Controlled vocabularies and semantics in systems biology

Cited by (283)

Items 201–283 of 283

1. Understanding characteristics of semantic associations in health consumer generated knowledge representation in social media
   Min Sook Park · 2019 · J. Assoc. Inf. Sci. Technol.
2. Dynamic Flux Balance Analysis Models in SBML
   Matthias König, Leandro H. Watanabe, Jan Grzegorzewski, C. Myers · 2018 · bioRxiv
3. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
   Vincent Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, M. Dinh, V. Loux, C. Froidevaux, V. Fromion · 2017 · Journal of Biomedical Semantics
4. Challenges in adapting text mining for full text articles to assist pathway curation
   K. E. Ravikumar, K. Wagholikar, Hong-Fang Liu · 2014 · ACM International Conference on Bioinformatics, Computational Biology and Biomedicine
5. Function of dynamic models in systems biology: linking structure to behaviour
   C. Knüpfer, C. Beckstein · 2013 · Journal of Biomedical Semantics
6. GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML
   S. Vlaic, B. Hoffmann, P. Kupfer, Michael Weber, A. Dräger · 2013 · Bioinform.
7. Genome-scale model management and comparison.
   Stephan Pabinger, Z. Trajanoski · 2013 · Methods in molecular biology
8. Controlled annotations for systems biology.
   N. Juty, C. Laibe, N. Le Novère · 2013 · Methods in molecular biology
9. SIMPROV: Provenance capturing for simulation studies
   Andreas Ruscheinski, Anja Wolpers, Philipp Henning, Pia Wilsdorf, Adelinde M. Uhrmacher · 2025 · PLoS ONE
10. An automated model annotation system (AMAS) for SBML models
    Woosub Shin, J. Gennari, J. Hellerstein, H. Sauro · 2023 · bioRxiv
11. Design considerations for representing systems biology information with the Systems Biology Graphical Notation
    Falk Schreiber, Tobias Czauderna · 2022 · Journal of Integrative Bioinformatics
12. The Practice of Ensuring Repeatable and Reproducible Computational Models
    H. Sauro · 2021 · arXiv (Cornell University)
13. A large-scale assessment of exact lumping of quantitative models in the BioModels repository
    Isabel Cristina Pérez-Verona, M. Tribastone, Andrea Vandin · 2021 · Theoretical Computer Science
14. bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks
    A. Naldi · 2018 · bioRxiv
15. A Linked Data Visualiser for Finite Element Biosimulations
    Muntazir Mehdi, Yasar Khan, Joao Jares, André Freitas, Alok Kumar Jha, Antonis I. Sakellarios, Ratnesh Sahay · 2016 · International Journal of Semantic Computing
16. From standardized modeling formats to modeling languages and back — An exploration based on SBML and ML-Rules
    Sebastian Nahring, R. Ewald, A. Uhrmacher, Carsten Maus · 2013 · Online World Conference on Soft Computing in Industrial Applications
17. Standardized network reconstruction of E. coli metabolism
    Kieran Smallbone · 2013 · arXiv (Cornell University)
18. Standardized network reconstruction of CHO cell metabolism
    Kieran Smallbone · 2013
19. Computer Science Methods for Effective and Sustainable Simulation Studies (Dagstuhl Seminar 22401)
    Wen-Tong Cai, C. Carothers, D. Nicol, A. Uhrmacher · 2022 · Dagstuhl Reports
20. Challenges and promises of self-adaptive simulation models
    Adelinde M. Uhrmacher, Pia Wilsdorf, Justin Noah Kreikemeyer · 2024 · SIMULATION
21. EFECT: A Method to Quantify the Reproducibility of Stochastic Simulations
    T. J. Sego, Matthias Konig, Luis L. Fonseca, D. Pathirana, Frank T. Bergmann, Hern'an E. Grecco, Mauro Silberberg, Subhasis Ray, Baylor Fain, Adam C. Knapp et al. · 2024
22. Standardizing Extracted Data Using Automated Application of Controlled Vocabularies
    Caroline Foster, Jessica Wignall, Samuel Kovach, Neepa Y. Choksi, Dave Allen, Joanne Trgovcich, Johanna R. Rochester, Patricia C. Ceger, Amber B. Daniel, Jon T. Hamm et al. · 2024 · Environmental Health Perspectives
23. NBSIMGEN: Jupyter Notebook Extension for Generating Simulation Experiments
    Pia Wilsdorf, Anton Willy Kirchhübel, Adelinde M. Uhrmacher · 2023 · Winter Simulation Conference
24. From quantitative SBML models to Boolean networks
    Athénaïs Vaginay, T. Boukhobza, Malika Smaïl-Tabbone · 2022 · Applied Network Science
25. Towards reusable process-based models of dynamical systems: A case study in the domain of aquatic ecosystems
    Ilin Tolovski, Ana Kostovska, Nikola Simidjievski, L. Todorovski, S. Džeroski, P. Panov · 2019 · International Convention on Information and Communication Technology, Electronics and Microelectronics
26. JigCell Model Connector: building large molecular network models from components
    Thomas C. Jones, Stefan Hoops, L. Watson, Alida Palmisano, J. Tyson, C. Shaffer · 2018 · International Conference on Advances in System Simulation
27. Notions of similarity for computational biology models
    Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian rer. nat. Knüpfer, Wolfram Liebermeister, Dagmar Waltemath · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
28. Challenges in horizontal model integration
    K. Kolczyk, C. Conradi · 2016 · BMC Systems Biology
29. Automatising the analysis of stochastic biochemical time-series
    G. Caravagna, Luca De Sano, M. Antoniotti · 2015 · BMC Bioinformatics
30. SBtab - Conventions for structured data tables in Systems Biology
    Wolfram Liebermeister, Timo Lubitz, Jens Hahn · 2015
31. BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology
    A. F. Villaverde, D. Henriques, Kieran Smallbone, S. Bongard, J. Schmid, Damjan Cicin-Sain, A. Crombach, J. Sáez-Rodríguez, K. Mauch, E. Balsa-Canto et al. · 2014 · arXiv.org
32. SPNConverter: a new link between static and dynamic complex network analysis
    Jennifer E. Dent, Xin-Yi Yang, C. Nardini · 2013 · Bioinform.
33. FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast (preprint)
    Kausthubh Ramachandran, Matthias König, Martin Scharm, Tung V. N. Nguyen, Henning Hermjakob, Dagmar Waltemath, Rahuman S. Malik Sheriff · 2022 · Preprints.org
34. Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa
    Ina Koch · 2019 · Carl Adam Petri: Ideas, Personality, Impact
35. Input Encoding Proposal for Behavioral Experiments with a Virtual C. elegans Representation
    G. Epelde, A. Mujika, Roberto Álvarez, P. Leškovský, A. De Mauro, F. Krewer, A. Blau · 2015 · International Congress on Neurotechnology, Electronics and Informatics
36. Standards, Platforms, and Applications
    Stanley Gu, H. Sauro · 2014 · Elsevier eBooks
37. Computational Infrastructures for Data and Knowledge Management in Systems Biology
    F. Georgatos, S. Ballereau, J. Pellet, M. Ghanem, Nathan D. Price, L. Hood, Yi-Ke Guo, D. Boutigny, C. Auffray, R. Balling et al. · 2013
38. SBOL converter: enabling backward compatibility for biological designs
    Metehan Ünal, Chris J. Myers, I. T. Medeni, Jacob Beal, P. Vaidyanathan, Lukas Buecherl, F. Buson, Georgie Hau Sørensen, Gonzalo Vidal, Carolus Vitalis et al. · 2026 · Journal of Integrative Bioinformatics
39. METEOR: joint genome-scale reconstruction and enzyme prediction
    Ke-Xin Niu, Maxat Kulmanov, R. Hoehndorf · 2026 · bioRxiv
40. MCC: automated mass and charge curation at the genome scale applied to C. tuberculostearicum
    Reihaneh Mostolizadeh, Finn Mier, Andreas Dräger · 2025 · Microbiology Spectrum
41. The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling
    Leon Martin, Konstantin Bülau, Marius Pille, Rico Andre Schmitt, Christoph Huettl, Jil Mona Meier, Halgurd Taher, Dionysios Perdikis, Michael Schirner, Leon Stefanovski et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
42. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
    Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, Andreas Dräger · 2023 · Frontiers in Bioinformatics
43. Exploring the evolution of biochemical models at the network level
    Tom Gebhardt, Vasundra Touré, D. Waltemath, O. Wolkenhauer, Martin Scharm · 2022 · PLoS ONE
44. Genome-scale Model Constrained by Proteomics Reveals Metabolic Rearrangements in the Heterologous Host Streptomyces coelicolor
    Snorre Sulheim, T. Kumelj, Dino van Dissel, Ali Salehzadeh-Yazdi, Chao Du, G. V. van Wezel, K. Nieselt, E. Almaas, A. Wentzel, E. Kerkhoven · 2019 · bioRxiv
45. Epithelial Modelling Platform: A Tool for Model Discovery and Assembly with the Physiome Model Repository
    D. Sarwar, Yuda Munarko, D. Nickerson · 2019 · bioRxiv
46. Annotations for Rule-Based Models
    M. Cavaliere, V. Danos, Ricardo Honorato-Zimmer, W. Waites · 2018 · Methods in molecular biology
47. Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse
    J. Medley, Kiri Choi, Matthias König, Lucian P. Smith, Stanley Gu, J. Hellerstein, S. Sealfon, H. Sauro · 2017 · bioRxiv
48. From cell to silicon: Translation of a genetic circuit to finite state machine implementation
    Urooj Ainuddin, M. Khurram · 2016 · InTech
49. Streamlining metadata for economic time series data: A project report
    Genevieve Podleski · 2015 · ASIS&T Annual Meeting
50. Extending inner-ear anatomical concepts in the Foundational Model of Anatomy (FMA) ontology
    Yasar Khan, Muntazir Mehdi, A. Jha, Saleem Raza, André Freitas, Marggie Jones, Ratnesh Sahay · 2015 · International Conferences on Biological Information and Biomedical Engineering
51. Invited presentations, junior research groups and research highlights at GCB 2015
    A. Mosig, J. Rahnenführer, M. Eisenacher, S. Rahmann · 2015 · PeerJ Preprints
52. Inferring semantic similarity through correlating information contents of gene ontology terms
    Mingxin Gan, Rui Jiang · 2013 · IEEE International Conference on Bioinformatics and Biomedicine
53. LibKiSAO: a Java library for Querying KiSAO
    A. Zhukova, R. Adams, C. Laibe, N. Le Novère · 2012 · BMC Research Notes
54. Towards Automation of IoT Analytics: An Ontology-Driven Approach
    S. Dey, Arijit Mukherjee · 2017
55. Ontologies in Chemoinformatics
    Janna Hastings, C. Steinbeck · 2017
56. Finding patterns in biochemical reaction networks
    R. Henkel, Fabienne Lambusch, O. Wolkenhauer, K. Sandkuhl, Christian Rosenke, Dagmar Waltemath · 2016 · PeerJ Preprints
57. Biological Network Modeling and Analysis
    S. Janowski, B. Kaltschmidt, C. Kaltschmidt · 2014 · Approaches in Integrative Bioinformatics
58. Qualitative Modelling of Metabolic Networks
    F. Jourdan · 2013 · Advances in botanical research
59. Nutrient control enables metabolic reconstruction of Lacticaseibacillus rhamnosus GG and analysis of secretions
    G. Richmond, Emanuel Cunha, Libusha Kelly, Óscar Dias, R. Chang · 2026 · mSystems
60. Standards in systems and synthetic biology: status, developments, and tools in 2026
    Falk Schreiber, Martin Golebiewski, Padraig Gleeson, Sarah Keating, Matthias König, Augustin Luna, Elebeoba E. May, Göksel Mısırlı, Chris J. Myers, David Phillip Nickerson et al. · 2026 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
61. Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions
    G. Richmond, Emanuel Cunha, Libusha Kelly, Óscar Dias, R. Chang · 2026 · bioRxiv
62. Optotransduction Pathway, Exploring Connections with Inflammation
    A. Ravoni, Veronica Paparozzi, T. Guarnieri, Cecilia Sanzini, Luigi Manni, C. Nardini · 2026 · Biomolecules
63. Interoperability to Improve Science-Based Decision Making: Adapting a Risk Analysis Framework to Improve Translational Environmental Health Science.
    John M. Johnston, Edward J. Perkins, Pierre D. Glynn, K. von Stackelberg, B. Hope, Matthew C. Harwell · 2026 · Electronics
64. MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology
    K. Robasky, James Morrissey, Markus Riedl, A. Dräger, Nicole Borth, Michael J. Betenbaugh, Nathan E. Lewis · 2026 · bioRxiv
65. Frame-based mathematical models – a tool for the study of molecular genetic systems
    F. V. Kazantsev, S. Lashin, Y. Matushkin · 2025 · Vavilovskii zhurnal genetiki i selektsii
66. Self-Adaptive Simulation Models: A Case Study in Cell Biology
    Pia Wilsdorf, Philipp Henning, Justin Noah Kreikemeyer, Marcel Kliefoth, Simone Baltrusch, Adelinde M. Uhrmacher · 2025 · International Symposium on Distributed Simulation and Real Time Applications (DS-RT)
67. In Pursuit of Total Reproducibility
    M. Research, Education · 2025
68. Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models
    Gioele Lazzari, Giovanna E. Felis, Elisa Salvetti, Matteo Calgaro, Francesca Di Cesare, Bas Teusink, Nicola Vitulo · 2025 · mSystems
69. Exploring the adaptability and robustness of the central carbon metabolism of Mycoplasma pneumoniae
    Niels A. Zondervan, Eva Yus, Daniel C. Sévin, Sira Martínez, Carolina Gallo, Peter J. Schaap, María Lluch‐Senar, Luis G. Serrano, Vítor A. P. Martins dos Santos, Maria Suarez Diez · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
70. Modelling techniques for biomolecular networks
    Gerhard Mayer · 2020 · arXiv (Cornell University)
71. Closing the gap between formats for storing layout information in systems biology
    D. Hoksza, P. Gawron, M. Ostaszewski, J. Hasenauer, Reinhard Schneider · 2020 · Briefings Bioinform.
72. Modelling and measurement in synthetic biology
    W. Waites · 2020
73. Knowledge-based scaling for biological models. (Généralisation de modèles métaboliques par connaissances)
    A. Zhukova · 2014
74. Annotation-Based Feature Extraction from Sets of SBML Models
    Rebekka Alm, Dagmar Waltemath, Olaf Wolkenauer, R. Henkel · 2014 · Data Integration in the Life Sciences
75. Chemical Ontologies for Standardization, Knowledge Discovery, and Data Mining
    Janna Hastings, C. Steinbeck · 2013
76. Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology
    Kiri Choi, Jonathan R. Karr, H. Sauro · 2021 · Elsevier eBooks
77. Prediction and visualization of the carcinogenic potential of chemicals with short-term omics assays
    Michael Römer · 2017
78. Simulation and optimization of logical and kinetic biochemical models
    Roland Keller · 2016
79. Ontologies in Cheminformatics
    Janna Hastings, C. Steinbeck · 2016
80. Development and Dissemination of Computational Methods for Genome-scale Modeling
    A. Ebrahim · 2016
81. Getting Science to Scale: Accelerating the Development of Translational Computational Models
    Y. Vodovotz, G. An · 2015
82. Computational Tools and Resources for Integrative Modeling in Systems Biology
    Christoph Wierling, Hendrik Hache · 2013 · Springer eBooks
83. Annotation-based storage and retrieval of models and simulation descriptions in computational biology
    Dagmar Waltemath · 2011 · Ros Dok Rostocker Dokumentenserver (Universitätsbibliothek Rostock)