Anika Küken
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View article: A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions
A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions Open
View article: Kinetic modules are sources of concentration robustness in biochemical networks
Kinetic modules are sources of concentration robustness in biochemical networks Open
Modules represent fundamental building blocks of cellular networks and are thought to facilitate robustness of phenotypes against perturbations. While reaction kinetic shapes the concentration of components and reaction rates, its use in i…
View article: Imposing multireaction dependencies provides an innovative strategy to alter metabolic functions
Imposing multireaction dependencies provides an innovative strategy to alter metabolic functions Open
Metabolism operates under physico-chemical constraints that result in multireaction dependencies. Understanding how multireaction dependencies affect metabolic phenotypes remains challenging, hindering their biotechnological applications. …
View article: A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae
A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae Open
Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translati…
View article: The effective deficiency of biochemical networks
The effective deficiency of biochemical networks Open
The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of…
View article: Nonstoichiometric balanced complexes: Implications on the effective deficiency of the underlying metabolic network
Nonstoichiometric balanced complexes: Implications on the effective deficiency of the underlying metabolic network Open
The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of…
View article: Light-independent regulation of algal photoprotection by CO2 availability
Light-independent regulation of algal photoprotection by CO2 availability Open
Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO 2 conditions. When light energy exceeds CO 2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the C…
View article: The unraveling of balanced complexes in metabolic networks
The unraveling of balanced complexes in metabolic networks Open
View article: The hidden simplicity of metabolic networks is revealed by multireaction dependencies
The hidden simplicity of metabolic networks is revealed by multireaction dependencies Open
Understanding the complexity of metabolic networks has implications for manipulation of their functions. The complexity of metabolic networks can be characterized by identifying multireaction dependencies that are challenging to determine …
View article: Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants
Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants Open
View article: Light-independent regulation of algal photoprotection by CO<sub>2</sub>availability
Light-independent regulation of algal photoprotection by CO<sub>2</sub>availability Open
Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO 2 conditions. When light energy exceeds CO 2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the C…
View article: A structural property for reduction of biochemical networks
A structural property for reduction of biochemical networks Open
View article: Nonstoichiometric balanced complexes: Implications on the effective deficiency of the underlying metabolic network
Nonstoichiometric balanced complexes: Implications on the effective deficiency of the underlying metabolic network Open
The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of…
View article: Characterization of effects of genetic variants via genome-scale metabolic modelling
Characterization of effects of genetic variants via genome-scale metabolic modelling Open
Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipu…
View article: The unraveling of balanced complexes in metabolic networks
The unraveling of balanced complexes in metabolic networks Open
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employ…
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…
View article: Characterization of maximal enzyme catalytic rates in central metabolism of <i>Arabidopsis thaliana</i>
Characterization of maximal enzyme catalytic rates in central metabolism of <i>Arabidopsis thaliana</i> Open
SUMMARY Availability of plant‐specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measured in vitro , ofte…
View article: Integrating molecular markers into metabolicmodels improves genomic selection for Arabidopsis growth
Integrating molecular markers into metabolicmodels improves genomic selection for Arabidopsis growth Open
The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant g…
View article: Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth Open
The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant g…
View article: Cellular determinants of metabolite concentration ranges
Cellular determinants of metabolite concentration ranges Open
Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components. However, cellular mechanisms ensuring that a component's concentration resides in a given range remain elusive…
View article: Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways Open
Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biologic…
View article: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts
Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts Open
Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimen…
View article: Cellular determinants of metabolite concentration ranges
Cellular determinants of metabolite concentration ranges Open
Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components. However, cellular mechanisms ensuring that a component’s concentration resides in a given range remain elusive…
View article: Author response: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts
Author response: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts Open
View article: Author response: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts
Author response: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts Open
View article: A network property necessary for concentration robustness
A network property necessary for concentration robustness Open
View article: Observability of plant metabolic networks is reflected in the correlation of metabolic profiles.
Observability of plant metabolic networks is reflected in the correlation of metabolic profiles. Open
Understanding whether the functionality of a biological system can be characterized by measuring few selected components is key to targeted phenotyping techniques in systems biology. Methods from observability theory have proven useful in …
View article: Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence?
Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? Open
Arguably, the biggest challenge of modern plant systems biology lies in predicting the performance of plant species, and crops in particular, upon different intracellular and external perturbations. Recently, an increased growth of Arabido…