COPASI—a COmplex PAthway SImulator

• estim8 - An FMI-compliant Python toolbox for bioprocess modeling and parameter estimation

  2026 The Journal of Open Source Software article Computer Science Modeling and Simulation Systems Open access

  0

  citations
• A comparative computational analysis of IFN-alpha pharmacokinetics and its induced cellular response in mice and humans

  2025 PLoS Computational Biology article Immunology and Microbiology interferon and immune responses Open access

  3

  citations
• MxlPy - Python Package for Mechanistic Learning in Life Science

  2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Explainable Artificial Intelligence (XAI) Open access

  0

  citations
• Structural Systems Biology Toolkit (SSBtoolkit): From Molecular Structure to Subcellular Signaling Pathways

  2025 Journal of Chemical Information and Modeling article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access

  0

  citations
• MxlPy—Python package for mechanistic learning and hybrid modelling in life science

  2024 Bioinformatics Advances software-paper Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  1

  citations
• Enhanced cell wall mechanics in VirtualLeaf enable realistic simulations of plant tissue dynamics

  2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Polysaccharides and Plant Cell Walls Open access

  0

  citations
• Context, Composition, Automation, and Communication: The C 2 AC Roadmap for Modeling and Simulation

  2024 ACM Transactions on Modeling and Computer Simulation article Decision Sciences Simulation Techniques and Applications

  19

  citations
• Cardinality optimization in constraint-based modelling: application to human metabolism

  2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access

  10

  citations
• Tumor-mediated immunosuppression and cytokine spreading affects the relation between EMT and PD-L1 status

  2023 Frontiers in Immunology article Medicine Cancer Immunotherapy and Biomarkers Open access

  4

  citations
• EnzymeML: seamless data flow and modeling of enzymatic data

  2023 Nature Methods article Computer Science Research Data Management Practices

  37

  citations
• Bidirectional crosstalk between epithelial–mesenchymal plasticity and IFN γ -induced PD-L1 expression promotes tumour progression

  2022 Royal Society Open Science article Medicine Cancer Cells and Metastasis Open access

  11

  citations
• Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling

  2022 PLoS Computational Biology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  9

  citations
• Bayesian calibration, process modeling and uncertainty quantification in biotechnology

  2022 PLoS Computational Biology article Decision Sciences Optimal Experimental Design Methods Open access cited by 1 patent

  34

  citations
• Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumor progression

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Cells and Metastasis Open access

  1

  citations
• Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation

  2022 Journal of Personalized Medicine article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  116

  citations
• Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis

  2022 Journal of Theoretical Biology article Biochemistry, Genetics and Molecular Biology Angiogenesis and VEGF in Cancer Open access

  6

  citations
• Bayesian calibration, process modeling and uncertainty quantification in biotechnology

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Gaussian Processes and Bayesian Inference Open access

  4

  citations
• pyFOOMB: Python framework for object oriented modeling of bioprocesses

  2021 Engineering in Life Sciences article Computer Science Modeling and Simulation Systems Open access

  30

  citations
• pyFOOMB: Python Framework for Object Oriented Modelling of Bioprocesses

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Modeling and Simulation Systems Open access

  3

  citations

19 results