Controlled vocabularies and semantics in systems biology

Cited by (283)

Items 101–200 of 283

1. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
   Dawson D. Payne, Alina Renz, Laura J. Dunphy, T. Lewis, A. Dräger, J. Papin · 2021 · bioRxiv
2. Reusing simulation experiment specifications to support developing models by successive extension
   Dan-Hua Peng, Tom Warnke, Fiete Haack, A. Uhrmacher · 2016 · Simulation modelling practice and theory
3. Annotation-based feature extraction from sets of SBML models
   Rebekka Alm, Dagmar Waltemath, M. Wolfien, O. Wolkenhauer, R. Henkel · 2015 · Journal of Biomedical Semantics
4. Challenges for an enzymatic reaction kinetics database
   Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, A. Weidemann, Wolfgang Müller, Isabel Rojas · 2014 · The FEBS Journal
5. Relating simulation studies by provenance—Developing a family of Wnt signaling models
   Budde, Kai, Smith, Jacob, Wilsdorf, Pia, Haack, Fiete, Uhrmacher, Adelinde M. · 2021 · PLOS Computational Biology
6. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
   Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski, M. Hucka, N. Le Novère, C. Myers, D. Nickerson, B. Sommer, D. Walthemath · 2016 · Journal of Integrative Bioinformatics
7. Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
   Goksel Misirli, M. Cavaliere, W. Waites, Matthew R. Pocock, C. Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, V. Danos, A. Wipat · 2015 · Bioinform.
8. Data management and data enrichment for systems biology projects.
   Ulrike Wittig, Maja Rey, A. Weidemann, Wolfgang Müller · 2017 · Journal of Biotechnology
9. Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility
   Jonathan R. Karr, Rahuman S. Malik-Sheriff, James Osborne, Gilberto C. González-Parra, Eric Forgoston, Ruth Bowness, Ya-Ling Liu, R. Thompson, W. Garira, J. Barhak et al. · 2022 · Frontiers in Systems Biology
10. Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus
    Alina Renz, Andreas Dräger · 2021 · npj Systems Biology and Applications
11. Knowledge representation and data sharing to unlock crop variation for nutritional food security
    Liliana Andrés-Hernández, A. Baten, Razlin Azman Halimi, R. Walls, G. King · 2020 · Crop science
12. Proceedings of the 2017 Winter Simulation Conference
    W. K. Chan, A. D'Ambrogio, G. Zacharewicz, N. Mustafee, G. Wainer, E. Page · 2017
13. From FAIR to CURE: Guidelines for Computational Models of Biological Systems
    Herbert M. Sauro, E. Agmon, M. Blinov, J. Gennari, Joseph L. Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E. Jardine, Elebeoba E. May, David P. Nickerson et al. · 2025 · arXiv.org
14. Synthetic biology open language (SBOL) version 3.1.0
    Lukas Buecherl, Tom Mitchell, James Scott-Brown, P. Vaidyanathan, G. Vidal, Hasan Baig, Bryan A. Bartley, Jacob Beal, M. Crowther, Pedro Fontanarrosa et al. · 2023 · Journal of Integrative Bioinformatics
15. Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology
    M. Blinov, J. Gennari, Jonathan R. Karr, I. Moraru, D. Nickerson, H. Sauro · 2021 · Current Opinion in Systems Biology
16. Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/ β -catenin signaling pathway
    Danhua Peng, Tom Warnke, Fiete Haack, Adelinde M. Uhrmacher · 2017 · SIMULATION
17. The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
    Smith, Lucian P., Bergmann, Frank T., Garny, Alan, Helikar, Tomáš, Karr, Jonathan, Nickerson, David, Sauro, Herbert, Waltemath, Dagmar, König, Matthias · 2021 · Journal of Integrative Bioinformatics
18. Specifications of standards in systems and synthetic biology: status and developments in 2020
    Schreiber, Falk, Sommer, Björn, Czauderna, Tobias, Golebiewski, Martin, Gorochowski, Thomas E., Hucka, Michael, Keating, Sarah M., König, Matthias, Myers, Chris, Nickerson, David et al. · 2020 · Journal of Integrative Bioinformatics
19. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
    Sarah M. Alghamdi, Beth A. Sundberg, John P. Sundberg, Paul N. Schofield, Robert Hoehndorf · 2019 · Scientific Reports
20. A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
    Dietrich Rebholz-Schuhmann, Christoph Grabmüller, Silvestras Kavaliauskas, Samuel Croset, Peter M. Woollard, R. Backofen, W. Filsell, Dominic Clark · 2014 · Drug Discovery Today
21. Hierarchical modeling for synthetic biology.
    D. Chandran, H. Sauro · 2012 · ACS Synthetic Biology
22. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
    Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novère, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C. et al. · 2015 · Journal of Integrative Bioinformatics
23. Graph databases in systems biology: a systematic review
    Ilya Mazein, Adrien Rougny, Alexander Mazein, Ron Henkel, Lea Gütebier, Lea Michaelis, Marek Ostaszewski, Reinhard Schneider, Venkata Satagopam, Lars Juhl Jensen et al. · 2024 · Briefings in Bioinformatics
24. Ten simple rules for creating reusable pathway models for computational analysis and visualization
    K. Hanspers, M. Kutmon, S. Coort, D. Digles, Lauren J Dupuis, F. Ehrhart, Finterly Hu, E. Lopes, Marvin Martens, Nhung Pham et al. · 2021 · PLoS Comput. Biol.
25. SBOannotator: a Python tool for the automated assignment of systems biology ontology terms
    Nantia Leonidou, Elisabeth Fritze, Alina Renz, A. Dräger · 2023 · Bioinform.
26. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
    Falk Schreiber, B. Sommer, Gary D Bader, Padraig Gleeson, Martin Golebiewski, M. Hucka, Sarah M. Keating, Matthias König, C. Myers, D. Nickerson et al. · 2019 · Journal of Integrative Bioinformatics
27. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
    C. Madsen, Ángel Goñi Moreno, Zachary Palchick, U. P, Nicholas Roehner, Bryan A. Bartley, Swapnil P. Bhatia, Shyam P. Bhakta, Mike Bissell, Kevin Clancy et al. · 2019 · Journal of Integrative Bioinformatics
28. phraSED-ML: A paraphrased, human-readable adaptation of SED-ML
    Kiri Choi, Lucian P. Smith, J. Medley, Herbert M. Sauro · 2016 · J. Bioinform. Comput. Biol.
29. Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform
    K. Wolstencroft, S. Owen, Olga Krebs, Wolfgang Müller, Quyen Nguyen, J. Snoep, C. Goble · 2013 · International Workshop on the Semantic Web
30. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
    Frank T. Bergmann, Jonathan Cooper, N. Le Novère, D. Nickerson, Dagmar Waltemath · 2015 · Journal of Integrative Bioinformatics
31. ModelBricks—modules for reproducible modeling improving model annotation and provenance
    Ann E. Cowan, Pedro Mendes, Michael L. Blinov · 2019 · npj Systems Biology and Applications
32. COMODI: an ontology to characterise differences in versions of computational models in biology
    Martin Scharm, Dagmar Waltemath, P. Mendes, O. Wolkenhauer · 2016 · Journal of Biomedical Semantics
33. Structure, function, and behaviour of computational models in systems biology
    Christian rer. nat. Knüpfer, Clemens Beckstein, Peter Dittrich, Nicolas Gambardella Le Novère · 2013 · BMC Systems Biology
34. Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
    Dagmar Waltemath, Frank T. Bergmann, R. Adams, N. Le Novère · 2011 · Nature Precedings
35. The synthetic biology open language.
    C. Myers, Kevin Clancy, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Jacqueline Quinn, Nicholas Roehner, H. Sauro · 2015 · Methods in molecular biology
36. A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism
    Garrett W. Roell, C. Schenk, Winston E. Anthony, Rhiannon Carr, A. Ponukumati, Joonhoon Kim, E. Akhmatskaya, Marcus B. Foston, G. Dantas, T. Moon et al. · 2023 · ACS Synthetic Biology
37. Examining organic acid production potential and growth‐coupled strategies in Issatchenkia orientalis using constraint‐based modeling
    Patrick F. Suthers, Costas D. Maranas · 2022 · Biotechnology Progress
38. Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species
    Iván Domenzain, Fei-Ran Li, E. Kerkhoven, V. Siewers · 2021 · FEMS Yeast Research
39. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
    M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, Aurelio Orta-Resendiz, Vidisha Singh, S. Aghamiri, M. Acencio, E. Glaab et al. · 2020 · bioRxiv
40. Synthetic biology open language visual (SBOL visual) version 2.2
    Hasan Baig, Pedro Fontanarrosa, V. Kulkarni, James Alastair McLaughlin, P. Vaidyanathan, Bryan A. Bartley, Swapnil P. Bhatia, Shyam P. Bhakta, Mike Bissell, Kevin Clancy et al. · 2020 · Journal of Integrative Bioinformatics
41. CSEO – the Cigarette Smoke Exposure Ontology
    E. Younesi, Sam Ansari, Michaela Gündel, Shiva Ahmadi, C. Coggins, J. Hoeng, M. Hofmann-Apitius, M. Peitsch · 2014 · Journal of Biomedical Semantics
42. Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products
    Mingxin Gan · 2014 · Comput. Math. Methods Medicine
43. A Distinct Expression Pattern of the Long 3′-Untranslated Region Dicer mRNA and Its Implications for Posttranscriptional Regulation in Colorectal Cancer
    Yasushi Hamaya, S. Kuriyama, T. Takai, Ken-ichi Yoshida, Takanori Yamada, M. Sugimoto, S. Osawa, K. Sugimoto, H. Miyajima, Shigeru Kanaoka · 2012 · Clinical and Translational Gastroenterology
44. Clinical Applications of Metabolic Models in SBML Format
    Alina Renz, Reihaneh Mostolizadeh, A. Dräger · 2020 · Elsevier eBooks
45. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine
    Vasundra Touré, A. Dräger, Augustin Luna, U. Dogrusoz, Adrien Rougny · 2020 · Systems Medicine
46. HuPSON: the human physiology simulation ontology
    Michaela Gündel, E. Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bi-Jun Zhang, B. de Bono, Heinz-Theodor Mevissen, M. Hofmann-Apitius · 2013 · Journal of Biomedical Semantics
47. Musculoskeletal Modelling and the Physiome Project
    Justin W. Fernandez, Ju Zhang, V. Shim, Jacob T. Munro, Massimo Sartori, T. Besier, D. Lloyd, D. Nickerson, P. Hunter · 2018 · Courses and lectures
48. Reproducibility of Model-Based Results in Systems Biology
    Dagmar Waltemath, R. Henkel, Felix Winter, O. Wolkenhauer · 2013 · Springer eBooks
49. Synthetic biology open language visual (SBOL Visual) version 2.3
    Hasan Baig, Pedro Fontanarossa, V. Kulkarni, James Alastair McLaughlin, P. Vaidyanathan, Bryan A. Bartley, Shyam P. Bhakta, Swapnil P. Bhatia, Mike Bissell, Kevin Clancy et al. · 2021 · Journal of Integrative Bioinformatics
50. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
    Alina Renz, Lina Widerspick, Andreas Dräger · 2021 · Metabolites
51. Nanoinformatics: Opportunities and challenges in the development and delivery of healthcare products in developing countries
    Professor Wilson Nwankwo, K. Ukhurebor · 2021 · IOP Conference Series: Earth and Environment
52. SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
    Adrien Rougny, Vasundra Touré, J. Albanese, D. Waltemath, Denis Shirshov, A. Sorokin, Gary D Bader, M. Blinov, A. Mazein · 2020 · bioRxiv
53. Integration of Structured Biological Data Sources using Biological Expression Language
    Charles Tapley Hoyt, D. Domingo-Fernándéz, S. Mubeen, J. Llaó, Andrej Konotopez, C. Ebeling, C. Birkenbihl, Ozlem Muslu, Brad English, Simon Müller et al. · 2019 · bioRxiv
54. Identifying frequent patterns in biochemical reaction networks: a workflow
    Fabienne Lambusch, Dagmar Waltemath, O. Wolkenhauer, K. Sandkuhl, Christian Rosenke, R. Henkel · 2018 · PeerJ Preprints
55. A brief history of COMBINE
    Chris John Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Gambardella Le Novère, David Phillip Nickerson, Falk Schreiber, Dagmar Waltemath · 2017 · Winter Simulation Conference
56. 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 Keating, Matthias König, Chris John Myers, David Phillip Nickerson, Björn Sommer, Dagmar Waltemath et al. · 2024 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
57. From knowledge to models: Automated modeling in systems and synthetic biology
    B. Gyori, John A. Bachman · 2021 · Current Opinion in Systems Biology
58. Converting Alzheimer's Disease Map into a Heavyweight Ontology: A Formal Network to Integrate Data
    Vincent Henry, I. Moszer, O. Dameron, M. Potier, M. Hofmann-Apitius, O. Colliot · 2018 · Data Integration in the Life Sciences
59. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
    Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski, M. Hucka, Sarah M. Keating, N. Le Novère, C. Myers, D. Nickerson, B. Sommer et al. · 2018 · Journal of Integrative Bioinformatics
60. Qualitative dynamics semantics for SBGN process description
    Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Paulevé · 2016 · BMC Systems Biology
61. The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models
    R. Adams, N. Tsorman, K. Stratford, O. Akman, Stephen Gilmore, N. Juty, N. Le Novère, A. Millar · 2012 · Journal of Biological Rhythms
62. Tav4SB: integrating tools for analysis of kinetic models of biological systems
    M. Rybiński, Michal Lula, Pawel Banasik, S. Lasota, A. Gambin · 2012 · BMC Systems Biology
63. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling
    Nantia Leonidou, Yufan Xia, Lea Friedrich, Monika Schütz, Andreas Dräger · 2024 · PLoS Pathogens
64. SBOL Visual 2 Ontology
    Goksel Misirli, J. Beal, Thomas E. Gorochowski, G. Stan, A. Wipat, C. Myers · 2020 · bioRxiv
65. A physiome interoperability roadmap for personalized drug development
    Simon Thomas, Katherine Wolstencroft, Bernard de Bono, Peter John Hunter · 2016 · Interface Focus
66. In Silico Cell: Challenges and Perspectives
    Ilya R. Akberdin · 2013 · Mathematical Biology and Bioinformatics
67. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
    Frank T. Bergmann, Jonathan Cooper, N. Le Novère, D. Nickerson, Dagmar Waltemath · 2015 · Journal of Integrative Bioinformatics
68. Simulation Experiment Description Markup Language (SED-ML)
    Dagmar Waltemath, N. Le Novère · 2014 · Encyclopedia of Computational Neuroscience
69. Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks–What about specialised metabolism?
    Delphine Nègre, A. Larhlimi, Samuel Bertrand · 2023 · bioRxiv
70. A semantics, energy-based approach to automate biomodel composition
    Niloofar Shahidi, M. Pan, K. Tran, E. Crampin, D. Nickerson · 2021 · bioRxiv
71. Synthetic Biology Curation Tools (SYNBICT).
    Nicholas Roehner, Jeanet V. Mante, C. Myers, J. Beal · 2021 · ACS Synthetic Biology
72. Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node
    Christopher Schölzel, Valeria Blesius, G. Ernst, A. Goesmann, Andreas Dominik · 2021 · bioRxiv
73. BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
    Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, D. Natale, Jonathan R. Karr · 2019 · Genome Biology
74. The Dangers of Plug-and-Play Simulation Using Shared Models
    E. De Schutter · 2014 · Neuroinformatics
75. Towards a semantic representation for multi-scale finite element biosimulation experiments
    André Freitas, Margaret Jones, Kartik Asooja, Christos Bellos, Steve J. Elliott, S. Stenfelt, Panagiotis Hasapis, Christos Georgousopoulos, T. Marquardt, N. Filipović et al. · 2013 · International Conferences on Biological Information and Biomedical Engineering
76. SED-ED, a workflow editor for computational biology experiments written in SED-ML
    R. Adams · 2012 · Bioinform.
77. From FAIR to CURE: guidelines for computational models of biological systems
    Herbert M. Sauro, E. Agmon, M. Blinov, John H. Gennari, Joseph L. Hellerstein, Adel Heydarabadipour, Bartholomew E. Jardine, E. May, D. Nickerson, Lucian P. Smith et al. · 2026 · npj Systems Biology and Applications
78. Simulation studies of social systems: telling the story based on provenance patterns
    Pia Wilsdorf, Oliver Reinhardt, Toby Prike, Martin Hinsch, Jakub Bijak, Adelinde M. Uhrmacher · 2024 · Royal Society Open Science
79. Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
    Leonardo Giannantoni, Roberta Bardini, Alessandro Savino, Stefano Di Carlo · 2024 · BMC Bioinformatics
80. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
    Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, A. Dräger · 2023 · PLoS Comput. Biol.
81. Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022
    Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, M. Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, B. Sommer, D. Waltemath et al. · 2023 · Journal of Integrative Bioinformatics
82. Specifications of standards in systems and synthetic biology: status and developments in 2021
    Falk Schreiber, Padraig Gleeson, Martin Golebiewski, T. Gorochowski, M. Hucka, Sarah M. Keating, Matthias König, C. Myers, D. Nickerson, B. Sommer et al. · 2021 · Journal of Integrative Bioinformatics
83. LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules
    Sawal Maskey, Young‐Rae Cho · 2019 · BMC Genomics
84. Extracting reproducible simulation studies from model repositories using the combinearchive toolkit
    Martin Scharm, Dagmar Waltemath · 2015 · Datenbanksysteme für Business, Technologie und Web
85. Combining computational models, semantic annotations, and associated simulation experiments in a graph database
    R. Henkel, O. Wolkenhauer, D. Walthemath · 2014
86. A dedicated database system for handling multi-level data in systems biology
    Natapol Pornputtapong, K. Wanichthanarak, A. Nilsson, I. Nookaew, Jens C. O. Nielsen · 2014 · Source Code for Biology and Medicine
87. Biomedical Ontologies: Coverage, Access and Use
    João D. Ferreira, David Carriço Teixeira, Cátia Pesquita · 2020 · Elsevier eBooks
88. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
    Natalie Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Michael Hucka, Varun B. Kothamachu, David Phillip Nickerson, Stuart Owen, Jürgen Pahle, Ulrike Wittig et al. · 2019 · Methods in molecular biology
89. Biological and Medical Ontologies: Systems Biology Ontology (SBO)
    Anna Bernasconi, M. Masseroli · 2019 · Encyclopedia of Bioinformatics and Computational Biology
90. Data Formats for Systems Biology and Quantitative Modeling
    Martin Golebiewski · 2019 · Encyclopedia of Bioinformatics and Computational Biology
91. Platforms for Genetic Design Automation
    Chris John Myers · 2013 · Methods in microbiology
92. A Large-Scale Assessment of Exact Model Reduction in the BioModels Repository
    Isabel Cristina Pérez-Verona, M. Tribastone, Andrea Vandin · 2019 · Computational Methods in Systems Biology
93. A linked data platform for finite element biosimulations
    Muntazir Mehdi, Yasar Khan, André Freitas, J. Jares, S. Decker, Ratnesh Sahay · 2015 · International Conference on Semantic Systems
94. iBIRA – integrated bioinformatics information resource access
    S. Ram, N. L. Rao · 2012
95. Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
    M. Dumontier, L. Chepelev, R. Hoehndorf · 2013 · Springer eBooks
96. Reproducibility in systems biology modelling
    Tiwari, Krishna, Kananathan, Sarubini, Roberts, Matthew G, Meyer, Johannes P, Sharif Shohan, Mohammad Umer, Xavier, Ashley, Maire, Matthieu, Zyoud, Ahmad, Men, Jinghao, Ng, Szeyi et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
97. Standardized Representation of Parts and Assembly for Build Planning.
    Jacob Beal, Vinoo Selvarajah, Gaël Chambonnier, Traci L. Haddock, A. Vignoni, Gonzalo Vidal, Nicholas Roehner · 2023 · ACS Synthetic Biology
98. SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
    Jin Xu · 2023 · bioRxiv
99. Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing.
    Bryan A. Bartley · 2022 · ACS Synthetic Biology
100. Overview: Standards for Modeling in Systems Medicine
     Andreas Dräger, Dagmar Waltemath · 2020 · Elsevier eBooks