Publikationen der Gruppe

Zeitschriftenartikel (102)

  1. 1.
    Scheunemann, M.; Brady, S. M.; Nikoloski, Z.: Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models. Scientific Reports 8 (1), 7919 (2018)
  2. 2.
    Annunziata, M. G.; Apelt, F.; Carillo, P.; Krause, U.; Feil, R.; Mengin, V.; Lauxmann, M.; Koehl, K. I.; Nikoloski, Z.; Stitt, M. et al.; Lunn, J. E.; Raines, C.: Getting back to nature: a reality check for experiments in controlled environments. Journal of Experimental Botany 68 (16), S. 4463 - 4477 (2017)
  3. 3.
    Apelt, F.; Breuer, D.; Olas, J. J.; Annunziata, M. G.; Flis, A.; Nikoloski, Z.; Kragler, F.; Stitt, M.: Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement. Plant Physiology 174 (3), S. 1949 - 1968 (2017)
  4. 4.
    Breuer, D.; Nowak, J.; Ivako, A.; Somssich, M.; Persson, S.; Nikoloski, Z.: System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells. Proceedings of the National Academy of Sciences of the United States of America 114 (28), S. E5741 - E5749 (2017)
  5. 5.
    Estevez, S.; Nikoloski, Z.: On the effects of alternative optima in context-specific metabolic model predictions. PLoS Computational Biology (2017)
  6. 6.
    Robaina-Estévez, S.; Daloso, D. M.; Zhang, Y.; Fernie, A. R.; Nikoloski, Z.: Resolving the central metabolism of Arabidopsis guard cells. Scientific Reports 7, 8307 (2017)
  7. 7.
    Ruprecht, C.; Lohaus, R.; Vanneste, K.; Mutwil, M.; Nikoloski, Z.; Van de Peer, Y.; Persson, S.: Revisiting ancestral polyploidy in plants. Science Advances 3 (7), e1603195 (2017)
  8. 8.
    Swiadek, M.; Proost, S.; Sieh, D.; Yu, J.; Todesco, M.; Jorzig, C.; Cubillos, A.; Plötner, B.; Nikoloski, Z.; Chae, E. et al.; Giavalisco, P.; Fischer, A.; Schröder, F.; Kim, S.-T.; Weigel, D.; Laitinen, R.: Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana. New Phytologist 213 (2), S. 900 - 915 (2017)
  9. 9.
    Westhues, M.; Schrag, T. A.; Heuer, C.; Thaller, G.; Utz, H. F.; Schipprack, W.; Thiemann, A.; Seifert, F.; Ehret, A.; Schlereth, A. et al.; Stitt, M.; Nikoloski, Z.; Willmitzer, L.; Schoen, C. C.; Scholten, S.; Melchinger, A. E.: Omics-based hybrid prediction in maize. THEORETICAL AND APPLIED GENETICS 130 (9), S. 1927 - 1939 (2017)
  10. 10.
    Zhang, Y.; Beard, K. F. M.; Swart, C.; Bergmann, S.; Krahnert, I.; Nikoloski, Z.; Graf, A.; Ratcliffe, R. G.; Sweetlove, L. J.; Fernie, A. R. et al.; Obata, T.: Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle. Nature Communications (2017)
  11. 11.
    de Abreu e Lima, F.; Westhues, M.; Cuadros-Inostroza, Á.; Willmitzer, L.; Melchinger, A. E.; Nikoloski, Z.: Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field. The Plant Journal 90 (2), S. 319 - 329 (2017)
  12. 12.
    Gago, J.; Daloso, D. M.; Figueroa, C. M.; Flexas, J.; Fernie, A. R.; Nikoloski, Z.: Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach. Plant Physiology 171 (1), S. 265 - 279 (2016)
  13. 13.
    Omranian, N.; Eloundou-Mbebi, J. M. O.; Mueller-Roeber, B.; Nikoloski, Z.: Gene regulatory network inference using fused LASSO on multiple data sets. Scientific Reports 6, 20533 (2016)
  14. 14.
    Basler, G.; Nikoloski, Z.; Larhlimi, A.; Barabasi, A.-L.; Liu, Y.-Y.: Control of fluxes in metabolic networks. Genome Research 26 (7), S. 956 - 968 (2016)
  15. 15.
    Basler, G.; Küken, A.; Fernie, A. R.; Nikoloski, Z.: Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? Frontiers in Bioengineering and Biotechnology 4, 31 (2016)
  16. 16.
    Beleggia, R.; Rau, D.; Laido, G.; Platani, C.; Nigro, F.; Fragasso, M.; De Vita, P.; Scossa, F.; Fernie, A. R.; Nikoloski, Z. et al.; Papa, R.: Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels. Molecular Biology and Evolution 33 (7), S. 1740 - 1753 (2016)
  17. 17.
    Eloundou-Mbebi, J. M. O.; Küken, A.; Omranian, N.; Kleessen, S.; Neigenfind, J.; Basler, G.; Nikoloski, Z.: A network property necessary for concentration robustness. Nature Communications 7, 13255 (2016)
  18. 18.
    Estevez, S.; Nikoloski, Z.: Metabolic Network Constrains Gene Regulation of C4 Photosynthesis: The Case of Maize. Plant & Cell Physiology 57 (5), S. 933 - 943 (2016)
  19. 19.
    Florez-Sarasa, I. D.; Ribas-Carbo, M.; Fernandez Del-Saz, N.; Schwahn, K.; Nikoloski, Z.; Fernie, A. R.; Flexas, J.: Unravelling the invivo regulation and metabolic role of the alternative oxidase pathway in C-3 species under photoinhibitory conditions. New Phytologist 212 (1), S. 66 - 79 (2016)
  20. 20.
    Liu, Z.; Omranian, N.; Neumetzler, L.; Wang, T.; Herter, T.; Usadel, B.; Demura, T.; Giavalisco, P.; Nikoloski, Z.; Persson, S.: A transcriptional and metabolic framework for secondary wall formation in arabidopsis. Plant Physiology 172 (2), S. 1334 - 1351 (2016)
  21. 21.
    Orf, I.; Timm, S.; Bauwe, H.; Fernie, A. R.; Hagemann, M.; Kopka, J.; Nikoloski, Z.: Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles. Journal of Experimental Botany 67 (10), S. 2941 - 2952 (2016)
  22. 22.
    Ruprecht, C.; Mendrinna, A.; Tohge, T.; Sampathkumar, A.; Klie, S.; Fernie, A. R.; Nikoloski, Z.; Persson, S.; Mutwil, M.: FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. Plant Physiology 170 (3), S. 1878 - 1894 (2016)
  23. 23.
    Sajitz-Hermstein, M.; Nikoloski, Z.: Functional centrality as a predictor of shifts in metabolic flux states. BMC research notes 9 (1), 317 (2016)
  24. 24.
    Sajitz-Hermstein, M.; Töpfer, N.; Kleessen, S.; Fernie, A. R.; Nikoloski, Z.: iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. Bioinformatics 32 (17), S. i755 - i762 (2016)
  25. 25.
    Sajitz-Hermstein, M.; Nikoloski, Z.: Multi-objective shadow prices point at principles of metabolic regulation. Biosystems [Elektronische Ressource]: Journal of Biological and Information Processing Sciences 146, S. 91 - 101 (2016)
  26. 26.
    Schwahn, K.; Küken, A.; Kliebenstein, D.J.; Fernie, A. R.; Nikoloski, Z.: Observability of plant metabolic networks is reflected in the correlation of metabolic profiles. Plant Physiology 172 (2), S. 1324 - 1333 (2016)
  27. 27.
    Scossa, F.; Brotman, Y.; de Abreu e Lima, F.; Willmitzer, L.; Nikoloski, Z.; Tohge, T.; Fernie, A. R.: Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. Plant Science 242, S. 47 - 64 (2016)
  28. 28.
    Shaik, S. S.; Obata, T.; Hebelstrup, K. H.; Schwahn, K.; Fernie, A. R.; Mateiu, R. V.; Blennow, A.: Starch Granule Re-Structuring by Starch Branching Enzyme and Glucan Water Dikinase Modulation Affects Caryopsis Physiology and Metabolism. PLoS One 11 (2), e0149613 (2016)
  29. 29.
    Rosado-Souza, L.; Scossa, F.; Chaves, I. S.; Kleessen, S.; Salvador, L. F. D.; Milagre, J. C.; Finger, F.; Bhering, L. L.; Sulpice, R.; Araujo, W. L. et al.; Nikoloski, Z.; Fernie, A. R.; Nunes-Nesi, A.: Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions. Planta 242 (3), S. 677 - 691 (2015)
  30. 30.
    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. Plant, Cell and Environment 38 (8), S. 1457 - 1470 (2015)
  31. 31.
    Cui, X.; Lv, Y.; Chen, M.; Nikoloski, Z.; Twell, D.; Zhang, D.: Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome. Molecular Plant 8 (6), S. 935 - 945 (2015)
  32. 32.
    Kleessen, S.; Irgang, S.; Klie, S.; Giavalisco, P.; Nikoloski, Z.: Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment. The Plant Journal 81 (5), S. 822 - 835 (2015)
  33. 33.
    Alseekh, S.; Tohge, T.; Wendenburg, R.; Scossa, F.; Omranian, N.; Li, J.; Kleessen, S.; Giavalisco, P.; Pleban, T.; Mueller-Roeber, B. et al.; Zamir, D.; Nikoloski, Z.; Fernie, A. R.: Identification and mode of inheritance of quantitative trait Loci for secondary metabolite abundance in tomato. The Plant Cell 27 (3), S. 485 - 512 (2015)
  34. 34.
    Apelt, F.; Breuer, D.; Nikoloski, Z.; Stitt, M.; Kragler, F.: Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth. The Plant Journal 82 (4), S. 693 - 706 (2015)
  35. 35.
    Arnold, A.; Sajitz-Hermstein, M.; Nikoloski, Z.: Effects of Varying Nitrogen Sources on Amino Acid Synthesis Costs in Arabidopsis thaliana under Different Light and Carbon-Source Conditions. PLoS One 10 (2), e0116536 (2015)
  36. 36.
    Breuer, D.; Nikoloski, Z.: DeFiNe: an optimisation-based method for robust disentangling of filamentous networks. Scientific Reports 5, 18267 (2015)
  37. 37.
    Estevez, S.; Nikoloski, Z.: Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization. PLoS One 10 (7), e0131875 (2015)
  38. 38.
    Heise, R.; Fernie, A. R.; Stitt, M.; Nikoloski, Z.: Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana. Frontiers in Plant Science 6, 386 (2015)
  39. 39.
    Nikoloski, Z.; Perez-Storey, R.; Sweetlove, L. J.: Inference and Prediction of Metabolic Network Fluxes. Plant Physiology 169 (3), S. 1443 - 1455 (2015)
  40. 40.
    Omranian, N.; Mueller-Roeber, B.; Nikoloski, Z.: Segmentation of biological multivariate time-series data. Scientific Reports 5, S. 8937 - 8937 (2015)
  41. 41.
    Omranian, N.; Kleessen, S.; Tohge, T.; Klie, S.; Basler, G.; Mueller-Roeber, B.; Fernie, A. R.; Nikoloski, Z.: Differential metabolic and coexpression networks of plant metabolism. Trends in Plant Science 20 (5), S. 266 - 268 (2015)
  42. 42.
    Toepfer, N.; Kleessen, S.; Nikoloski, Z.: Integration of metabolomics data into metabolic networks. Frontiers in Plant Science 6, 49 (2015)
  43. 43.
    Toubiana, D.; Batushansky, A.; Tzfadia, O.; Scossa, F.; Khan, A.; Barak, S.; Zamir, D.; Fernie, A. R.; Nikoloski, Z.; Fait, A.: Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds. The Plant Journal 81 (1), S. 121 - 133 (2015)
  44. 44.
    Weiwei, W.; Li, K.; Alseekh, S.; Omranian, N.; Zhao, L.; Zhou, Y.; Xiao, Y.; Jin, M.; Yang, N.; Liu, H. et al.; Florian, A.; Li, W.; Pan, Q.; Nikoloski, Z.; Yan, J.; Fernie, A. R.: Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. The Plant Cell 27 (7), S. 1839 - 1856 (2015)
  45. 45.
    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), S. 1901 - 1912 (2014)
  46. 46.
    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 (2014)
  47. 47.
    Arnold, A.; Nikoloski, Z.: In search for an accurate model of the photosynthetic carbon metabolism. Mathematics and Computers in Simulation 96, S. 171 - 194 (2014)
  48. 48.
    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 (2014)
  49. 49.
    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)
  50. 50.
    Breuer, D.; Timme, M.; Memmesheimer, R.-M.: Statistical Physics of Neural Systems with Nonadditive Dendritic Coupling. Physical Review X (2014)
  51. 51.
    Breuer, D.; Nikoloski, Z.: img2net: automated network-based analysis of imaged phenotypes. Bioinformatics 30 (22), S. 3291 - 2 (2014)
  52. 52.
    Estevez, S.; Nikoloski, Z.: Generalized framework for context-specific metabolic model extraction methods. Frontiers in Plant Science 5, S. 491 - 491 (2014)
  53. 53.
    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 Special Issue), S. 893 - 911 (2014)
  54. 54.
    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), S. 1803 - 1824 (2014)
  55. 55.
    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 metabolomicsd. Scientific Reports (2014)
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