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  1. Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

    Article • mSystems, June 2025, ASM Journals

    Jun.-Prof. Dr. Andreas Dräger

  2. MCC: Automated Mass and Charge Curation at Genome-Scale Applied toC. tuberculostearicum

    Article • November 2024, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  3. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling

    Article • PLoS Pathogens, September 2024, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  4. Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities

    Article • Microbiology Spectrum, June 2024, ASM Journals

    Jun.-Prof. Dr. Andreas Dräger

  5. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs

    Article • March 2024, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  6. Perspectives on computational modeling of biological systems and the significance of the SysMod community

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  7. Genome-scale metabolic model ofStaphylococcus epidermidisATCC 12228 matchesin vitroconditions

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  8. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs

    Article • November 2023, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  9. Genome-Scale Modeling ofRothia mucilaginosaReveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  10. Exploring the metabolic profiling ofA. baumanniifor antimicrobial development using genome-scale modelling

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  11. Advancements in computational modelling of biological systems: seventh annual SysMod meeting

    Article • Bioinformatics, September 2023, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  12. SBOannotator: a Python tool for the automated assignment of systems biology ontology terms

    Article • Bioinformatics, July 2023, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  13. Genome-scale metabolic models consistently predictin vitrocharacteristics ofCorynebacterium striatum

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  14. standard-GEM: standardization of open-source genome-scale metabolic models

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Dr John M Hancock, Jun.-Prof. Dr. Andreas Dräger

  15. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

    Article • PLoS Computational Biology, March 2023, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  16. SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms

    Article • February 2023, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  17. Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

    Article • Communications Biology, February 2023, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  18. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells

    Article • January 2023, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  19. Hierarchical modelling of microbial communities

    Article • Bioinformatics, January 2023, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  20. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs

    Article • October 2022, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  21. Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

    Article • Bioinformatics, September 2022, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  22. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells

    Article • July 2022, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  23. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells

    Article • March 2022, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  24. A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice

    Article • Biology, February 2022, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  25. COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

    Article • Molecular Systems Biology, December 2021, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  26. High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

    Article • Frontiers in Microbiology, November 2021, Frontiers

    Jun.-Prof. Dr. Andreas Dräger

  27. SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

    Article • Processes, October 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  28. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

    Article • npj Systems Biology and Applications, October 2021, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  29. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

    Article • Molecular Systems Biology, October 2021, EMBO

    Jun.-Prof. Dr. Andreas Dräger

  30. The systems biology simulation core library

    Article • Bioinformatics, September 2021, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  31. SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

    Article • August 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  32. 114 highly specific computer models of the threatening pathogen Staphylococcus aureus

    Article • npj Systems Biology and Applications, June 2021, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  33. The community for data-driven computational modelling and multi-scale analysis of biological systems

    Article • Bioinformatics, June 2021, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  34. Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms GK1 as Potential Antiviral Target

    Article • Genes, May 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  35. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target

    Article • April 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  36. Genome-scale modeling ofPseudomonas aeruginosaPA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  37. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

    Article • Metabolites, April 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  38. <span data-preserver-spaces="true">Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of <em><span data-preserver-spaces="true">Staphylococcus aureus</em>

    Article • April 2021, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  39. An updated genome-scale metabolic network reconstruction ofPseudomonas aeruginosaPA14 to characterize mucin-driven shifts in bacterial metabolism

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  40. Overview: Standards for Modeling in Systems Medicine

    Article • January 2021, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  41. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine

    Article • January 2021, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  42. Clinical Applications of Metabolic Models in SBML Format

    Article • January 2021, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  43. The Systems Biology Simulation Core Library

    Article • December 2020, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  44. A computer model identifies a human enzyme as a potential target to treat COVID-19

    Article • Bioinformatics, December 2020, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  45. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

    Article • Immunity, December 2020, Elsevier

    Jun.-Prof. Dr. Andreas Dräger, Prof. Markus Ralser

  46. Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection

    Article • Biology, November 2020, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  47. Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications

    Article • November 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  48. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  49. A Computational Model to Inform Effective Control Interventions against Yersinia enterocolitica Coinfection

    Article • October 2020, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  50. Model-based prediction of bacterial population dynamics in gastrointestinal infection

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  51. SBML Level 3: an extensible format for the exchange and reuse of biological models

    Article • Molecular Systems Biology, August 2020, EMBO

    Jun.-Prof. Dr. Andreas Dräger

  52. Community standards to facilitate development and address challenges in metabolic modeling

    Article • Molecular Systems Biology, August 2020, EMBO

    Jun.-Prof. Dr. Andreas Dräger

  53. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

    Article • Scientific Data, July 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  54. Visualizing metabolic network dynamics through time-series metabolomic data

    Article • BMC Bioinformatics, July 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  55. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

    Article • Journal of Integrative Bioinformatics, July 2020, De Gruyter

    Fengkai Zhang, Jun.-Prof. Dr. Andreas Dräger

  56. A file format to store and distribute maps of biological processes.

    Article • Journal of Integrative Bioinformatics, June 2020, De Gruyter

    Jun.-Prof. Dr. Andreas Dräger

  57. We want to collaborate on exchanging what we know on how the new coronavirus works

    Article • Scientific Data, May 2020, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  58. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

    Article • Nature Biotechnology, March 2020, Springer Science + Business Media

    Dr.-Ing. Birgitta Elisabeth Ebert, Jun.-Prof. Dr. Andreas Dräger

  59. MEMOTE for standardized genome-scale metabolic model testing

    Article • Nature Biotechnology, March 2020, Springer Science + Business Media

    Dr.-Ing. Birgitta Elisabeth Ebert, Jun.-Prof. Dr. Andreas Dräger

  60. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

    Article • Nucleic Acids Research, November 2019, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  61. Community standards to facilitate development and address challenges in metabolic modeling

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  62. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

    Article • Journal of Integrative Bioinformatics, June 2019, De Gruyter

    Jun.-Prof. Dr. Andreas Dräger

  63. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

    Article • Journal of Integrative Bioinformatics, June 2019, De Gruyter

    Jun.-Prof. Dr. Andreas Dräger

  64. The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes

    Article • BMC Bioinformatics, April 2019, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  65. Insights into Dynamic Network States Using Metabolomic Data

    Article • January 2019, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  66. Harmonizing semantic annotations for computational models in biology

    Article • Briefings in Bioinformatics, November 2018, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  67. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

    Article • Nucleic Acids Research, August 2018, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  68. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

    Article • Journal of Integrative Bioinformatics, April 2018, De Gruyter

    Brett G Olivier, Jun.-Prof. Dr. Andreas Dräger

  69. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

    Article • Journal of Integrative Bioinformatics, March 2018, De Gruyter

    Brett G Olivier, Jun.-Prof. Dr. Andreas Dräger

  70. Recon3D enables a three-dimensional view of gene variation in human metabolism

    Article • Nature Biotechnology, February 2018, Nature

    Ines Thiele , Jun.-Prof. Dr. Andreas Dräger

  71. Harmonizing semantic annotations for computational models in biology

    Article • January 2018, Cold Spring Harbor Laboratory Press

    Jun.-Prof. Dr. Andreas Dräger

  72. A Padawan Programmer’s Guide to Developing Software Libraries

    Article • Cell Systems, November 2017, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  73. Visualization and creation of biochemical networks with Escher

    Article • August 2017, Faculty of 1000, Ltd.

    Jun.-Prof. Dr. Andreas Dräger

  74. Evaluation of rate law approximations in bottom-up kinetic models of metabolism

    Article • BMC Systems Biology, June 2016, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  75. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii

    Article • Algal Research, April 2016, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  76. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

    Article • PLOS One, February 2016, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  77. Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

    Article • PLoS Computational Biology, January 2016, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  78. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

    Article • Nucleic Acids Research, October 2015, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  79. Do genome-scale models need exact solvers or clearer standards?

    Article • Molecular Systems Biology, October 2015, EMBO

    Professor Sang Yup Lee, Jun.-Prof. Dr. Andreas Dräger

  80. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

    Article • BMC Systems Biology, October 2015, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  81. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

    Article • PLoS Computational Biology, August 2015, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  82. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

    Article • Proceedings of the National Academy of Sciences, August 2015, Proceedings of the National Academy of Sciences

    Jun.-Prof. Dr. Andreas Dräger

  83. JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.

    Article • Bioinformatics, June 2015, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  84. Cooperative development of logical modelling standards and tools with CoLoMoTo

    Article • Bioinformatics, January 2015, Oxford University Press (OUP)

    Professor Denis Thieffry, Professor Julio Saez-Rodriguez, Jun.-Prof. Dr. Andreas Dräger

  85. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

    Article • Computation, December 2014, MDPI AG

    Jun.-Prof. Dr. Andreas Dräger

  86. Improving Collaboration by Standardization Efforts in Systems Biology

    Article • Frontiers in Bioengineering and Biotechnology, December 2014, Frontiers

    Jun.-Prof. Dr. Andreas Dräger

  87. Controlled vocabularies and semantics in systems biology

    Article • Molecular Systems Biology, April 2014, EMBO

    Professor Douglas B Kell, Jun.-Prof. Dr. Andreas Dräger

  88. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors

    Article • PLOS One, December 2013, PLOS

    Jun.-Prof. Dr. Andreas Dräger

  89. Parkinson’s disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein

    Article • BMC Neuroscience, November 2013, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  90. GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML

    Article • Bioinformatics, June 2013, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  91. Path2Models: large-scale generation of computational models from biochemical pathway maps

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Professor Douglas B Kell, Professor Julio Saez-Rodriguez, Jun.-Prof. Dr. Andreas Dräger

  92. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Professor Denis Thieffry, Professor Julio Saez-Rodriguez, Jun.-Prof. Dr. Andreas Dräger

  93. Metabolic Networks

    Article • January 2013, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  94. Parameter Estimation, Metabolic Network Modeling

    Article • January 2013, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  95. Precise generation of systems biology models from KEGG pathways

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  96. The systems biology simulation core algorithm

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  97. Qualitative translation of relations from BioPAX to SBML qual

    Article • Bioinformatics, August 2012, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  98. CySBML: a Cytoscape plugin for SBML

    Article • Bioinformatics, July 2012, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  99. ProDGe: investigating protein-protein interactions at the domain level

    Article • Nature Photonics, August 2011, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  100. Inferring statin-induced gene regulatory relationships in primary human hepatocytes

    Article • Bioinformatics, July 2011, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  101. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

    Article • Bioinformatics, June 2011, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  102. JSBML: a flexible Java library for working with SBML

    Article • Bioinformatics, June 2011, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  103. Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization

    Article • June 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Jun.-Prof. Dr. Andreas Dräger

  104. Automating Mathematical Modeling of Biochemical Reaction Networks

    Article • January 2010, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  105. ModuleMaster: A new tool to decipher transcriptional regulatory networks

    Article • Biosystems, January 2010, Elsevier

    Jun.-Prof. Dr. Andreas Dräger

  106. BowTieBuilder: modeling signal transduction pathways

    Article • BMC Systems Biology, June 2009, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  107. SBML2LATEX: Conversion of SBML files into human-readable reports

    Article • Bioinformatics, March 2009, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  108. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

    Article • BMC Systems Biology, January 2009, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  109. BioJava: an open-source framework for bioinformatics

    Article • Bioinformatics, August 2008, Oxford University Press (OUP)

    Jun.-Prof. Dr. Andreas Dräger

  110. SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

    Article • BMC Systems Biology, April 2008, Springer Science + Business Media

    Jun.-Prof. Dr. Andreas Dräger

  111. Benchmarking evolutionary algorithms on convenience kinetics models of the valine and leucine biosynthesis in C. glutamicum

    Article • September 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Jun.-Prof. Dr. Andreas Dräger

  112. Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum

    Article • September 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Jun.-Prof. Dr. Andreas Dräger

  113. INFERRING GENE REGULATORY NETWORKS BY MACHINE LEARNING METHODS

    Article • January 2007, World Scientific Pub Co Pte Lt

    Jun.-Prof. Dr. Andreas Dräger