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ORCIDDagmar Waltemath
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- affiliation: University of Rostock, Germany
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2020 – today
- 2022
[j40]Anna Niarakis
, Dagmar Waltemath, James 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)- [c12]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 - [c11]Ron Henkel, Lea Gütebier, Dagmar Waltemath:
CovidGraph: Integrating COVID-19 Data. MIE 2022: 711-712 - 2021
- [j39]Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly 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]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]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]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) - [c10]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]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]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]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]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]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
- 2019
- [j31]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]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]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
- [j28]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]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]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) - [j25]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]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]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]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]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) - [i5]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
- [j20]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]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) - [j18]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) - [c8]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 - [i4]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
- [j17]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]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]Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor 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]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]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]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]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 - [i3]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]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]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]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]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]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]Martin Scharm, Dagmar Waltemath:
Extracting reproducible simulation studies from model repositories using the combinearchive toolkit. BTW Workshops 2015: 137-142 - [i2]Ron Henkel, Fabienne Lambusch, Dagmar Waltemath:
Finding pattern in biochemical reaction networks - a sub-graph mining approach. PeerJ Prepr. 3: e1479 (2015) - 2014
- [j6]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) - [c5]Rebekka Alm, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel:
Annotation-Based Feature Extraction from Sets of SBML Models. DILS 2014: 81-95 - [c4]Ron Henkel, Dagmar Waltemath:
MaSyMoS: Finding Hidden Treasures in Model Repositories. SWAT4LS 2014 - [c3]Christian Rosenke, Dagmar Waltemath:
How Can Semantic Annotations Support the Identification of Network Similarities? SWAT4LS 2014 - [c2]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 - [p1]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 - [r1]Dagmar Waltemath, Nicolas Le Novère:
Simulation Experiment Description Markup Language (SED-ML). Encyclopedia of Computational Neuroscience 2014 - [i1]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]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]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
- [j4]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) - [j3]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) - [j2]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
- [j1]Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère, Dagmar Waltemath:
Ranked retrieval of Computational Biology models. BMC Bioinform. 11: 423 (2010)
Coauthor Index
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