Kleessen, S.; Klie, S.; Nikoloski, Z.: Concurrent Conditional Clustering of Multiple Networks: COCONETS. PLoS One 9 (8), e103637 (2014)

Klie, S.; Osorio, S.; Tohge, T.; Drincovich, M. F.; Fait, A.; Giovannoni, J. J.; Fernie, A. R.; Nikoloski, Z.: Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species. Plant Physiology 164 (1), pp. 55 - 68 (2014)

Meret, M.; Kopetzki, D.; Degenkolbe, T.; Kleessen, S.; Nikoloski, Z.; Tellstroem, V.; Barsch, A.; Kopka, J.; Antonietti, M.; Willmitzer, L.: From systems biology to systems chemistry: metabolomic procedures enable insight into complex chemical reaction networks in water. RSC Advances 4 (32), pp. 16777 - 16781 (2014)

Mettler, T.; Mühlhaus, T.; Hemme, D.; Schöttler, M. A.; Rupprecht, J.; Idoine, A.; Veyel, D.; Pal, S. K.; Yaneva-Roder, L.; Winck, F. V. et al.; Sommer, F.; Vosloh, D.; Seiwert, B.; Erban, A.; Burgos, A.; Arvidsson, S.; Schönfelder, S.; Arnold, A.; Günther, M.; Krause, U.; Lohse, M.; Kopka, J.; Nikoloski, Z.; Mueller-Roeber, B.; Willmitzer, L.; Bock, R.; Schroda, M.; Stitt, M.: Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. The Plant Cell 26 (6), pp. 2310 - 2350 (2014)

Toepfer, N.; Scossa, F.; Fernie, A. R.; Nikoloski, Z.: Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses. PLoS Computational Biology 10 (6), e1003656 (2014)

Sajitz-Hermstein, M.; Nikoloski, Z.: Structural control of metabolic flux. PLoS Computational Biology 9 (12), e1003368 (2013)

Hochberg, U.; Degu, A.; Toubiana, D.; Gendler, T.; Nikoloski, Z.; Rachmilevitch, S.; Fait, A.: Metabolic profiling and network analysis reveal coordinated changes in grapevine water stress response. BMC Plant Biology 13 (184) (2013)

Kleessen, S.; Klie, S.; Nikoloski, Z.: Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales. The Plant Cell 25 (6), pp. 1917 - 1927 (2013)

Toepfer, N.; Caldana, C.; Grimbs, S.; Willmitzer, L.; Fernie, A. R.; Nikoloski, Z.: Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis. The Plant Cell 25 (4), pp. 1197 - 1211 (2013)

Neigenfind, J.; Grimbs, S.; Nikoloski, Z.: On the relation between reactions and complexes of (bio)chemical reaction networks. Journal of Theoretical Biology 317, pp. 359 - 365 (2013)

Omranian, N.; Klie, S.; Mueller-Roeber, B.; Nikoloski, Z.: Network-Based Segmentation of Biological Multivariate Time Series. PLoS One 8 (5), p. e62974 (2013)

Sulpice, R.; Nikoloski, Z.; Tschoep, H.; Antonio, C.; Kleeson, S.; Lahrlimi, A.; Selbig, J.; Hirofumi, I.; Gibon, Y.; Fernie, A. R. et al.; Stitt, M.: Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiology 162 (1), pp. 347 - 363 (2013)

Szecowka, M.; Heise, R.; Tohge, T.; Nunes-Nesi, A.; Vosloh, D.; Huege, J.; Feil, R.; Lunn, J.; Nikoloski, Z.; Stitt, M. et al.; Fernie, A. R.; Arrivault, S.: Metabolic Fluxes in an Illuminated Arabidopsis Rosette. The Plant Cell 25 (2), pp. 694 - 714 (2013)

Winck, F. V.; Arvidsson, S.; Mauricio Riano-Pachon, D.; Hempel, S.; Koseska, A.; Nikoloski, Z.; Urbina Gomez, D. A.; Rupprecht, J.; Mueller-Roeber, B.: Genome-Wide Identification of Regulatory Elements and Reconstruction of Gene Regulatory Networks of the Green Alga Chlamydomonas reinhardtii under Carbon Deprivation. PLoS One 8 (11), e79909 (2013)

Xue, W.; Batushansky, A.; Toubiana, D.; Botnick, I.; Szymanski, J.; Khozin-Goldberg, I.; Nikoloski, Z.; Lewinsohn, E.; Fait, A.: The Investment in Scent: Time-Resolved Metabolic Processes in Developing Volatile-Producing Nigella sativa L. Seeds. PLoS One 8 (9), e73061 (2013)

Zakharova, A.; Nikoloski, Z.; Koseska, A.: Dimensionality reduction of multistable biological systems. Bulletin of Mathematical Biology 75 (3), pp. 373 - 392 (2013)

Araujo, W. L.; Nunes-Nesi, A.; Nikoloski, Z.; Sweetlove, L. J.; Fernie, A. R.: Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant, Cell and Environment 35 (1), pp. 1 - 21 (2012)

Basler, G.; Grimbs, S.; Nikoloski, Z.: Optimizing metabolic pathways by screening for feasible synthetic reactions. Biosystems 109 (2), pp. 186 - 191 (2012)

Güell, O.; Sagués, F.; Basler, G.; Nikoloski, Z.; Serrano, M. S.: Assessing the significance of knockout cascades in metabolic networks. Journal of Computational Interdisciplinary Sciences 3 (1-2), pp. 45 - 53 (2012)

Kleessen, S.; Antonio, C.; Sulpice, R.; Laitinen, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nature Communications 3, p. 1319 (2012)

Kleessen, S.; Araujo, W. L.; Fernie, A. R.; Nikoloski, Z.: Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain. Journal of Biological Chemistry 287 (14), pp. 11122 - 11131 (2012)

Kleessen, S.; Fernie, A. R.; Nikoloski, Z.: A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms. Frontiers in Plant Science 3, p. 217 (2012)

Kleessen, S.; Nikoloski, Z.: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6 (1), p. 16 (2012)

Klie, S.; Caldana, C.; Nikoloski, Z.: Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions. Frontiers in Plant Science 3, p. 249 (2012)

Klie, S.; Nikoloski, Z.: The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. Frontiers in Genetics 3, p. 115 (2012)

Omidbakhshfard, M. A.; Omranian, N.; Ahmadi, F. S.; Nikoloski, Z.; Mueller-Roeber, B.: Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana. Plant Signaling & Behavior 7 (9), pp. 1095 - 1102 (2012)

Omranian, N.; Mueller-Roeber, B.; Nikoloski, Z.: PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana. Molecular BioSystems 8 (4), pp. 1121 - 1127 (2012)

Osorio, S.; Alba, R.; Nikoloski, Z.; Kochevenko, A.; Fernie, A. R.; Giovannoni, J. J.: Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior. Plant Physiology 159 (4), pp. 1713 - 1729 (2012)

Sajitz-Hermstein, M.; Nikoloski, Z.: Restricted cooperative games on metabolic networks reveal functionally important reactions. Journal of Theoretical Biology 314, pp. 192 - 203 (2012)

Toepfer, N.; Jozefczuk, S.; Nikoloski, Z.: Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Systems Biology 6 (1), p. 148 (2012)

Toubiana, D.; Semel, Y.; Tohge, T.; Beleggia, R.; Cattivelli, L.; Rosental, L.; Nikoloski, Z.; Zamir, D.; Fernie, A. R.; Fait, A.: Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations. PLoS Genetics 8 (3), p. e1002612 (2012)

Basler, G.; Ebenhoeh, O.; Selbig, J.; Nikoloski, Z.: Mass-balanced randomization of metabolic networks. Bioinformatics 27 (10), pp. 1397 - 1403 (2011)

Basler, G.; Grimbs, S.; Ebenhoeh, O.; Selbig, J.; Nikoloski, Z.: Evolutionary significance of metabolic network properties. Journal of the Royal Society Interface 9 (71), pp. 1168 - 1176 (2011)

Basler, G.; Nikoloski, Z.; Ebenhoeh, O.; Handorf, T.: Biosynthetic potentials from species-specific metabolic networks. Genome Informatics 20, pp. 135 - 148 (2008)

Handorf, T.; Christian, N.; Ebenhoeh, O.; Kahn, D.: An environmental perspective on metabolism. Journal of Theoretical Biology 252 (3), pp. 530 - 537 (2008)

Kersten, B.; Nagel, A.; Riano-Pachon, D.M.; Neigenfind, J.; Weber, E.; Wagner, R.; Diehl, S.: Die GABI-Primaerdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXPress: Informationen aus der Deutschen Genomforschung 1, pp. 17 - 19 (2008)

Kruse, K.; Ebenhoeh, O.: Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds. Genome Informatics 20, pp. 91 - 101 (2008)

Matthaeus, F.; Salazar, C.; Ebenhoeh, O.: Biosynthetic potentials of metabolites and their hierarchical organization. PLoS Computational Biology 4 (4), p. e1000049 (2008)

May, P.; Wienkoop, S.; Kempa, S.; Usadel, B.; Christian, N.; Rupprecht, J.; Weiss, J.; Recuenco-Munoz, L.; Ebenhoeh, O.; Weckwerth, W. et al.; Walther, D.: Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179 (1), pp. 157 - 166 (2008)

Nikoloski, Z.; Grimbs, S.; Selbig, J.; Ebenhoeh, O.: Hardness and Approximability of the Inverse Scope Problem. Algorithms in Bioinformatics, Wabi 2008 5251, pp. 99 - 112 (2008)

Christian, N.; Handorf, T.; Ebenhoeh, O.: Metabolic Synergy: Increasing Biosynthetic Capabilities by Network Cooperation. Genome Informatics 18 (1), pp. 320 - 329 (2007)

Küken, A.; Nikoloski, Z.: Genome-scale modeling of photorespiratory pathway manipulation. In: Methods in Molecular Biology, Vol. 1653, pp. 195 - 202. Elsevier, Cambridge, MA (2017)

Omranian, N.; Nikoloski, Z.: Computational Approaches to Study Gene Regulatory Networks. In: Plant gene Regulatory Networks, Vol. 1629, pp. 283 - 295. Springer, heidelberg (2017)

Angeleska, A.; Kleessen, S.; Nikoloski, Z.: The Sequence Reconstruction Problem. In: Discrete and Topological Models in Molecular Biology, pp. 23 - 43 (Eds. Jonoska , N.; Saito, M.). Springer-Verlag, Berlin, Heidelberg (2014)

Kartal, O.; Ebenhoeh, O.: The glucan, water dikinase - a kinetic model to understand the initial step in starch mobilization in plant leaves. In: From Computational Biophysics to Systems Biology, Vol. 40, pp. 245 - 248 (Eds. Hansmann, U.H.E.; Meinke, J.H.; Mohanty, S.; Nadler, W.; Zimmermann, O.). John von Neumann Institute for Computing, Jülich, GER (2008)

Sajitz-Hermstein, M.; Nikoloski, Z.: Sensitivity of Contending Cellular Objectives in the Central Carbon Metabolism of Escherichia Coli. In: Information Processing in Cells and Tissues, pp. 169 - 172. 10th International Conference on Information Processing in Cells and Tissues (IPCAT), San Diego, CA, September 14, 2015 - September 16, 2015. (2015)

Larhlimi, A.; Basler, G.; Grimbs, S.; Selbig, J.; Nikoloski, Z.: Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. In: 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB), pp. I502 - I508. 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB) , Basel, SWITZERLAND. (2012)

Medeiros, D. B.; Daloso, D. M.; Fernie, A. R.; Nikoloski, Z.; Araujo, W. L.: Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control. (2015)

Toepfer, N.; Kleessen, S.; Nikoloski, Z.: Integration of metabolomics data into metabolic networks. (2015)

Estevez, S.; Nikoloski, Z.: Generalized framework for context-specific metabolic model extraction methods. (2014)

Arnold, A.; Nikoloski, Z.: Comprehensive classification and perspective for modelling photorespiratory metabolism. (2013)

Fernie, A. R.; Bauwe, H.; Eisenhut, M.; Florian, A.; Hanson, D. T.; Hagemann, M.; Keech, O.; Mielewczik, M.; Nikoloski, Z.; Peterhansel, C. et al.; Roje, S.; Sage, R.; Timm, S.; von Cammerer, S.; Weber, A. P.; Westhoff, P.: Perspectives on plant photorespiratory metabolism. (2013)

Toubiana, D.; Fernie, A. R.; Nikoloski, Z.; Fait, A.: Network analysis: tackling complex data to study plant metabolism. (2013)

Klie, S.; Mutwil, M.; Persson, S.; Nikoloski, Z.: Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. (2012)

Larhlimi, A.; Blachon, S.; Selbig, J.; Nikoloski, Z.: Robustness of metabolic networks: A review of existing definitions. (2011)