Jakob Vanhoefer
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View article: Non-Negative Universal Differential Equations With Applications in Systems Biology
Non-Negative Universal Differential Equations With Applications in Systems Biology Open
Universal differential equations (UDEs) leverage the respective advantages of mechanistic models and artificial neural networks and combine them into one dynamic model. However, these hybrid models can suffer from unrealistic solutions, su…
View article: Non-Negative Universal Differential Equations With Applications in Systems Biology
Non-Negative Universal Differential Equations With Applications in Systems Biology Open
View article: pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models Open
Summary Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. pyPESTO is a modu…
View article: pyPESTO: A modular and scalable tool for parameter estimation for dynamic models
pyPESTO: A modular and scalable tool for parameter estimation for dynamic models Open
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a mod…
View article: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms Open
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a…
View article: COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms Open
View article: yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML
yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML Open
Vanhoefer et al., (2021). yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. Journal of Open Source Software, 6(61), 3215, https://doi.org/10.21105/joss.03215
View article: COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modeling
COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modeling Open
View article: COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021)
COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms (vol 17, e10387, 2021) Open
Graphical Abstract
View article: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms Open
We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the dis…
View article: COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling
COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling Open
Epidemiological models are widely used to analyse the spread of diseases such as the global COVID-19 pandemic caused by SARS-CoV-2. However, all models are based on simplifying assumptions and on sparse data. This limits the reliability of…
View article: Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible
Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible Open
View article: Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible
Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible Open
Null models for the effect of combination therapies are widely used to evaluate synergy and antagonism of drugs. Due to the relevance of null models, their suitability is continuously discussed. Here, we contribute to the discussion by inv…