List of works - Zoran Nikoloski

A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis.

scientific article

A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids

scientific article published in 2022

A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms

scientific article published on 25 September 2012

A network property necessary for concentration robustness

scientific article published on 19 October 2016

A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells

scientific article published on 19 January 2021

A new network model explains the evolution of plant-specific metabolic networks

article

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

scientific article published on September 2010

A quantitative comparison of Calvin-Benson cycle models.

scientific article published on 14 October 2011

Advances in metabolic flux analysis toward genome-scale profiling of higher organisms

scholarly article by Georg Basler published in October 2018

Algebraic connectivity may explain the evolution of gene regulatory networks

article

Analysis of Short-Term Metabolic Alterations in Arabidopsis Following Changes in the Prevailing Environmental Conditions

scientific article published on 06 February 2014

Analysis of metabolic alterations inArabidopsisfollowing changes in the carbon dioxide and oxygen partial pressures

scientific article published on 25 August 2014

AtRsgA from Arabidopsis thaliana controls maturation of the small subunit of the chloroplast ribosome

article published in 2017

BIOSYNTHETIC POTENTIALS FROM SPECIES-SPECIFIC METABOLIC NETWORKS

Biological cluster evaluation for gene function prediction

scientific article published on 08 January 2010

Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production.

scientific article published on 7 May 2014

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

scientific article published on 23 March 2022

Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles

scientific article published on 11 March 2016

Canalization of Tomato Fruit Metabolism

scientific article published in November 2017

Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

scientific article published on 23 December 2021

Cellular determinants of metabolite concentration ranges

scientific article published on 24 January 2019

Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement

scientific article published on 30 May 2017

Classification-driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots.

scientific article published on 26 April 2018

Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds.

scientific article published on 16 December 2014

Complexity of automated gene annotation

scientific article published on 08 January 2011

Comprehensive classification and perspective for modelling photorespiratory metabolism.

scientific article published on 10 April 2013

Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions

scientific article published on 16 November 2012

Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways

article

Computational Approaches to Study Gene Regulatory Networks

scientific article published on January 2017

Concurrent conditional clustering of multiple networks: COCONETS

scientific article

Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species

scientific article published on 15 November 2013

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

scientific article published on 9 July 2015

Control of fluxes in metabolic networks

scientific article published on 19 May 2016

Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns

article

Correlation Model of Worm Propagation on Scale-Free Networks

article

Data Integration, Metabolic Networks and Systems Biology

Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism.

scientific article

Data integration through proximity-based networks provides biological principles of organization across scales

scientific article

Data-driven reconstruction of directed networks

DeFiNe: an optimisation-based method for robust disentangling of filamentous networks

scientific article

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

scientific article

Deducing hybrid performance from parental metabolic profiles of young primary roots of maize by using a multivariate diallel approach

scientific article published on 7 January 2014

Differential metabolic and coexpression networks of plant metabolism

article

Dimensionality reduction of bistable biological systems

scientific article published on 8 February 2013

Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

scientific article

Editorial: Engineering Synthetic Metabolons: From Metabolic Modeling to Rational Design of Biosynthetic Devices

scientific article

Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana.

scientific article published on 17 August 2012

Effects of microcompartmentation on flux distribution and metabolic pools in chloroplasts

scientific article published on 11 October 2018

Effects of varying nitrogen sources on amino acid synthesis costs in Arabidopsis thaliana under different light and carbon-source conditions

scientific article published on 23 February 2015

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

scientific article published on 4 December 2017

Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels

scientific article published on 05 April 2016

Evolutionary significance of metabolic network properties

scientific article published on 30 November 2011

Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions

scientific article

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.

scientific article published on 11 January 2016

Flux profiling of photosynthetic carbon metabolism in intact plants

article

Flux-based hierarchical organization of Escherichia coli ’s metabolic network

scientific article published on 10 August 2019

Flux-based hierarchical organization of Escherichia coli's metabolic network

scientific article published on 20 April 2020

From systems biology to systems chemistry: metabolomic procedures enable insight into complex chemical reaction networks in water

scholarly article in RSC Advances, vol. 4 no. 32, 2014

Functional centrality as a predictor of shifts in metabolic flux states

scientific article

Gene regulatory network inference using fused LASSO on multiple data sets

scientific article

Generalized framework for context-specific metabolic model extraction methods

scientific article published on 19 September 2014

Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population.

scientific article

Genome-Scale Modeling of Photorespiratory Pathway Manipulation

scientific article

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

scientific article published in 2014

Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.

scientific article

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

scientific article published on 05 June 2015

Getting back to nature: a reality check for experiments in controlled environments

scientific article

Hardness and Approximability of the Inverse Scope Problem

Heterogeneous Combinatorial Candidate Generation

Identification and classification of ncRNA molecules using graph properties

scientific article published in April 2009

Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato

scientific article published on 13 March 2015

Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions

scientific article published in 2013

In search for an accurate model of the photosynthetic carbon metabolism

article

Inference and Prediction of Metabolic Network Fluxes

scientific article published on 21 September 2015

Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views

scientific article published on 29 June 2012

Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat

scientific article published on 13 December 2017

Inner composition alignment for inferring directed networks from short time series

scientific article

Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth

scientific article published on 15 May 2020

Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis

scientific article

Integration of metabolomics data into metabolic networks

scientific article

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

scientific article

Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment

scientific article

Integrative comparative analyses of transcript and metabolite profiles from pepper and tomato ripening and development stages uncovers species-specific patterns of network regulatory behavior

scientific article published on 8 June 2012

Integrative field scale phenotyping for investigating metabolic components of water stress within a vineyard

scientific article published on 30 October 2017

JMassBalance: mass-balanced randomization and analysis of metabolic networks

scientific article

Large-scale co-expression approach to dissect secondary cell wall formation across plant species

scientific article published on July 2011

Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

scientific article published on 30 August 2017

Mass-balanced randomization of metabolic networks

scientific article published on 23 March 2011

Metabolic Network Constrains Gene Regulation of C4 Photosynthesis: The Case of Maize

scientific article

Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues

scientific article published on 20 June 2011

Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana

scientific article published on 28 March 2014

Metabolic fluxes in an illuminated Arabidopsis rosette

scientific article published on 26 February 2013

Metabolic networks are NP-hard to reconstruct

scientific article

Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations

scientific article

Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field

scientific article published on 25 January 2017

Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics ⬇️

scientific article published on 27 May 2014

Metabolite profiling and integrative modeling reveal metabolic constraints for carbon partitioning under nitrogen starvation in the green algae Haematococcus pluvialis.

scientific article

Metabolite profiling and network analysis reveal coordinated changes in grapevine water stress response

scientific article

Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways

scientific article published on 12 July 2020

Model-based confirmation of alternative substrates of mitochondrial electron transport chain

scientific article

Modeling alternatives for interpreting the change in oxygen‐consumption rates during hypoxic conditions ⬇️

scientific article published on February 23, 2011

Multi-objective shadow prices point at principles of metabolic regulation

scientific article published on 13 June 2016

Network analysis: tackling complex data to study plant metabolism

scientific article

Network-based segmentation of biological multivariate time series

scientific article

Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana

scientific article published on 2 September 2016

Observability of Plant Metabolic Networks Is Reflected in the Correlation of Metabolic Profiles

scientific article

Omics-Based Hybrid Prediction In Maize

Omics-based hybrid prediction in maize.

scientific article

On Finding Graph Clusterings with Maximum Modularity

On Modularity Clustering

On the effects of alternative optima in context-specific metabolic model predictions

scientific article

On the relation between reactions and complexes of (bio)chemical reaction networks

scientific article published on 22 October 2012

Optimizing metabolic pathways by screening for feasible synthetic reactions

scientific article

PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana

scientific article

Perspectives on plant photorespiratory metabolism

scientific article published on 10 December 2012

Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence?

scientific article published on 7 April 2016

Phytotyping4D: a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth

article

PlaNet: combined sequence and expression comparisons across plant networks derived from seven species

scientific article published on 25 March 2011

Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana

scientific article

Probabilistic Inductive Classes of Graphs

Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle

scientific article

Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale

scientific article published in 2023

Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles

scientific article

Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach.

scientific article

Resolving the central metabolism of Arabidopsis guard cells

scientific article published on 16 August 2017

Restricted cooperative games on metabolic networks reveal functionally important reactions

scientific article published on 23 August 2012

Revisiting ancestral polyploidy in plants

scientific article published on 05 July 2017

Robustness of metabolic networks: a review of existing definitions

scientific article published on 25 June 2011

Segmentation of biological multivariate time-series data

scientific article

Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli

scholarly article by Max Sajitz-Hermstein & Zoran Nikoloski published 2015 in Lecture Notes in Computer Science

Spatiotemporal dynamics of the Calvin cycle: multistationarity and symmetry breaking instabilities.

scientific article published on 12 November 2010

Stability of metabolic correlations under changing environmental conditions in Escherichia coli--a systems approach

scientific article

Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data

scientific article published on 18 December 2017

Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks

scientific article published on September 2012

Structural control of metabolic flux

scientific article (publication date: 2013)

Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana

scientific article

Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data

scientific article published on 30 June 2020

System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells.

scientific article

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii

scholarly article by Tabea Mettler et al published June 2014 in The Plant Cell

The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science

scientific article published on 28 June 2012

The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism

scientific article published on 15 August 2019

The Sequence Reconstruction Problem

The hidden simplicity of metabolic networks is revealed by multireaction dependencies

scientific article published in 2022

The investment in scent: time-resolved metabolic processes in developing volatile-producing Nigella sativa L. seeds

scientific article (publication date: 2013)

Topological properties accurately predict cell division events and organization of shoot apical meristem in <i>Arabidopsis thaliana</i>

scientific article published in 2022

Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco

scientific article published on 17 December 2021

Toward mechanistic modeling and rational engineering of plant respiration

scientific article published in 2023

Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study

scientific article

Unraveling the lipid metabolism in maize with time-resolved multi-omics data

scientific article published on 31 January 2018

Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions

scientific article published on 20 June 2016

Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control

scientific article

Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses

scientific article (publication date: June 2014)

Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome

scientific article

iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models

scientific article published on September 2016

img2net: automated network-based analysis of imaged phenotypes

scientific article published on 26 July 2014

List of works by Zoran Nikoloski

A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis.

A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids

A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms

A network property necessary for concentration robustness

A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells

A new network model explains the evolution of plant-specific metabolic networks

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

A quantitative comparison of Calvin-Benson cycle models.

Advances in metabolic flux analysis toward genome-scale profiling of higher organisms

Algebraic connectivity may explain the evolution of gene regulatory networks

Analysis of Short-Term Metabolic Alterations in Arabidopsis Following Changes in the Prevailing Environmental Conditions

Analysis of metabolic alterations inArabidopsisfollowing changes in the carbon dioxide and oxygen partial pressures

AtRsgA from Arabidopsis thaliana controls maturation of the small subunit of the chloroplast ribosome

BIOSYNTHETIC POTENTIALS FROM SPECIES-SPECIFIC METABOLIC NETWORKS

Biological cluster evaluation for gene function prediction

Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production.

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles

Canalization of Tomato Fruit Metabolism

Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

Cellular determinants of metabolite concentration ranges

Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement

Classification-driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots.

Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds.

Complexity of automated gene annotation

Comprehensive classification and perspective for modelling photorespiratory metabolism.

Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions

Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways

Computational Approaches to Study Gene Regulatory Networks

Concurrent conditional clustering of multiple networks: COCONETS

Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species

Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization

Control of fluxes in metabolic networks

Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns

Correlation Model of Worm Propagation on Scale-Free Networks

Data Integration, Metabolic Networks and Systems Biology

Data Integration, Metabolic Networks and Systems Biology

Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism.

Data integration through proximity-based networks provides biological principles of organization across scales

Data-driven reconstruction of directed networks

DeFiNe: an optimisation-based method for robust disentangling of filamentous networks

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

Deducing hybrid performance from parental metabolic profiles of young primary roots of maize by using a multivariate diallel approach

Differential metabolic and coexpression networks of plant metabolism

Dimensionality reduction of bistable biological systems

Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

Editorial: Engineering Synthetic Metabolons: From Metabolic Modeling to Rational Design of Biosynthetic Devices

Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana.

Effects of microcompartmentation on flux distribution and metabolic pools in chloroplasts

Effects of varying nitrogen sources on amino acid synthesis costs in Arabidopsis thaliana under different light and carbon-source conditions

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana

Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels

Evolutionary significance of metabolic network properties

Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.

Flux profiling of photosynthetic carbon metabolism in intact plants

Flux-based hierarchical organization of Escherichia coli ’s metabolic network

Flux-based hierarchical organization of Escherichia coli's metabolic network

From systems biology to systems chemistry: metabolomic procedures enable insight into complex chemical reaction networks in water

Functional centrality as a predictor of shifts in metabolic flux states

Gene regulatory network inference using fused LASSO on multiple data sets

Generalized framework for context-specific metabolic model extraction methods

Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population.

Genome-Scale Modeling of Photorespiratory Pathway Manipulation

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

Getting back to nature: a reality check for experiments in controlled environments

Hardness and Approximability of the Inverse Scope Problem

Heterogeneous Combinatorial Candidate Generation

Identification and classification of ncRNA molecules using graph properties

Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato

Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions

In search for an accurate model of the photosynthetic carbon metabolism

Inference and Prediction of Metabolic Network Fluxes

Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views

Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat

Inner composition alignment for inferring directed networks from short time series

Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth