Publications of the Group

Bellucci, E.; Bitocchi, E.; Ferrarini, A.; Benazzo, A.; Biagetti, E.; Klie, S.; Minio, A.; Rau, D.; Rodriguez, M.; Panziera, A. et al.; Venturini, L.; Attene, G.; Albertini, E.; Jackson, S. A.; Nanni, L.; Fernie, A. R.; Nikoloski, Z.; Bertorelle, G.; Delledonne, M.; Papa, R.: Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. The Plant Cell 26 (5), pp. 1901 - 1912 (2014)

Kleessen, S.; Laitinen, R.; Fusari, C. M.; Antonio, C.; Sulpice, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana. Nature Communications 5, 3537 (2014)

Arnold, A.; Nikoloski, Z.: In search for an accurate model of the photosynthetic carbon metabolism. Mathematics and Computers in Simulation 96, pp. 171 - 194 (2014)

Feher, K.; Lisec, J.; Römisch-Margl, L.; Selbig, J.; Gierl, A.; Piepho, H.-P.; Nikoloski, Z.; Willmitzer, L.: Deducing Hybrid Performance from Parental Metabolic Profiles of Young Primary Roots of Maize by Using a Multivariate Diallel Approach. PLoS ONE 9 (1), e85435 (2014)

Breuer, D.; Ivakov, A.; Sampathkumar, A.; Hollandt, F.; Persson, S.; Nikoloski, Z.: Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles. Interface: Journal of the Royal Society 11 (97), 20140362 (2014)

Breuer, D.; Nikoloski, Z.: img2net: automated network-based analysis of imaged phenotypes. Bioinformatics 30 (22), pp. 3291 - 2 (2014)

Breuer, D.; Timme, M.; Memmesheimer, R.-M.: Statistical Physics of Neural Systems with Nonadditive Dendritic Coupling. Physical Review X 4 (1), 011053 (2014)

Florian, A.; Nikoloski, Z.; Sulpice, R.; Timm, S.; Araujo, W. L.; Tohge, T.; Bauwe, H.; Fernie, A. R.: Analysis of Short-Term Metabolic Alterations in Arabidopsis Following Changes in the Prevailing Environmental Conditions. Molecular Plant 7 (5 - SI), pp. 893 - 911 (2014)

Heise, R.; Arrivault, S.; Szecowka, M.; Tohge, T.; Nunes-Nesi, A.; Stitt, M.; Nikoloski, Z.; Fernie, A. R.: Flux profiling of photosynthetic carbon metabolism in intact plants. Nature Protocols 9 (8), pp. 1803 - 1824 (2014)

Hu, C.; Shi, J.; Quan, S.; Cui, B.; Kleessen, S.; Nikoloski, Z.; Tohge, T.; Alexander, D.; Guo, L.; Lin, H. et al.; Wang, J.; Cui, X.; Rao, J.; Luo, Q.; Zhao, X.; Fernie, A. R.; Zhang, D.: Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics. Scientific Reports 4, 5067 (2014)

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)

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)

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