Zoran Nikoloski
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View article: <scp>NeuralFlux</scp> : Estimation of Reaction Fluxes at a Genome‐Scale Level From Time‐Resolved Isotope Labelling Patterns Using Deep Learning
<span>NeuralFlux</span> : Estimation of Reaction Fluxes at a Genome‐Scale Level From Time‐Resolved Isotope Labelling Patterns Using Deep Learning Open
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: Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning
Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning Open
Developing crop varieties that maintain productivity under drought is essential for future food security. Here, we investigated the potential of time-resolved high-throughput phenotyping to predict harvest-related traits and identify droug…
View article: Rho <scp>GTPase</scp> overexpression impacts leaf internal architecture and mesophyll conductance in Arabidopsis
Rho <span>GTPase</span> overexpression impacts leaf internal architecture and mesophyll conductance in Arabidopsis Open
Summary Leaves are built from multiple cell types and are structured to enable the conversion of carbon dioxide and water into sugars in the process of photosynthesis. Understanding how cell architecture impacts the movement of CO 2 within…
View article: The sucrose–trehalose 6-phosphate nexus is conserved in flowering plants with different phloem loading and carbon storage strategies
The sucrose–trehalose 6-phosphate nexus is conserved in flowering plants with different phloem loading and carbon storage strategies Open
Trehalose 6-phosphate (Tre6P) is a signalling metabolite that maintains sucrose homeostasis and links plant growth and development to the availability of sucrose. Most of our knowledge of the nexus between Tre6P and sucrose comes from stud…
View article: Gene expression and protein abundance: Just how associated are these molecular traits?
Gene expression and protein abundance: Just how associated are these molecular traits? Open
The ability to accurately predict the abundance of proteins from the expression of the corresponding genes has enormous potential for the advancement of biotechnological applications using metabolic engineering and synthetic biology approa…
View article: Constraint‐based metabolic modeling reveals metabolic properties underpinning the unprecedented growth of <i>Chlorella ohadii</i>
Constraint‐based metabolic modeling reveals metabolic properties underpinning the unprecedented growth of <i>Chlorella ohadii</i> Open
Summary Comparative molecular and physiological analyses of organisms from one taxonomic group grown under similar conditions offer a strategy to identify gene targets for trait improvement. While this strategy can also be performed in sil…
View article: Evaluating plant growth–defense trade-offs by modeling the interaction between primary and secondary metabolism
Evaluating plant growth–defense trade-offs by modeling the interaction between primary and secondary metabolism Open
Understanding the molecular mechanisms behind plant response to stress can enhance breeding strategies and help us design crop varieties with improved stress tolerance, yield, and quality. To investigate resource redistribution from growth…
View article: High-throughput Raman-activated cell sorting of microalgal genome-wide edited library revealed a new regulatory pathway for carotenoid synthesis
High-throughput Raman-activated cell sorting of microalgal genome-wide edited library revealed a new regulatory pathway for carotenoid synthesis Open
Functional genomics has been hampered by the paucity of efficient methods that connect genotype and metabolic phenotype at single-cell resolution. Using the industrial microalga Nannochloropsis oceanica as a model, we introduced a platform…
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: Towards genetic architecture and genomic prediction of crop traits from time-series data: Challenges and breakthroughs
Towards genetic architecture and genomic prediction of crop traits from time-series data: Challenges and breakthroughs Open
Advances in remote and proximal sensing have facilitated temporal high-throughput phenotyping of crop populations grown in field conditions. The resulting time-series phenotypic data capture single or multiple growth- and yield-related tra…
View article: Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize
Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize Open
Hyperspectral reflectance provides rapid and precise phenotyping of plants in a non-destructive manner both in field and well-controlled settings. The resulting data have been used to devise machine learning (ML) models for paired measurem…
View article: Precision modification and de novo design of metabolic pathways to enhance crop nutritional quality and stress tolerance
Precision modification and de novo design of metabolic pathways to enhance crop nutritional quality and stress tolerance Open
View article: Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize
Generalizability of machine learning models for plant traits using hyperspectral reflectance data: The case of maize Open
View article: CSR Calculator: An R package and Shiny application for assigning plant ecological strategies using trait data
CSR Calculator: An R package and Shiny application for assigning plant ecological strategies using trait data Open
1. The competitor, stress-tolerator, ruderal (CSR) theory, first proposed by John Philip Grime, is a useful framework for understanding plant ecological strategies and predicting responses to environmental changes and pressures. However, c…
View article: Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning
Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning Open
Developing crop varieties that maintain productivity under drought is essential for future food security. Here, we investigated the potential of time-resolved high-throughput phenotyping to predict harvest-related traits and identify droug…
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: Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives
Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives Open
Traits in any organism are not independent, but show considerable integration, observed in a form of couplings and trade-offs. Therefore, improvement in one trait may affect other traits, often in undesired direction. To account for this p…
View article: Comparative analysis of genomic prediction approaches for multiple time-resolved traits in maize
Comparative analysis of genomic prediction approaches for multiple time-resolved traits in maize Open
Ability to accurately predict multiple growth-related traits over plant developmental trajectories has the potential to revolutionize crop breeding and precision agriculture. Despite increased availability of time-resolved data for multipl…
View article: Predicting plant trait dynamics from genetic markers
Predicting plant trait dynamics from genetic markers Open
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: Flux-sum coupling analysis of metabolic network models
Flux-sum coupling analysis of metabolic network models Open
Metabolites acting as substrates and regulators of all biochemical reactions play an important role in maintaining the functionality of cellular metabolism. Despite advances in the constraint-based framework for genome-scale metabolic mode…
View article: Phototropin connects blue light perception to starch metabolism in green algae
Phototropin connects blue light perception to starch metabolism in green algae Open
View article: Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms
Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms Open
Advances in genomics technologies have generated large data sets that provide tremendous insights into the genetic diversity of taxonomic groups. However, it remains challenging to pinpoint the effect of genetic diversity on different trai…
View article: Advances in multi-trait genomic prediction approaches: Classification, comparative analysis, and perspectives
Advances in multi-trait genomic prediction approaches: Classification, comparative analysis, and perspectives Open
Traits in any organism are not independent, but show considerable integration, observed in a form of couplings and trade-offs. Therefore, improvement in one trait may affect other traits, often in undesired direction. To account for this p…
View article: Smart integrated biorefineries in bioeconomy: A concept toward zero-waste, emission reduction, and self-sufficient energy production
Smart integrated biorefineries in bioeconomy: A concept toward zero-waste, emission reduction, and self-sufficient energy production Open
Integrated biorefineries play a transformative role in sustainable development by converting biomass and biogenic residues into high-value products while minimizing waste, emissions, and resource inefficiencies. This review explores innova…
View article: Protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes
Protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes Open
Integrating enzyme parameters into constraint-based models have significantly improved the prediction of physiological and molecular traits. To further improve these models, we integrated promiscuous enzyme activities that jointly comprise…
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: Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models
Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models Open
Microbial consortia play pivotal roles in nutrient cycling across diverse ecosystems, where the functionality and composition of microbial communities are shaped by metabolic interactions. Despite the critical importance of understanding t…