Treasures in Model Repositories. SWAT4LS 2014
[c3]
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Christian Rosenke, Dagmar Waltemath:
How Can Semantic Annotations Support the Identification of Network Similarities? SWAT4LS 2014
[c2]
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Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltemath:
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results. SWAT4LS 2014
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  - books/sp/14/LangeHMWW14
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Matthias Lange, Ron Henkel, Wolfgang Müller, Dagmar Waltemath, Stephan Weise:
Information Retrieval in Life Sciences: A Programmatic Survey. Approaches in Integrative Bioinformatics 2014: 73-109
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Dagmar Waltemath, Nicolas Le Novère:
Simulation Experiment Description Markup Language (SED-ML). Encyclopedia of Computational Neuroscience 2014
[i1]
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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, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive: One File To Share Them All. CoRR abs/1407.4992 (2014)
2013
[j5]
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Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer:
Improving the reuse of computational models through version control. Bioinform. 29(6): 742-748 (2013)
2012
[c1]
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Ron Henkel, Nicolas Le Novère, Olaf Wolkenhauer, Dagmar Waltemath:
Considerations of graph-based concepts to manage of computational biology models and associated simulations. GI-Jahrestagung 2012: 1545-1551
2011
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Dagmar Waltemath:
Annotation-based storage and retrieval of models and simulation descriptions in computational biology. Rostock University, Germany, 2011
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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:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (2011)
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Dagmar Waltemath, Ron Henkel, Holger Meyer, Andreas Heuer:
Das Sombi-Framework zum Ermitteln geeigneter Suchfunktionen für biologische Modelldatenbasen. Datenbank-Spektrum 11(1): 27-36 (2011)
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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, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011)
2010
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Ron Henkel, Lukas Endler, André Peters, Nicolas Le Novère, Dagmar Waltemath:
Ranked retrieval of Computational Biology models. BMC Bioinform. 11: 423 (2010)

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