Philipp Wendering
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View article: KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits
KineticGP: a computational framework for genomic prediction of leaf photosynthesis traits Open
Crop traits are the integrated outcome of genetic factors, environment effects, and their complex interactions, rendering accurate prediction from genetic markers alone a challenging problem. Here we present KineticGP, a computational fram…
View article: Kinetic parameter prediction using neural networks identifies limitations to C<sub>4</sub> photosynthesis
Kinetic parameter prediction using neural networks identifies limitations to C<sub>4</sub> photosynthesis Open
Large-scale kinetic models of photosynthesis enable time-resolved predictions of traits related to this key process, and provide the means to identify factors limiting photosynthesis. However, their use is currently limited by the lack of …
View article: Metabolic modeling identifies determinants of thermal growth responses in <i>Arabidopsis thaliana</i>
Metabolic modeling identifies determinants of thermal growth responses in <i>Arabidopsis thaliana</i> Open
Summary Temperature is a critical environmental factor affecting nearly all plant processes, including growth, development, and yield. Yet, despite decades of research, we lack the ability to predict plant performance at different temperat…
View article: Predicting plant thermal responses using a temperature-aware plant metabolic model: a primer
Predicting plant thermal responses using a temperature-aware plant metabolic model: a primer Open
Understanding plant temperature responses at a molecular level can speed up the development of climate-resilient crops. However, the threats due to anthropogenic warming necessitate imminent solutions to ensure food security. Modelling pla…
View article: Die Rolle von Photorespiration unter dynamischen Lichtbedingungen
Die Rolle von Photorespiration unter dynamischen Lichtbedingungen Open
Plants use photosynthesis to convert light into metabolic energy. This energy is used to produce carbohydrates and to fuel other metabolic pathways. In nature, the availability of light and thereby metabolic energy can fluctuate strongly, …
View article: Histone retention preserves epigenetic marks during heat stress‐induced transcriptional memory in plants
Histone retention preserves epigenetic marks during heat stress‐induced transcriptional memory in plants Open
View article: Growth in fluctuating light buffers plants against photorespiratory perturbations
Growth in fluctuating light buffers plants against photorespiratory perturbations Open
View article: Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning Open
Quantification of how different environmental cues affect protein allocation can provide important insights for understanding cell physiology. While absolute quantification of proteins can be obtained by resource-intensive mass-spectrometr…
View article: Model-driven insights into the effects of temperature on metabolism
Model-driven insights into the effects of temperature on metabolism Open
Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future clima…
View article: Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning Open
Quantification of how different environmental cues affect protein allocation can provide important insights for understanding cell physiology. While absolute quantification of proteins can be obtained by resource-intensive mass-spectrometr…
View article: Data integration across conditions improves turnover number estimates and metabolic predictions
Data integration across conditions improves turnover number estimates and metabolic predictions Open
Turnover numbers characterize a key property of enzymes, and their usage in constraint-based metabolic modeling is expected to increase the prediction accuracy of diverse cellular phenotypes. In vivo turnover numbers can be obtained by int…
View article: Toward mechanistic modeling and rational engineering of plant respiration
Toward mechanistic modeling and rational engineering of plant respiration Open
Plant respiration not only provides energy to support all cellular processes, including biomass production, but also plays a major role in the global carbon cycle. Therefore, modulation of plant respiration can be used to both increase the…
View article: Data integration across conditions improves turnover number estimates and metabolic predictions
Data integration across conditions improves turnover number estimates and metabolic predictions Open
Turnover numbers characterize a key property of enzymes, and their usage in constraint-based metabolic modeling is expected to increase prediction accuracy of diverse cellular phenotypes. In vivo turnover numbers can be obtained by ranking…
View article: COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions Open
Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabol…
View article: Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions Open
Generated draft and consensus reconstructions for the manuscript "COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions" (Wendering & Nikoloski).
View article: Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
Dataset - COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions Open
Generated draft and consensus reconstructions for the manuscript "COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions" (Wendering & Nikoloski).
View article: Genome-Scale Modeling Specifies the Metabolic Capabilities of <i>Rhizophagus irregularis</i>
Genome-Scale Modeling Specifies the Metabolic Capabilities of <i>Rhizophagus irregularis</i> Open
Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to d…
View article: Genome-scale modeling specifies the metabolic capabilities of <i>Rhizophagus irregularis</i>
Genome-scale modeling specifies the metabolic capabilities of <i>Rhizophagus irregularis</i> Open
Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challengi…
View article: A structural property for reduction of biochemical networks
A structural property for reduction of biochemical networks Open
View article: COMMIT: Consideration of metabolite leakage and community composition improves microbial community models
COMMIT: Consideration of metabolite leakage and community composition improves microbial community models Open
Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabol…
View article: A structural property for reduction of biochemical networks
A structural property for reduction of biochemical networks Open
Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state me…