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ORCIDZoran Nikoloski
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2020 – today
- 2024
[j35]Zahra Razaghi-Moghadam
, Fayaz Soleymani Babadi, Zoran Nikoloski:
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. PLoS Comput. Biol. 20(11): 1012576 (2024)- 2023
- [j34]Alain J. Mbebi, Zoran Nikoloski:
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput. Biol. 19(7) (2023) - [j33]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) - [j32]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) - 2022
- [j31]Sara Omranian, Zoran Nikoloski:
CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. Appl. Netw. Sci. 7(1): 71 (2022) - [j30]Philipp Wendering, Zoran Nikoloski:
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Comput. Biol. 18(3) (2022) - 2021
- [j29]Sara Omranian, Angela Angeleska, Zoran Nikoloski:
PC2P: parameter-free network-based prediction of protein complexes. Bioinform. 37(1): 73-81 (2021) - [j28]Zahra Razaghi-Moghadam, Zoran Nikoloski:
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. Bioinform. 37(12): 1717-1723 (2021) - [j27]Alain J. Mbebi, Hao Tong, Zoran Nikoloski:
L2, 1-norm regularized multivariate regression model with applications to genomic prediction. Bioinform. 37(18): 2896-2904 (2021) - [j26]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): 3848-3855 (2021) - [j25]Angela Angeleska, Sara Omranian, Zoran Nikoloski:
Coherent network partitions: Characterizations with cographs and prime graphs. Theor. Comput. Sci. 894: 3-11 (2021) - [c6]Sara Omranian, Zoran Nikoloski:
CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs. COMPLEX NETWORKS 2021: 605-615 - 2020
- [j24]Jacqueline Nowak, Kristin Gennermann, Staffan Persson, Zoran Nikoloski:
CytoSeg 2.0: automated extraction of actin filaments. Bioinform. 36(9): 2950-2951 (2020) - [j23]Semidán Robaina-Estévez, Zoran Nikoloski:
Flux-based hierarchical organization of Escherichia coli's metabolic network. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j22]Angela Angeleska, Zoran Nikoloski:
Coherent network partitions. Discret. Appl. Math. 266: 283-290 (2019) - [j21]Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski:
Cellular determinants of metabolite concentration ranges. PLoS Comput. Biol. 15(1) (2019) - 2017
- [j20]Semidán Robaina-Estévez, Zoran Nikoloski:
On the effects of alternative optima in context-specific metabolic model predictions. PLoS Comput. Biol. 13(5) (2017) - 2016
- [j19]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): 755-762 (2016) - [j18]Max Sajitz-Hermstein, Zoran Nikoloski:
Multi-objective shadow prices point at principles of metabolic regulation. Biosyst. 146: 91-101 (2016) - [i1]David Breuer, Zoran Nikoloski:
DeFiNe: an optimisation-based method for robust disentangling of filamentous networks. CoRR abs/1601.00847 (2016) - 2015
- [c5]Max Sajitz-Hermstein, Zoran Nikoloski:
Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli. IPCAT 2015: 169-172 - 2014
- [j17]David Breuer, Zoran Nikoloski:
img2net: automated network-based analysis of imaged phenotypes. Bioinform. 30(22): 3291-3292 (2014) - [j16]Sebastian Klie, Zoran Nikoloski, Joachim Selbig:
Biological Cluster Evaluation for Gene Function Prediction. J. Comput. Biol. 21(6): 428-445 (2014) - [j15]Anne Arnold, Zoran Nikoloski:
In search for an accurate model of the photosynthetic carbon metabolism. Math. Comput. Simul. 96: 171-194 (2014) - [j14]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) - [p1]Angela Angeleska, Sabrina Kleessen, Zoran Nikoloski:
The Sequence Reconstruction Problem. Discrete and Topological Models in Molecular Biology 2014: 23-43 - 2013
- [j13]Max Sajitz-Hermstein, Zoran Nikoloski:
Structural Control of Metabolic Flux. PLoS Comput. Biol. 9(12) (2013) - [c4]Fahad Khalid, Zoran Nikoloski, Peter Tröger, Andreas Polze:
Heterogeneous Combinatorial Candidate Generation. Euro-Par 2013: 751-762 - [c3]Georg Basler, Abdelhalim Larhlimi, Sergio Grimbs, Zoran Nikoloski:
Computational metabolic engineering of Arabidopsis thaliana for increased biomass production. IWBBIO 2013: 223 - 2012
- [j12]Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski:
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. Bioinform. 28(18): 502-508 (2012) - [j11]Georg Basler, Sergio Grimbs, Zoran Nikoloski:
Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosyst. 109(2): 186-191 (2012) - [j10]Sabrina Kleessen, Zoran Nikoloski:
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Syst. Biol. 6: 16 (2012) - [j9]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: 148 (2012) - 2011
- [j8]Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski:
Mass-balanced randomization of metabolic networks. Bioinform. 27(10): 1397-1403 (2011) - [j7]Georg Basler, Zoran Nikoloski:
JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinform. 27(19): 2761-2762 (2011) - [j6]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): 212-223 (2011) - [j5]Zoran Nikoloski, Sergio Grimbs, Sebastian Klie, Joachim Selbig:
Complexity of automated gene annotation. Biosyst. 104(1): 1-8 (2011) - [j4]Abdelhalim Larhlimi, Sylvain Blachon, Joachim Selbig, Zoran Nikoloski:
Robustness of metabolic networks: A review of existing definitions. Biosyst. 106(1): 1-8 (2011) - [j3]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: 292 (2011) - 2010
- [j2]Max Sajitz-Hermstein, Zoran Nikoloski:
A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana. Bioinform. 26(18) (2010)
2000 – 2009
- 2008
- [j1]Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner:
On Modularity Clustering. IEEE Trans. Knowl. Data Eng. 20(2): 172-188 (2008) - [c2]Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhöh:
Hardness and Approximability of the Inverse Scope Problem. WABI 2008: 99-112 - 2007
- [c1]Ulrik Brandes, Daniel Delling, Marco Gaertler, Robert Görke, Martin Hoefer, Zoran Nikoloski, Dorothea Wagner:
On Finding Graph Clusterings with Maximum Modularity. WG 2007: 121-132
Coauthor Index
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