Zoran Nikoloski

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 19

Top Topics

Metabolic Pathways

Computational Biology

Protein Complexes

Escherichia Coli

Top Venues

PLoS Comput. Biol.

Math. Comput. Simul.

Publications

Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS Comput. Biol. 19 (9) (2023)
Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Comput. Biol. 19 (10) (2023)
Alain J. Mbebi, Zoran Nikoloski
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput. Biol. 19 (7) (2023)
Philipp Wendering, Zoran Nikoloski
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Comput. Biol. 18 (3) (2022)
Sara Omranian, Zoran Nikoloski
CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Appl. Netw. Sci. 7 (1) (2022)
Rudan Xu, Zahra Razaghi-Moghadam, Zoran Nikoloski
Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli. Bioinform. 37 (21) (2021)
Sara Omranian, Zoran Nikoloski
CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs. COMPLEX NETWORKS (2021)
Zahra Razaghi-Moghadam, Zoran Nikoloski
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. Bioinform. 37 (12) (2021)
Sara Omranian, Angela Angeleska, Zoran Nikoloski
PC2P: parameter-free network-based prediction of protein complexes. Bioinform. 37 (1) (2021)
Alain J. Mbebi, Hao Tong, Zoran Nikoloski
L2, 1-norm regularized multivariate regression model with applications to genomic prediction. Bioinform. 37 (18) (2021)
Angela Angeleska, Sara Omranian, Zoran Nikoloski
Coherent network partitions: Characterizations with cographs and prime graphs. Theor. Comput. Sci. 894 (2021)
Jacqueline Nowak, Kristin Gennermann, Staffan Persson, Zoran Nikoloski
CytoSeg 2.0: automated extraction of actin filaments. Bioinform. 36 (9) (2020)
Semidán Robaina-Estévez, Zoran Nikoloski
Flux-based hierarchical organization of Escherichia coli's metabolic network. PLoS Comput. Biol. 16 (4) (2020)
Angela Angeleska, Zoran Nikoloski
Coherent network partitions. Discret. Appl. Math. 266 (2019)
Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski
Cellular determinants of metabolite concentration ranges. PLoS Comput. Biol. 15 (1) (2019)
Semidán Robaina-Estévez, Zoran Nikoloski
On the effects of alternative optima in context-specific metabolic model predictions. PLoS Comput. Biol. 13 (5) (2017)
Max Sajitz-Hermstein, Nadine Töpfer, Sabrina Kleessen, Alisdair R. Fernie, Zoran Nikoloski
iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. Bioinform. 32 (17) (2016)
David Breuer, Zoran Nikoloski
DeFiNe: an optimisation-based method for robust disentangling of filamentous networks. CoRR (2016)
Max Sajitz-Hermstein, Zoran Nikoloski
Multi-objective shadow prices point at principles of metabolic regulation. Biosyst. 146 (2016)
Max Sajitz-Hermstein, Zoran Nikoloski
Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli. IPCAT (2015)
David Breuer, Zoran Nikoloski
img2net: automated network-based analysis of imaged phenotypes. Bioinform. 30 (22) (2014)
Sebastian Klie, Zoran Nikoloski, Joachim Selbig
Biological Cluster Evaluation for Gene Function Prediction. J. Comput. Biol. 21 (6) (2014)
Anne Arnold, Zoran Nikoloski
In search for an accurate model of the photosynthetic carbon metabolism. Math. Comput. Simul. 96 (2014)
Nadine Töpfer, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski
Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses. PLoS Comput. Biol. 10 (6) (2014)
Max Sajitz-Hermstein, Zoran Nikoloski
Structural Control of Metabolic Flux. PLoS Comput. Biol. 9 (12) (2013)
Fahad Khalid, Zoran Nikoloski, Peter Tröger, Andreas Polze
Heterogeneous Combinatorial Candidate Generation. Euro-Par (2013)
Georg Basler, Abdelhalim Larhlimi, Sergio Grimbs, Zoran Nikoloski
Computational metabolic engineering of Arabidopsis thaliana for increased biomass production. IWBBIO (2013)
Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. Bioinform. 28 (18) (2012)
Georg Basler, Sergio Grimbs, Zoran Nikoloski
Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosyst. 109 (2) (2012)
Sabrina Kleessen, Zoran Nikoloski
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Syst. Biol. 6 (2012)
Nadine Töpfer, Szymon Jozefczuk, Zoran Nikoloski
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Syst. Biol. 6 (2012)
Georg Basler, Zoran Nikoloski
: mass-balanced randomization and analysis of metabolic networks. Bioinform. 27 (19) (2011)
Abdelhalim Larhlimi, Sylvain Blachon, Joachim Selbig, Zoran Nikoloski
Robustness of metabolic networks: A review of existing definitions. Biosyst. 106 (1) (2011)
Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski
Mass-balanced randomization of metabolic networks. Bioinform. 27 (10) (2011)
Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. BMC Bioinform. 12 (2011)
Sergio Grimbs, Anne Arnold, Aneta Koseska, Jürgen Kurths, Joachim Selbig, Zoran Nikoloski
Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities. Biosyst. 103 (2) (2011)
Zoran Nikoloski, Sergio Grimbs, Sebastian Klie, Joachim Selbig
Complexity of automated gene annotation. Biosyst. 104 (1) (2011)
Max Sajitz-Hermstein, Zoran Nikoloski
. Bioinform. 26 (18) (2010)
Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhöh
Hardness and Approximability of the Inverse Scope Problem. WABI (2008)
Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner
On Modularity Clustering. IEEE Trans. Knowl. Data Eng. 20 (2) (2008)
Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner
On Finding Graph Clusterings with Maximum Modularity. WG (2007)