On Finding Graph Clusterings with Maximum Modularity. - Ulrik Brandes; Daniel Delling; Marco Gaertler; Robert Görke; Martin Hoefer 001; Zoran Nikoloski; Dorothea Wagner (WG, 2007)

Hardness and Approximability of the Inverse Scope Problem. - Zoran Nikoloski; Sergio Grimbs; Joachim Selbig; Oliver Ebenhöh (WABI, 2008)

On Modularity Clustering. - Ulrik Brandes; Daniel Delling; Marco Gaertler; Robert Görke; Martin Hoefer 001; Zoran Nikoloski; Dorothea Wagner (IEEE Trans. Knowl. Data Eng., 2008)

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana. - Max Sajitz-Hermstein; Zoran Nikoloski (Bioinform., 2010)

Mass-balanced randomization of metabolic networks. - Georg Basler; Oliver Ebenhöh; Joachim Selbig; Zoran Nikoloski (Bioinform., 2011)

JMassBalance: mass-balanced randomization and analysis of metabolic networks. - Georg Basler; Zoran Nikoloski (Bioinform., 2011)

Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities. - Sergio Grimbs; Anne Arnold; Aneta Koseska; Jürgen Kurths; Joachim Selbig; Zoran Nikoloski (Biosyst., 2011)

Robustness of metabolic networks: A review of existing definitions. - Abdelhalim Larhlimi; Sylvain Blachon; Joachim Selbig; Zoran Nikoloski (Biosyst., 2011)

Complexity of automated gene annotation. - Zoran Nikoloski; Sergio Grimbs; Sebastian Klie; Joachim Selbig (Biosyst., 2011)

Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. - Sabrina Hempel; Aneta Koseska; Zoran Nikoloski; Jürgen Kurths (BMC Bioinform., 2011)

Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. - Abdelhalim Larhlimi; Georg Basler; Sergio Grimbs; Joachim Selbig; Zoran Nikoloski (Bioinform., 2012)

Optimizing metabolic pathways by screening for feasible synthetic reactions. - Georg Basler; Sergio Grimbs; Zoran Nikoloski (Biosyst., 2012)

Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. - Sabrina Kleessen; Zoran Nikoloski (BMC Syst. Biol., 2012)

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. - Nadine Töpfer; Szymon Jozefczuk; Zoran Nikoloski (BMC Syst. Biol., 2012)

Heterogeneous Combinatorial Candidate Generation. - Fahad Khalid; Zoran Nikoloski; Peter Tröger; Andreas Polze (Euro-Par, 2013)

Computational metabolic engineering of Arabidopsis thaliana for increased biomass production. - Georg Basler; Abdelhalim Larhlimi; Sergio Grimbs; Zoran Nikoloski (IWBBIO, 2013)

Structural Control of Metabolic Flux. - Max Sajitz-Hermstein; Zoran Nikoloski (PLoS Comput. Biol., 2013)

img2net: automated network-based analysis of imaged phenotypes. - David Breuer; Zoran Nikoloski (Bioinform., 2014)

Biological Cluster Evaluation for Gene Function Prediction. - Sebastian Klie; Zoran Nikoloski; Joachim Selbig (J. Comput. Biol., 2014)

In search for an accurate model of the photosynthetic carbon metabolism. - Anne Arnold; Zoran Nikoloski (Math. Comput. Simul., 2014)

Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses. - Nadine Töpfer; Federico Scossa; Alisdair R. Fernie; Zoran Nikoloski (PLoS Comput. Biol., 2014)

The Sequence Reconstruction Problem. - Angela Angeleska; Sabrina Kleessen; Zoran Nikoloski (Discrete and Topological Models in Molecular Biology, 2014)

Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli. - Max Sajitz-Hermstein; Zoran Nikoloski (IPCAT, 2015)

iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. - Max Sajitz-Hermstein; Nadine Töpfer; Sabrina Kleessen; Alisdair R. Fernie; Zoran Nikoloski (Bioinform., 2016)

Multi-objective shadow prices point at principles of metabolic regulation. - Max Sajitz-Hermstein; Zoran Nikoloski (Biosyst., 2016)

DeFiNe: an optimisation-based method for robust disentangling of filamentous networks. - David Breuer; Zoran Nikoloski (CoRR, 2016)

On the effects of alternative optima in context-specific metabolic model predictions. - Semidán Robaina-Estévez; Zoran Nikoloski (PLoS Comput. Biol., 2017)

Coherent network partitions. - Angela Angeleska; Zoran Nikoloski (Discret. Appl. Math., 2019)

Cellular determinants of metabolite concentration ranges. - Anika Küken; Jeanne M. O. Eloundou-Mbebi; Georg Basler; Zoran Nikoloski (PLoS Comput. Biol., 2019)

CytoSeg 2.0: automated extraction of actin filaments. - Jacqueline Nowak; Kristin Gennermann; Staffan Persson; Zoran Nikoloski (Bioinform., 2020)

Flux-based hierarchical organization of Escherichia coli's metabolic network. - Semidán Robaina-Estévez; Zoran Nikoloski (PLoS Comput. Biol., 2020)

L2, 1-norm regularized multivariate regression model with applications to genomic prediction. - Alain J. Mbebi; Hao Tong; Zoran Nikoloski (Bioinform., 2021)

PC2P: parameter-free network-based prediction of protein complexes. - Sara Omranian; Angela Angeleska; Zoran Nikoloski (Bioinform., 2021)

GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. - Zahra Razaghi-Moghadam; Zoran Nikoloski (Bioinform., 2021)

Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli. - Rudan Xu; Zahra Razaghi-Moghadam; Zoran Nikoloski (Bioinform., 2021)

Coherent network partitions: Characterizations with cographs and prime graphs. - Angela Angeleska; Sara Omranian; Zoran Nikoloski (Theor. Comput. Sci., 2021)

CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. - Sara Omranian; Zoran Nikoloski (Appl. Netw. Sci., 2022)

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. - Philipp Wendering; Zoran Nikoloski (PLoS Comput. Biol., 2022)

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. - Seirana Hashemi; Zahra Razaghi-Moghadam; Zoran Nikoloski (PLoS Comput. Biol., 2023)

Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. - Alain J. Mbebi; Zoran Nikoloski (PLoS Comput. Biol., 2023)

PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. - Mauricio Alexander de Moura Ferreira; Wendel Batista da Silveira; Zoran Nikoloski (PLoS Comput. Biol., 2023)

Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. - Zahra Razaghi-Moghadam; Fayaz Soleymani Babadi; Zoran Nikoloski (PLoS Comput. Biol., 2024)

Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives. - Alain J. Mbebi; Facundo Mercado; David Hobby; Hao Tong; Zoran Nikoloski (Briefings Bioinform., 2025)

Flux-sum coupling analysis of metabolic network models. - Mihriban Seyis; Zahra Razaghi-Moghadam; Zoran Nikoloski (PLoS Comput. Biol., 2025)