Zoran Nikoloski

45 papers B 1C 1Journal 38Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
Accurate prediction of flux distributions compatible with metabolite concentration effects in genome-scale metabolic networks.
PLoS Comput. Biol.
Fayaz Soleymani Babadi, Zahra Razaghi-Moghadam, Zoran Nikoloski
2025 J jnl
Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives.
Briefings Bioinform.
Alain J. Mbebi, Facundo Mercado, David Hobby, Hao Tong, Zoran Nikoloski
2025 J jnl
Flux-sum coupling analysis of metabolic network models.
PLoS Comput. Biol.
Mihriban Seyis, Zahra Razaghi-Moghadam, Zoran Nikoloski
2024 J jnl
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes.
PLoS Comput. Biol.
Zahra Razaghi-Moghadam, Fayaz Soleymani Babadi, Zoran Nikoloski
2023 J jnl
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.
PLoS Comput. Biol.
Alain J. Mbebi, Zoran Nikoloski
2023 J jnl
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony.
PLoS Comput. Biol.
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
2023 J jnl
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models.
PLoS Comput. Biol.
Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski
2022 J jnl
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions.
PLoS Comput. Biol.
Philipp Wendering, Zoran Nikoloski
2022 J jnl
CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs.
Appl. Netw. Sci.
Sara Omranian, Zoran Nikoloski
2021 — conf
CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs.
COMPLEX NETWORKS
Sara Omranian, Zoran Nikoloski
2021 J jnl
Coherent network partitions: Characterizations with cographs and prime graphs.
Theor. Comput. Sci.
Angela Angeleska, Sara Omranian, Zoran Nikoloski
2021 J jnl
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level.
Bioinform.
Zahra Razaghi-Moghadam, Zoran Nikoloski
2021 J jnl
L2, 1-norm regularized multivariate regression model with applications to genomic prediction.
Bioinform.
Alain J. Mbebi, Hao Tong, Zoran Nikoloski
2021 J jnl
Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli.
Bioinform.
Rudan Xu, Zahra Razaghi-Moghadam, Zoran Nikoloski
2021 J jnl
PC2P: parameter-free network-based prediction of protein complexes.
Bioinform.
Sara Omranian, Angela Angeleska, Zoran Nikoloski
2020 J jnl
CytoSeg 2.0: automated extraction of actin filaments.
Bioinform.
Jacqueline Nowak, Kristin Gennermann, Staffan Persson, Zoran Nikoloski
2020 J jnl
Flux-based hierarchical organization of Escherichia coli's metabolic network.
PLoS Comput. Biol.
Semidán Robaina-Estévez, Zoran Nikoloski
2019 J jnl
Cellular determinants of metabolite concentration ranges.
PLoS Comput. Biol.
Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski
2019 J jnl
Coherent network partitions.
Discret. Appl. Math.
Angela Angeleska, Zoran Nikoloski
2017 J jnl
On the effects of alternative optima in context-specific metabolic model predictions.
PLoS Comput. Biol.
Semidán Robaina-Estévez, Zoran Nikoloski
2016 J jnl
DeFiNe: an optimisation-based method for robust disentangling of filamentous networks.
CoRR
David Breuer, Zoran Nikoloski
2016 J jnl
Multi-objective shadow prices point at principles of metabolic regulation.
Biosyst.
Max Sajitz-Hermstein, Zoran Nikoloski
2016 J jnl
iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models.
Bioinform.
Max Sajitz-Hermstein, Nadine Töpfer, Sabrina Kleessen, Alisdair R. Fernie, Zoran Nikoloski
2015 — conf
Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli.
IPCAT
Max Sajitz-Hermstein, Zoran Nikoloski
2014 J jnl
Biological Cluster Evaluation for Gene Function Prediction.
J. Comput. Biol.
Sebastian Klie, Zoran Nikoloski, Joachim Selbig
2014 J jnl
In search for an accurate model of the photosynthetic carbon metabolism.
Math. Comput. Simul.
Anne Arnold, Zoran Nikoloski
2014 — ch.
The Sequence Reconstruction Problem.
Discrete and Topological Models in Molecular Biology
Angela Angeleska, Sabrina Kleessen, Zoran Nikoloski
2014 J jnl
Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses.
PLoS Comput. Biol.
Nadine Töpfer, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski
2014 J jnl
img2net: automated network-based analysis of imaged phenotypes.
Bioinform.
David Breuer, Zoran Nikoloski
2013 — conf
Computational metabolic engineering of Arabidopsis thaliana for increased biomass production.
IWBBIO
Georg Basler, Abdelhalim Larhlimi, Sergio Grimbs, Zoran Nikoloski
2013 — conf
Heterogeneous Combinatorial Candidate Generation.
Euro-Par
Fahad Khalid, Zoran Nikoloski, Peter Tröger, Andreas Polze
2013 J jnl
Structural Control of Metabolic Flux.
PLoS Comput. Biol.
Max Sajitz-Hermstein, Zoran Nikoloski
2012 J jnl
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations.
BMC Syst. Biol.
Sabrina Kleessen, Zoran Nikoloski
2012 J jnl
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli.
BMC Syst. Biol.
Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski
2012 J jnl
Optimizing metabolic pathways by screening for feasible synthetic reactions.
Biosyst.
Georg Basler, Sergio Grimbs, Zoran Nikoloski
2012 J jnl
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks.
Bioinform.
Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski
2011 J jnl
Complexity of automated gene annotation.
Biosyst.
Zoran Nikoloski, Sergio Grimbs, Sebastian Klie, Joachim Selbig
2011 J jnl
Mass-balanced randomization of metabolic networks.
Bioinform.
Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski
2011 J jnl
Robustness of metabolic networks: A review of existing definitions.
Biosyst.
Abdelhalim Larhlimi, Sylvain Blachon, Joachim Selbig, Zoran Nikoloski
2011 J jnl
Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities.
Biosyst.
Sergio Grimbs, Anne Arnold, Aneta Koseska, Jürgen Kurths, Joachim Selbig, Zoran Nikoloski
2011 J jnl
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study.
BMC Bioinform.
Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths
2010 J jnl
A novel approach for determining environment-specific protein costs: the case of
Bioinform.
Max Sajitz-Hermstein, Zoran Nikoloski
2008 C conf
Hardness and Approximability of the Inverse Scope Problem.
WABI
Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhöh
2008 J jnl
On Modularity Clustering.
IEEE Trans. Knowl. Data Eng.
Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner
2007 B conf
On Finding Graph Clusterings with Maximum Modularity.
WG
Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner