Publications 2016

University of Potsdam - Institute of Biochemistry and Biology- Bioinformatics group - Publications - 2016

Basler, G.; Nikoloski, Z.; Larhlimi, A.; Barabasi, A.-L.; Liu, Y.-Y. (2016)
Control of fluxes in metabolic networks.
Genome Research 26 (7), S. 956 - 968

Basler, G.; Küken, A.; Fernie, A. R.; Nikoloski, Z. (2016)
Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence?
Frontiers in Bioengineering and Biotechnology 4, 31 (2016)

Beleggia, R.; Rau, D.; Laido, G.; Platani, C.; Nigro, F.; Fragasso, M.; De Vita, P.; Scossa, F.; Fernie, A. R.; Nikoloski, Z. et al. (2016)
Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels.
Molecular Biology and Evolution 33 (7), S. 1740 - 1753

C. Edlich-Muth, M. M. Muraya, T. Altmann and J. Selbig (2016)
Phenomic prediction of maize hybrids.
BioSystems 146, 102-109.

Eloundou-Mbebi, J. M. O.; Küken, A.; Omranian, N.; Kleessen, S.; Neigenfind, J.; Basler, G.; Nikoloski, Z. (2016)
A network property necessary for concentration robustness.
Nature Communications 7, 13255

Estevez, S.; Nikoloski, Z.
Metabolic Network Constrains Gene Regulation of C4 Photosynthesis: The Case of Maize.
Plant & Cell Physiology 57 (5), S. 933 - 943

Florez-Sarasa, I. D.; Ribas-Carbo, M.; Fernandez Del-Saz, N.; Schwahn, K.; Nikoloski, Z.; Fernie, A. R.; Flexas, J. (2016)
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

Gago, J.; Daloso, D. M.; Figueroa, C. M.; Flexas, J.; Fernie, A. R.; Nikoloski, Z. (2016):
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

M. Hermanussen, C. Aßmann, K. Staub and D. Groth (2016)
Monte Carlo simulation of body height in a spatial network.
Eur J Clin Nutr.70(6), 756.

M. Hermanussen, J. Ipsen, R. Mumm, C. Aßmann, J. Quitmann, A. Gomula, A. Lehmann, I. Jasch, V. Tassenaar, B. Bogin, T. Satake, C. Scheffler, J. Núñez, E. Godina, R. Hardeland, J. Boldsen, M. El-Shabrawi, M. Elhusseini, C. G. Barbu, R. Pop, J. Söderhäll, A. Merker, J. Swanson and D. Groth (2016)
Stunted Growth. Proceedings of the 23rd Aschauer Soiree, Held at Aschauhof, Germany, November 7th 2015.
Ped. Endocrinol. Rev. 13(4), 756-767.

M. Jargosch, S. Kröger, E. Gralinska, U. Klotz, Z. Fang, W. Chen, U. Leser, J. Selbig, D. Groth and R. Baumgrass (2016)
Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions.
Genet. Mol. Res. 15(2), gmr. 15028493.

Liu, Z.; Omranian, N.; Neumetzler, L.; Wang, T.; Herter, T.; Usadel, B.; Demura, T.; Giavalisco, P.; Nikoloski, Z.; Persson, S. (2016)
A transcriptional and metabolic framework for secondary wall formation in arabidopsis.
Plant Physiology 172 (2), S. 1334 - 1351

Omranian, N.; Eloundou-Mbebi, J. M. O.; Mueller-Roeber, B.; Nikoloski, Z. (2016)
Gene regulatory network inference using fused LASSO on multiple data sets.
Scientific Reports 6, 20533

Orf, I.; Timm, S.; Bauwe, H.; Fernie, A. R.; Hagemann, M.; Kopka, J.; Nikoloski, Z. (2016)
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)

D. Rajasundaram and J. Selbig (2016)
More effort - more results: recent advances in integrative 'omics' data analysis.
Curr Opin Plant Biol 30, 57-61.

Ruprecht, C.; Mendrinna, A.; Tohge, T.; Sampathkumar, A.; Klie, S.; Fernie, A. R.; Nikoloski, Z.; Persson, S.; Mutwil, M. (2016)
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.
Plant Physiology 170 (3), S. 1878 - 1894

Sajitz-Hermstein, M.; Nikoloski, Z. (2016)
Functional centrality as a predictor of shifts in metabolic flux states.
BMC research notes 9 (1), 317

Sajitz-Hermstein, M.; Töpfer, N.; Kleessen, S.; Fernie, A. R.; Nikoloski, Z. (2016)
iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models .
Bioinformatics 32 (17), S. i755 - i762

Sajitz-Hermstein, M.; Nikoloski, Z. (2016)
Multi-objective shadow prices point at principles of metabolic regulation.
Biosystems [Elektronische Ressource] : Journal of Biological and Information Processing Sciences 146, S. 91 - 101

Schwahn, K.; Küken, A.; Kliebenstein, D.J.; Fernie, A. R.; Nikoloski, Z. (2016)
Observability of plant metabolic networks is reflected in the correlation of metabolic profiles.
Plant Physiology 172 (2), S. 1324 - 1333

Scossa, F.; Brotman, Y.; de Abreu e Lima, F.; Willmitzer, L.; Nikoloski, Z.; Tohge, T.; Fernie, A. R. (2016)
Genomics-based strategies for the use of natural variation in the improvement of crop metabolism.
Plant Science 242, S. 47 - 64

Shaik, S. S.; Obata, T.; Hebelstrup, K. H.; Schwahn, K.; Fernie, A. R.; Mateiu, R. V.; Blennow, A. (2016)
Starch Granule Re-Structuring by Starch Branching Enzyme and Glucan Water Dikinase Modulation Affects Caryopsis Physiology and Metabolism.
PLoS One 11 (2), e0149613