| Year |
Citation |
Score |
| 2024 |
Habibpour M, Razaghi-Moghadam Z, Nikoloski Z. Prediction and integration of metabolite-protein interactions with genome-scale metabolic models. Metabolic Engineering. PMID 38367764 DOI: 10.1016/j.ymben.2024.02.008 |
0.389 |
|
| 2024 |
Ferreira MAM, Silveira WBD, Nikoloski Z. Protein constraints in genome-scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes. Biotechnology and Bioengineering. 121: 915-930. PMID 38178617 DOI: 10.1002/bit.28650 |
0.328 |
|
| 2023 |
Küken A, Treves H, Nikoloski Z. A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae. Frontiers in Plant Science. 14: 1140829. PMID 38078077 DOI: 10.3389/fpls.2023.1140829 |
0.348 |
|
| 2023 |
Córdoba SC, Tong H, Burgos A, Zhu F, Alseekh S, Fernie AR, Nikoloski Z. Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nature Communications. 14: 4897. PMID 37580345 DOI: 10.1038/s41467-023-40644-9 |
0.375 |
|
| 2023 |
Tong H, Laitinen RAE, Nikoloski Z. Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. The New Phytologist. 240: 426-438. PMID 37507350 DOI: 10.1111/nph.19154 |
0.327 |
|
| 2023 |
Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metabolic Engineering. 79: 97-107. PMID 37422133 DOI: 10.1016/j.ymben.2023.06.013 |
0.315 |
|
| 2023 |
Wendering P, Nikoloski Z. Model-driven insights into the effects of temperature on metabolism. Biotechnology Advances. 67: 108203. PMID 37348662 DOI: 10.1016/j.biotechadv.2023.108203 |
0.325 |
|
| 2023 |
Huß S, Nikoloski Z. Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis. Frontiers in Plant Science. 14: 1178239. PMID 37346134 DOI: 10.3389/fpls.2023.1178239 |
0.382 |
|
| 2023 |
Langary D, Küken A, Nikoloski Z. The unraveling of balanced complexes in metabolic networks. Scientific Reports. 13: 5712. PMID 37029206 DOI: 10.1038/s41598-023-32666-6 |
0.308 |
|
| 2023 |
Hashemi S, Laitinen R, Nikoloski Z. Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular Ecology. PMID 36773330 DOI: 10.1111/mec.16879 |
0.365 |
|
| 2022 |
Hashemi S, Razaghi-Moghadam Z, Laitinen RAE, Nikoloski Z. Relative flux trade-offs and optimization of metabolic network functionalities. Computational and Structural Biotechnology Journal. 20: 3963-3971. PMID 35950188 DOI: 10.1016/j.csbj.2022.07.038 |
0.374 |
|
| 2022 |
Huß S, Judd RS, Koper K, Maeda HA, Nikoloski Z. An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. PMID 35819300 DOI: 10.1111/tpj.15903 |
0.355 |
|
| 2022 |
Küken A, Langary D, Nikoloski Z. The hidden simplicity of metabolic networks is revealed by multireaction dependencies. Science Advances. 8: eabl6962. PMID 35353565 DOI: 10.1126/sciadv.abl6962 |
0.37 |
|
| 2022 |
Wendering P, Nikoloski Z. Genome-Scale Modeling Specifies the Metabolic Capabilities of . Msystems. 7: e0121621. PMID 35076269 DOI: 10.1128/msystems.01216-21 |
0.405 |
|
| 2021 |
Calderan-Rodrigues MJ, Luzarowski M, Monte-Bello CC, Minen RI, Zühlke BM, Nikoloski Z, Skirycz A, Caldana C. Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant . Frontiers in Plant Science. 12: 758933. PMID 35003157 DOI: 10.3389/fpls.2021.758933 |
0.36 |
|
| 2021 |
Hashemi S, Razaghi-Moghadam Z, Nikoloski Z. Identification of flux trade-offs in metabolic networks. Scientific Reports. 11: 23776. PMID 34893666 DOI: 10.1038/s41598-021-03224-9 |
0.392 |
|
| 2021 |
Zhu F, Alseekh S, Koper K, Tong H, Nikoloski Z, Naake T, Liu H, Yan J, Brotman Y, Wen W, Maeda H, Cheng Y, Fernie AR. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. The Plant Cell. PMID 34623442 DOI: 10.1093/plcell/koab251 |
0.334 |
|
| 2021 |
Küken A, Wendering P, Langary D, Nikoloski Z. A structural property for reduction of biochemical networks. Scientific Reports. 11: 17415. PMID 34465818 DOI: 10.1038/s41598-021-96835-1 |
0.342 |
|
| 2021 |
Camilo Moreno J, Rojas BE, Vicente R, Gorka M, Matz T, Chodasiewicz M, Peralta-Ariza JS, Zhang Y, Alseekh S, Childs D, Luzarowski M, Nikoloski Z, Zarivach R, Walther D, Hartman MD, et al. Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. The Embo Journal. e106800. PMID 34156108 DOI: 10.15252/embj.2020106800 |
0.312 |
|
| 2021 |
Tong H, Küken A, Razaghi-Moghadam Z, Nikoloski Z. Characterization of effects of genetic variants via genome-scale metabolic modelling. Cellular and Molecular Life Sciences : Cmls. PMID 33950314 DOI: 10.1007/s00018-021-03844-4 |
0.356 |
|
| 2021 |
Beleggia R, Omranian N, Holtz Y, Gioia T, Fiorani F, Nigro FM, Pecchioni N, De Vita P, Schurr U, David JL, Nikoloski Z, Papa R. Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation. International Journal of Molecular Sciences. 22. PMID 33946478 DOI: 10.3390/ijms22094790 |
0.304 |
|
| 2021 |
Seep L, Razaghi-Moghadam Z, Nikoloski Z. Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis. Scientific Reports. 11: 8544. PMID 33879809 DOI: 10.1038/s41598-021-87643-8 |
0.311 |
|
| 2021 |
Pries C, Razaghi-Moghadam Z, Kopka J, Nikoloski Z. Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Scientific Reports. 11: 4787. PMID 33637852 DOI: 10.1038/s41598-021-84114-y |
0.391 |
|
| 2021 |
Omranian S, Angeleska A, Nikoloski Z. PC2P: Parameter-free network-based prediction of protein complexes. Bioinformatics (Oxford, England). PMID 33416831 DOI: 10.7490/F1000Research.1118214.1 |
0.324 |
|
| 2020 |
Razaghi-Moghadam Z, Nikoloski Z. GeneReg: A constraint-based approach for design of feasible metabolic engineering strategies at the gene level. Bioinformatics (Oxford, England). PMID 33245091 DOI: 10.1093/bioinformatics/btaa996 |
0.303 |
|
| 2020 |
Correa SM, Alseekh S, Atehortúa L, Brotman Y, Ríos-Estepa R, Fernie AR, Nikoloski Z. Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. The Plant Journal : For Cell and Molecular Biology. PMID 33001507 DOI: 10.1111/Tpj.14906 |
0.438 |
|
| 2020 |
Küken A, Gennermann K, Nikoloski Z. Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. PMID 32656814 DOI: 10.1111/Tpj.14890 |
0.357 |
|
| 2020 |
Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Progress in Lipid Research. 101051. PMID 32640289 DOI: 10.1016/J.Plipres.2020.101051 |
0.476 |
|
| 2020 |
Razaghi-Moghadam Z, Nikoloski Z. Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data. Npj Systems Biology and Applications. 6: 21. PMID 32606380 DOI: 10.1038/s41540-020-0140-1 |
0.305 |
|
| 2020 |
Tong H, Küken A, Nikoloski Z. Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nature Communications. 11: 2410. PMID 32415110 DOI: 10.1038/S41467-020-16279-5 |
0.431 |
|
| 2020 |
Robaina-Estévez S, Nikoloski Z. Flux-based hierarchical organization of Escherichia coli's metabolic network. Plos Computational Biology. 16: e1007832. PMID 32310959 DOI: 10.1371/Journal.Pcbi.1007832 |
0.455 |
|
| 2020 |
Pott DM, de Abreu E Lima F, Soria C, Willmitzer L, Fernie AR, Nikoloski Z, Osorio S, Vallarino JG. Metabolic reconfiguration of strawberry physiology in response to postharvest practices. Food Chemistry. 321: 126747. PMID 32276147 DOI: 10.1016/J.Foodchem.2020.126747 |
0.405 |
|
| 2020 |
Clemente-Moreno MJ, Omranian N, Sáez PL, Figueroa CM, Del-Saz N, Elso M, Poblete L, Orf I, Cuadros-Inostroza A, Cavieres LA, Bravo L, Fernie AR, Ribas-Carbó M, Flexas J, Nikoloski Z, et al. Low temperature tolerance of the Antarctic species Deschampsia antarctica: a complex metabolic response associated with nutrient remobilization. Plant, Cell & Environment. PMID 32012308 DOI: 10.1111/Pce.13737 |
0.355 |
|
| 2020 |
Omidbakhshfard MA, Sujeeth N, Gupta S, Omranian N, Guinan KJ, Brotman Y, Nikoloski Z, Fernie AR, Mueller-Roeber B, Gechev TS. A Biostimulant Obtained from the Seaweed Protects from Severe Oxidative Stress. International Journal of Molecular Sciences. 21. PMID 31940839 DOI: 10.3390/Ijms21020474 |
0.345 |
|
| 2019 |
Langary D, Nikoloski Z. Inference of chemical reaction networks based on concentration profiles using an optimization framework. Chaos (Woodbury, N.Y.). 29: 113121. PMID 31779367 DOI: 10.1063/1.5120598 |
0.356 |
|
| 2019 |
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, ... Nikoloski Z, et al. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom. Nature Communications. 10: 4552. PMID 31591397 DOI: 10.1038/S41467-019-12407-Y |
0.469 |
|
| 2019 |
José Clemente-Moreno M, Omranian N, Sáez P, Figueroa CM, Del-Saz N, Elso M, Poblete L, Orf I, Cuadros-Inostroza A, Cavieres L, Bravo L, Fernie A, Ribas-Carbó M, Flexas J, Nikoloski Z, et al. Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis. The New Phytologist. PMID 31489634 DOI: 10.1111/Nph.16167 |
0.389 |
|
| 2019 |
Nunes-Nesi A, Alseekh S, de Oliveira Silva FM, Omranian N, Lichtenstein G, Mirnezhad M, González RRR, Garcia JSY, Conte M, Leiss KA, Klinkhamer PGL, Nikoloski Z, Carrari F, Fernie AR. Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics : Official Journal of the Metabolomic Society. 15: 46. PMID 30874962 DOI: 10.1007/S11306-019-1503-8 |
0.435 |
|
| 2019 |
Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nature Communications. 10: 737. PMID 30760717 DOI: 10.1038/S41467-019-08703-2 |
0.393 |
|
| 2019 |
Küken A, Eloundou-Mbebi JMO, Basler G, Nikoloski Z. Cellular determinants of metabolite concentration ranges. Plos Computational Biology. 15: e1006687. PMID 30677015 DOI: 10.1371/Journal.Pcbi.1006687 |
0.463 |
|
| 2019 |
Küken A, Nikoloski Z. Computational approaches to design and test plant synthetic metabolic pathways. Plant Physiology. PMID 30647083 DOI: 10.1104/Pp.18.01273 |
0.456 |
|
| 2018 |
Laitinen RAE, Nikoloski Z. Genetic basis of plasticity in plants. Journal of Experimental Botany. PMID 30445526 DOI: 10.1093/Jxb/Ery404 |
0.339 |
|
| 2018 |
Basler G, Fernie AR, Nikoloski Z. Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Bioscience Reports. PMID 30341247 DOI: 10.1042/Bsr20170224 |
0.418 |
|
| 2018 |
Küken A, Sommer F, Yaneva-Roder L, Mackinder LCM, Höhne M, Geimer S, Jonikas MC, Schroda M, Stitt M, Nikoloski Z, Mettler-Altmann T. Effects of microcompartmentation on flux distribution and metabolic pools in chloroplasts. Elife. 7. PMID 30306890 DOI: 10.7554/Elife.37960 |
0.441 |
|
| 2018 |
Vallarino JG, de Abreu E Lima F, Soria C, Tong H, Pott DM, Willmitzer L, Fernie AR, Nikoloski Z, Osorio S. Genetic diversity of strawberry germplasm using metabolomic biomarkers. Scientific Reports. 8: 14386. PMID 30258188 DOI: 10.1038/S41598-018-32212-9 |
0.48 |
|
| 2018 |
Janowski M, Zoschke R, Scharff L, Martinez Jaime S, Ferrari C, Proost S, Ng Wei Xiong J, Omranian N, Musialak-Lange M, Nikoloski Z, Graf A, Schöttler MA, Sampathkumar A, Vaid N, Mutwil M. AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. The Plant Journal : For Cell and Molecular Biology. PMID 30044525 DOI: 10.1111/Tpj.14040 |
0.335 |
|
| 2018 |
Scheunemann M, Brady SM, Nikoloski Z. Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models. Scientific Reports. 8: 7919. PMID 29784955 DOI: 10.1038/S41598-018-26232-8 |
0.417 |
|
| 2018 |
de Abreu E Lima F, Leifels L, Nikoloski Z. Regression-Based Modeling of Complex Plant Traits Based on Metabolomics Data. Methods in Molecular Biology (Clifton, N.J.). 1778: 321-327. PMID 29761449 DOI: 10.1007/978-1-4939-7819-9_23 |
0.389 |
|
| 2018 |
Schwahn K, Nikoloski Z. Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism. Frontiers in Plant Science. 9: 538. PMID 29731765 DOI: 10.3389/Fpls.2018.00538 |
0.424 |
|
| 2018 |
de Abreu E Lima F, Willmitzer L, Nikoloski Z. Classification-driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots. Plos One. 13: e0196038. PMID 29698533 DOI: 10.1371/Journal.Pone.0196038 |
0.346 |
|
| 2018 |
de Abreu E Lima F, Li K, Wen W, Yan J, Nikoloski Z, Willmitzer L, Brotman Y. Unraveling the lipid metabolism in maize with time-resolved multi-omics data. The Plant Journal : For Cell and Molecular Biology. PMID 29385634 DOI: 10.1111/Tpj.13833 |
0.4 |
|
| 2018 |
Küken A, Sommer F, Yaneva-Roder L, Mackinder LC, Höhne M, Geimer S, Jonikas MC, Schroda M, Stitt M, Nikoloski Z, Mettler-Altmann T. Author response: Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts Elife. DOI: 10.7554/Elife.37960.022 |
0.377 |
|
| 2017 |
Schwahn K, Beleggia R, Omranian N, Nikoloski Z. Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data. Frontiers in Plant Science. 8: 2152. PMID 29326746 DOI: 10.3389/Fpls.2017.02152 |
0.506 |
|
| 2017 |
Rodriguez Cubillos AE, Tong H, Alseekh S, de Abreu E Lima F, Yu J, Fernie AR, Nikoloski Z, Laitinen RAE. Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat. Heredity. PMID 29234160 DOI: 10.1038/S41437-017-0030-5 |
0.45 |
|
| 2017 |
Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M. Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. The New Phytologist. PMID 29205376 DOI: 10.1111/Nph.14921 |
0.339 |
|
| 2017 |
Gago J, Fernie AR, Nikoloski Z, Tohge T, Martorell S, Escalona JM, Ribas-Carbó M, Flexas J, Medrano H. Integrative field scale phenotyping for investigating metabolic components of water stress within a vineyard. Plant Methods. 13: 90. PMID 29093742 DOI: 10.1186/S13007-017-0241-Z |
0.33 |
|
| 2017 |
Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T, Ofner I, Zamir D, Nikoloski Z, Fernie AR. Canalization of Tomato Fruit Metabolism. The Plant Cell. PMID 29093214 DOI: 10.1105/Tpc.17.00367 |
0.397 |
|
| 2017 |
Wu S, Tohge T, Cuadros-Inostroza Á, Tong H, Tenenboim H, Kooke R, Méret M, Keurentjes JB, Nikoloski Z, Fernie AR, Willmitzer L, Brotman Y. Mapping the Arabidopsis metabolic landscape by untargeted metabolomics at different environmental conditions. Molecular Plant. PMID 28866081 DOI: 10.1016/J.Molp.2017.08.012 |
0.484 |
|
| 2017 |
Küken A, Nikoloski Z. Genome-Scale Modeling of Photorespiratory Pathway Manipulation. Methods in Molecular Biology (Clifton, N.J.). 1653: 195-202. PMID 28822134 DOI: 10.1007/978-1-4939-7225-8_13 |
0.433 |
|
| 2017 |
Robaina-Estévez S, Daloso DM, Zhang Y, Fernie AR, Nikoloski Z. Resolving the central metabolism of Arabidopsis guard cells. Scientific Reports. 7: 8307. PMID 28814793 DOI: 10.1038/S41598-017-07132-9 |
0.441 |
|
| 2017 |
Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S. Revisiting ancestral polyploidy in plants. Science Advances. 3: e1603195. PMID 28695205 DOI: 10.1126/Sciadv.1603195 |
0.318 |
|
| 2017 |
Annunziata MG, Apelt F, Carillo P, Krause U, Feil R, Mengin V, Lauxmann MA, Köhl K, Nikoloski Z, Stitt M, Lunn JE. Getting back to nature: a reality check for experiments in controlled environments. Journal of Experimental Botany. PMID 28673035 DOI: 10.1093/Jxb/Erx220 |
0.305 |
|
| 2017 |
Breuer D, Nowak J, Ivakov 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. PMID 28655850 DOI: 10.1073/Pnas.1706711114 |
0.315 |
|
| 2017 |
Omranian N, Nikoloski Z. Computational Approaches to Study Gene Regulatory Networks. Methods in Molecular Biology (Clifton, N.J.). 1629: 283-295. PMID 28623592 DOI: 10.1007/978-1-4939-7125-1_18 |
0.362 |
|
| 2017 |
Robaina-Estévez S, Nikoloski Z. On the effects of alternative optima in context-specific metabolic model predictions. Plos Computational Biology. 13: e1005568. PMID 28557990 DOI: 10.1371/Journal.Pcbi.1005568 |
0.419 |
|
| 2017 |
Zhang Y, Beard KFM, Swart C, Bergmann S, Krahnert I, Nikoloski Z, Graf A, Ratcliffe RG, Sweetlove LJ, Fernie AR, Obata T. Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle. Nature Communications. 8: 15212. PMID 28508886 DOI: 10.1038/Ncomms15212 |
0.374 |
|
| 2017 |
de Abreu E Lima F, Westhues M, Cuadros-Inostroza Á, Willmitzer L, Melchinger AE, Nikoloski Z. Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field. The Plant Journal : For Cell and Molecular Biology. PMID 28122143 DOI: 10.1111/Tpj.13495 |
0.387 |
|
| 2016 |
Eloundou-Mbebi JM, Küken A, Omranian N, Kleessen S, Neigenfind J, Basler G, Nikoloski Z. A network property necessary for concentration robustness. Nature Communications. 7: 13255. PMID 27759015 DOI: 10.1038/Ncomms13255 |
0.399 |
|
| 2016 |
Świadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, et al. Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana. The New Phytologist. PMID 27588563 DOI: 10.1111/Nph.14155 |
0.354 |
|
| 2016 |
Sajitz-Hermstein M, Töpfer N, Kleessen S, Fernie AR, Nikoloski Z. iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. Bioinformatics (Oxford, England). 32: i755-i762. PMID 27587698 DOI: 10.1093/Bioinformatics/Btw465 |
0.487 |
|
| 2016 |
Schwahn K, Küken A, Kliebenstein DJ, Fernie AR, Nikoloski Z. Observability of plant metabolic networks is reflected in the correlation of metabolic profiles. Plant Physiology. PMID 27566166 DOI: 10.1104/Pp.16.00900 |
0.467 |
|
| 2016 |
Li 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. PMID 27566165 DOI: 10.1104/Pp.16.01100 |
0.383 |
|
| 2016 |
Sajitz-Hermstein M, Nikoloski Z. Functional centrality as a predictor of shifts in metabolic flux states. Bmc Research Notes. 9: 317. PMID 27328671 DOI: 10.1186/S13104-016-2117-0 |
0.409 |
|
| 2016 |
Florez-Sarasa I, Ribas-Carbo M, Del-Saz NF, Schwahn K, Nikoloski Z, Fernie AR, Flexas J. Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions. The New Phytologist. PMID 27321208 DOI: 10.1111/Nph.14030 |
0.355 |
|
| 2016 |
Sajitz-Hermstein M, Nikoloski Z. Multi-objective shadow prices point at principles of metabolic regulation. Bio Systems. PMID 27312384 DOI: 10.1016/J.Biosystems.2016.04.005 |
0.465 |
|
| 2016 |
Voll LM, Nikoloski Z. Editorial: Engineering Synthetic Metabolons: From Metabolic Modeling to Rational Design of Biosynthetic Devices. Frontiers in Bioengineering and Biotechnology. 4: 39. PMID 27200344 DOI: 10.3389/Fbioe.2016.00039 |
0.334 |
|
| 2016 |
Basler G, Nikoloski Z, Larhlimi A, Barabási AL, Liu YY. Control of fluxes in metabolic networks. Genome Research. PMID 27197218 DOI: 10.1101/Gr.202648.115 |
0.464 |
|
| 2016 |
Beleggia R, Rau D, Laidò G, Platani C, Nigro F, Fragasso M, De Vita P, Scossa F, Fernie AR, Nikoloski Z, Papa R. Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels. Molecular Biology and Evolution. PMID 27189559 DOI: 10.1093/Molbev/Msw050 |
0.385 |
|
| 2016 |
Basler G, Küken A, Fernie AR, Nikoloski Z. Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? Frontiers in Bioengineering and Biotechnology. 4: 31. PMID 27092301 DOI: 10.3389/Fbioe.2016.00031 |
0.442 |
|
| 2016 |
Gago J, Daloso D, Figueroa CM, Flexas J, Fernie AR, Nikoloski Z. Relationships of leaf net photosynthesis, stomatal conductance, and mesophyll conductance to primary plant metabolism: a multi-species meta-analysis approach. Plant Physiology. PMID 26977088 DOI: 10.1104/Pp.15.01660 |
0.455 |
|
| 2016 |
Orf I, Timm S, Bauwe H, Fernie AR, 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. PMID 26969741 DOI: 10.1093/Jxb/Erw068 |
0.429 |
|
| 2016 |
Robaina-Estévez S, Nikoloski Z. Metabolic Network Constrains Gene Regulation of C4 Photosynthesis: The Case of Maize. Plant & Cell Physiology. PMID 26903529 DOI: 10.1093/Pcp/Pcw034 |
0.464 |
|
| 2016 |
Omranian N, Eloundou-Mbebi JM, Mueller-Roeber B, Nikoloski Z. Gene regulatory network inference using fused LASSO on multiple data sets. Scientific Reports. 6: 20533. PMID 26864687 DOI: 10.1038/Srep20533 |
0.392 |
|
| 2016 |
Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M. FamNet: A framework to identify multiplied modules driving pathway diversification in plants. Plant Physiology. PMID 26754669 DOI: 10.1104/Pp.15.01281 |
0.413 |
|
| 2016 |
Scossa F, Brotman Y, de Abreu e Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. Plant Science : An International Journal of Experimental Plant Biology. 242: 47-64. PMID 26566824 DOI: 10.1016/J.Plantsci.2015.05.021 |
0.408 |
|
| 2015 |
Breuer D, Nikoloski Z. DeFiNe: an optimisation-based method for robust disentangling of filamentous networks. Scientific Reports. 5: 18267. PMID 26666975 DOI: 10.1038/Srep18267 |
0.368 |
|
| 2015 |
Nikoloski Z, Perez-Storey R, Sweetlove LJ. Inference and Prediction of Metabolic Network Fluxes. Plant Physiology. 169: 1443-55. PMID 26392262 DOI: 10.1104/Pp.15.01082 |
0.518 |
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| 2015 |
Wen W, Li K, Alseek S, Omranian N, Zhao L, Zhou Y, Xiao Y, Jin M, Yang N, Liu H, Florian A, Li W, Pan Q, Nikoloski Z, Yan J, et al. Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. The Plant Cell. PMID 26187921 DOI: 10.1105/Tpc.15.00208 |
0.447 |
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| 2015 |
Robaina Estévez S, Nikoloski Z. Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization. Plos One. 10: e0131875. PMID 26158726 DOI: 10.1371/Journal.Pone.0131875 |
0.408 |
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| 2015 |
Heise R, Fernie AR, 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. PMID 26082786 DOI: 10.3389/Fpls.2015.00386 |
0.402 |
|
| 2015 |
Rosado-Souza L, Scossa F, Chaves IS, Kleessen S, Salvador LF, Milagre JC, Finger F, Bhering LL, Sulpice R, Araújo WL, Nikoloski Z, Fernie AR, Nunes-Nesi A. Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions. Planta. 242: 677-91. PMID 26007687 DOI: 10.1007/S00425-015-2332-2 |
0.446 |
|
| 2015 |
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 : For Cell and Molecular Biology. 82: 693-706. PMID 25801304 DOI: 10.1111/Tpj.12833 |
0.306 |
|
| 2015 |
Omranian N, Kleessen S, Tohge T, Klie S, Basler G, Mueller-Roeber B, Fernie AR, Nikoloski Z. Differential metabolic and coexpression networks of plant metabolism. Trends in Plant Science. 20: 266-8. PMID 25791509 DOI: 10.1016/J.Tplants.2015.02.002 |
0.515 |
|
| 2015 |
Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. The Plant Cell. 27: 485-512. PMID 25770107 DOI: 10.1105/Tpc.114.132266 |
0.476 |
|
| 2015 |
Omranian N, Mueller-Roeber B, Nikoloski Z. Segmentation of biological multivariate time-series data. Scientific Reports. 5: 8937. PMID 25758050 DOI: 10.1038/Srep08937 |
0.329 |
|
| 2015 |
Töpfer N, Kleessen S, Nikoloski Z. Integration of metabolomics data into metabolic networks. Frontiers in Plant Science. 6: 49. PMID 25741348 DOI: 10.3389/Fpls.2015.00049 |
0.486 |
|
| 2015 |
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: e0116536. PMID 25706533 DOI: 10.1371/Journal.Pone.0116536 |
0.327 |
|
| 2015 |
Medeiros DB, Daloso DM, Fernie AR, Nikoloski Z, Araújo WL. Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control. Plant, Cell & Environment. 38: 1457-70. PMID 25689387 DOI: 10.1111/Pce.12517 |
0.411 |
|
| 2015 |
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: 935-45. PMID 25670339 DOI: 10.1016/J.Molp.2014.12.008 |
0.3 |
|
| 2015 |
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 : For Cell and Molecular Biology. 81: 822-35. PMID 25600836 DOI: 10.1111/Tpj.12763 |
0.439 |
|
| 2015 |
Toubiana D, Batushansky A, Tzfadia O, Scossa F, Khan A, Barak S, Zamir D, Fernie AR, 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 : For Cell and Molecular Biology. 81: 121-33. PMID 25359542 DOI: 10.1111/Tpj.12717 |
0.389 |
|
| 2015 |
Sajitz-Hermstein M, Nikoloski Z. Sensitivity of contending cellular objectives in the central carbon metabolism of escherichia coli Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9303: 169-172. DOI: 10.1007/978-3-319-23108-2_14 |
0.316 |
|
| 2014 |
Robaina Estévez S, Nikoloski Z. Generalized framework for context-specific metabolic model extraction methods. Frontiers in Plant Science. 5: 491. PMID 25285097 DOI: 10.3389/Fpls.2014.00491 |
0.429 |
|
| 2014 |
Recht L, Töpfer N, Batushansky A, Sikron N, Gibon Y, Fait A, Nikoloski Z, Boussiba S, Zarka A. Metabolite profiling and integrative modeling reveal metabolic constraints for carbon partitioning under nitrogen starvation in the green algae Haematococcus pluvialis. The Journal of Biological Chemistry. 289: 30387-403. PMID 25183014 DOI: 10.1074/Jbc.M114.555144 |
0.411 |
|
| 2014 |
Kleessen S, Klie S, Nikoloski Z. Concurrent conditional clustering of multiple networks: COCONETS. Plos One. 9: e103637. PMID 25105292 DOI: 10.1371/Journal.Pone.0103637 |
0.371 |
|
| 2014 |
Breuer D, Nikoloski Z. img2net: automated network-based analysis of imaged phenotypes. Bioinformatics (Oxford, England). 30: 3291-2. PMID 25064565 DOI: 10.1093/Bioinformatics/Btu503 |
0.359 |
|
| 2014 |
Florian A, Timm S, Nikoloski Z, Tohge T, Bauwe H, Araújo WL, Fernie AR. Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures. Journal of Integrative Plant Biology. 56: 941-59. PMID 25040033 DOI: 10.1111/Jipb.12237 |
0.426 |
|
| 2014 |
Heise R, Arrivault S, Szecowka M, Tohge T, Nunes-Nesi A, Stitt M, Nikoloski Z, Fernie AR. Flux profiling of photosynthetic carbon metabolism in intact plants. Nature Protocols. 9: 1803-24. PMID 24992096 DOI: 10.1038/Nprot.2014.115 |
0.396 |
|
| 2014 |
Töpfer N, Scossa F, Fernie A, Nikoloski Z. Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. Plos Computational Biology. 10: e1003656. PMID 24946036 DOI: 10.1371/Journal.Pcbi.1003656 |
0.519 |
|
| 2014 |
Breuer D, Ivakov A, Sampathkumar A, Hollandt F, Persson S, Nikoloski Z. Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles. Journal of the Royal Society, Interface / the Royal Society. 11: 20140362. PMID 24920110 DOI: 10.1098/Rsif.2014.0362 |
0.4 |
|
| 2014 |
Sauvage C, Segura V, Bauchet G, Stevens R, Do PT, Nikoloski Z, Fernie AR, Causse M. Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits. Plant Physiology. 165: 1120-1132. PMID 24894148 DOI: 10.1104/Pp.114.241521 |
0.366 |
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| 2014 |
Mettler T, Mühlhaus T, Hemme D, Schöttler MA, Rupprecht J, Idoine A, Veyel D, Pal SK, Yaneva-Roder L, Winck FV, Sommer F, Vosloh D, Seiwert B, Erban A, Burgos A, ... ... Nikoloski Z, et al. 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: 2310-2350. PMID 24894045 DOI: 10.1105/Tpc.114.124537 |
0.377 |
|
| 2014 |
Hu C, Shi J, Quan S, Cui B, Kleessen S, Nikoloski Z, Tohge T, Alexander D, Guo L, Lin H, Wang J, Cui X, Rao J, Luo Q, Zhao X, et al. Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics. Scientific Reports. 4: 5067. PMID 24861081 DOI: 10.1038/Srep05067 |
0.485 |
|
| 2014 |
Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, Minio A, Rau D, Rodriguez M, Panziera A, Venturini L, Attene G, Albertini E, Jackson SA, Nanni L, ... ... Nikoloski Z, et al. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. The Plant Cell. 26: 1901-1912. PMID 24850850 DOI: 10.1105/Tpc.114.124040 |
0.339 |
|
| 2014 |
Arnold A, Nikoloski Z. Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. Plant Physiology. 165: 1380-1391. PMID 24808102 DOI: 10.1104/Pp.114.235358 |
0.495 |
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| 2014 |
Kleessen S, Laitinen R, Fusari CM, Antonio C, Sulpice R, Fernie AR, Stitt M, Nikoloski Z. Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana. Nature Communications. 5: 3537. PMID 24675291 DOI: 10.1038/Ncomms4537 |
0.386 |
|
| 2014 |
Florian A, Nikoloski Z, Sulpice R, Timm S, Araújo WL, Tohge T, Bauwe H, Fernie AR. Analysis of short-term metabolic alterations in Arabidopsis following changes in the prevailing environmental conditions. Molecular Plant. 7: 893-911. PMID 24503159 DOI: 10.1093/Mp/Ssu008 |
0.458 |
|
| 2014 |
Feher K, Lisec J, Römisch-Margl L, Selbig J, Gierl A, Piepho HP, 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: e85435. PMID 24409329 DOI: 10.1371/Journal.Pone.0085435 |
0.335 |
|
| 2014 |
Klie S, Osorio S, Tohge T, Drincovich MF, Fait A, Giovannoni JJ, Fernie AR, Nikoloski Z. Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. Plant Physiology. 164: 55-68. PMID 24243932 DOI: 10.1104/Pp.113.226142 |
0.433 |
|
| 2014 |
Klie S, Nikoloski Z, Selbig J. Biological cluster evaluation for gene function prediction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 428-45. PMID 20059365 DOI: 10.1089/Cmb.2009.0129 |
0.304 |
|
| 2014 |
Eloundou-Mbebi JMO, Kleeßen S, Mérèt M, Degenkolbe T, Willmitzer L, Nikoloski Z. A computational approach for reconstructing time-resolved chemical networks from time series metabolomics data F1000research. 5. DOI: 10.7490/F1000Research.1097154.1 |
0.328 |
|
| 2014 |
Méret 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: 16777-16781. DOI: 10.1039/C3Ra42384K |
0.362 |
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| 2014 |
Arnold A, Nikoloski Z. In search for an accurate model of the photosynthetic carbon metabolism Mathematics and Computers in Simulation. 96: 171-194. DOI: 10.1016/J.Matcom.2012.03.011 |
0.446 |
|
| 2013 |
Sajitz-Hermstein M, Nikoloski Z. Structural control of metabolic flux. Plos Computational Biology. 9: e1003368. PMID 24367246 DOI: 10.1371/Journal.Pcbi.1003368 |
0.461 |
|
| 2013 |
Hochberg U, Degu A, Toubiana D, Gendler T, Nikoloski Z, Rachmilevitch S, Fait A. Metabolite profiling and network analysis reveal coordinated changes in grapevine water stress response. Bmc Plant Biology. 13: 184. PMID 24256338 DOI: 10.1186/1471-2229-13-184 |
0.371 |
|
| 2013 |
Winck FV, Vischi Winck F, Arvidsson S, Riaño-Pachón DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, 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: e79909. PMID 24224019 DOI: 10.1371/Journal.Pone.0079909 |
0.338 |
|
| 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: e73061. PMID 24019893 DOI: 10.1371/Journal.Pone.0073061 |
0.398 |
|
| 2013 |
Töpfer N, Nikoloski Z. Large-scale modeling provides insights into Arabidopsis's acclimation to changing light and temperature conditions Plant Signaling and Behavior. 8. PMID 23838962 DOI: 10.4161/psb.25480 |
0.384 |
|
| 2013 |
Kleessen S, Klie S, Nikoloski Z. Data integration through proximity-based networks provides biological principles of organization across scales. The Plant Cell. 25: 1917-27. PMID 23749845 DOI: 10.1105/Tpc.113.111039 |
0.446 |
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| 2013 |
Omranian N, Klie S, Mueller-Roeber B, Nikoloski Z. Network-based segmentation of biological multivariate time series. Plos One. 8: e62974. PMID 23667552 DOI: 10.1371/Journal.Pone.0062974 |
0.415 |
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| 2013 |
Töpfer N, Caldana C, Grimbs S, Willmitzer L, Fernie AR, Nikoloski Z. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. The Plant Cell. 25: 1197-211. PMID 23613196 DOI: 10.1105/Tpc.112.108852 |
0.518 |
|
| 2013 |
Arnold A, Nikoloski Z. Comprehensive classification and perspective for modelling photorespiratory metabolism Plant Biology. 15: 667-675. PMID 23573904 DOI: 10.1111/J.1438-8677.2012.00708.X |
0.478 |
|
| 2013 |
Sulpice R, Nikoloski Z, Tschoep H, Antonio C, Kleessen S, Larhlimi A, Selbig J, Ishihara H, Gibon Y, Fernie AR, 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: 347-63. PMID 23515278 DOI: 10.1104/Pp.112.210104 |
0.473 |
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| 2013 |
Szecowka M, Heise R, Tohge T, Nunes-Nesi A, Vosloh D, Huege J, Feil R, Lunn J, Nikoloski Z, Stitt M, Fernie AR, Arrivault S. Metabolic fluxes in an illuminated Arabidopsis rosette. The Plant Cell. 25: 694-714. PMID 23444331 DOI: 10.1105/Tpc.112.106989 |
0.424 |
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| 2013 |
Toubiana D, Fernie AR, Nikoloski Z, Fait A. Network analysis: tackling complex data to study plant metabolism. Trends in Biotechnology. 31: 29-36. PMID 23245943 DOI: 10.1016/J.Tibtech.2012.10.011 |
0.499 |
|
| 2013 |
Fernie AR, Bauwe H, Eisenhut M, Florian A, Hanson DT, Hagemann M, Keech O, Mielewczik M, Nikoloski Z, Peterhänsel C, Roje S, Sage R, Timm S, von Cammerer S, Weber AP, et al. Perspectives on plant photorespiratory metabolism. Plant Biology (Stuttgart, Germany). 15: 748-53. PMID 23231538 DOI: 10.1111/J.1438-8677.2012.00693.X |
0.468 |
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| 2013 |
Neigenfind J, Grimbs S, Nikoloski Z. On the relation between reactions and complexes of (bio)chemical reaction networks. Journal of Theoretical Biology. 317: 359-65. PMID 23084997 DOI: 10.1016/J.Jtbi.2012.10.016 |
0.369 |
|
| 2013 |
Hempel S, Koseska A, Nikoloski Z. Data-driven reconstruction of directed networks European Physical Journal B. 86. DOI: 10.1140/Epjb/E2013-31111-8 |
0.319 |
|
| 2012 |
Kleessen S, Antonio C, Sulpice R, Laitinen R, Fernie AR, Stitt M, Nikoloski Z. Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nature Communications. 3: 1319. PMID 23271653 DOI: 10.1038/Ncomms2333 |
0.476 |
|
| 2012 |
Töpfer 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: 148. PMID 23194026 DOI: 10.1186/1752-0509-6-148 |
0.438 |
|
| 2012 |
Klie S, Caldana C, Nikoloski Z. Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions. Frontiers in Plant Science. 3: 249. PMID 23162561 DOI: 10.3389/Fpls.2012.00249 |
0.381 |
|
| 2012 |
Kleessen S, Fernie AR, 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: 217. PMID 23056002 DOI: 10.3389/Fpls.2012.00217 |
0.424 |
|
| 2012 |
Larhlimi A, Basler G, Grimbs S, Selbig J, Nikoloski Z. Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. Bioinformatics (Oxford, England). 28: i502-i508. PMID 22962473 DOI: 10.1093/Bioinformatics/Bts381 |
0.462 |
|
| 2012 |
Sajitz-Hermstein M, Nikoloski Z. Restricted cooperative games on metabolic networks reveal functionally important reactions. Journal of Theoretical Biology. 314: 192-203. PMID 22940237 DOI: 10.1016/J.Jtbi.2012.08.018 |
0.47 |
|
| 2012 |
Omidbakhshfard MA, Omranian N, Ahmadi FS, Nikoloski Z, Mueller-Roeber B. Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana. Plant Signaling & Behavior. 7: 1095-102. PMID 22899071 DOI: 10.4161/Psb.21218 |
0.303 |
|
| 2012 |
Klie S, Nikoloski Z. The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. Frontiers in Genetics. 3: 115. PMID 22754563 DOI: 10.3389/Fgene.2012.00115 |
0.398 |
|
| 2012 |
Klie S, Mutwil M, Persson S, Nikoloski Z. Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. Molecular Biosystems. 8: 2233-41. PMID 22744313 DOI: 10.1039/C2Mb25089F |
0.397 |
|
| 2012 |
Osorio S, Alba R, Nikoloski Z, Kochevenko A, Fernie AR, Giovannoni JJ. 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: 1713-29. PMID 22685169 DOI: 10.1104/Pp.112.199711 |
0.448 |
|
| 2012 |
Basler G, Grimbs S, Nikoloski Z. Optimizing metabolic pathways by screening for feasible synthetic reactions. Bio Systems. 109: 186-91. PMID 22575307 DOI: 10.1016/J.Biosystems.2012.04.007 |
0.45 |
|
| 2012 |
Toubiana D, Semel Y, Tohge T, Beleggia R, Cattivelli L, Rosental L, Nikoloski Z, Zamir D, Fernie AR, 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: e1002612. PMID 22479206 DOI: 10.1371/Journal.Pgen.1002612 |
0.482 |
|
| 2012 |
Kleessen S, Nikoloski Z. Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. Bmc Systems Biology. 6: 16. PMID 22409942 DOI: 10.1186/1752-0509-6-16 |
0.423 |
|
| 2012 |
Kleessen S, Araújo WL, Fernie AR, Nikoloski Z. Model-based confirmation of alternative substrates of mitochondrial electron transport chain. The Journal of Biological Chemistry. 287: 11122-31. PMID 22334689 DOI: 10.1074/Jbc.M111.310383 |
0.395 |
|
| 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: 1121-7. PMID 22327945 DOI: 10.1039/C2Mb05365A |
0.383 |
|
| 2012 |
Basler G, Grimbs S, Ebenhöh O, Selbig J, Nikoloski Z. Evolutionary significance of metabolic network properties. Journal of the Royal Society, Interface / the Royal Society. 9: 1168-76. PMID 22130553 DOI: 10.1098/Rsif.2011.0652 |
0.475 |
|
| 2012 |
Araújo WL, Nunes-Nesi A, Nikoloski Z, Sweetlove LJ, Fernie AR. Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant, Cell & Environment. 35: 1-21. PMID 21477125 DOI: 10.1111/J.1365-3040.2011.02332.X |
0.407 |
|
| 2011 |
Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S. Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Frontiers in Plant Science. 2: 23. PMID 22639584 DOI: 10.3389/Fpls.2011.00023 |
0.372 |
|
| 2011 |
Arnold A, Nikoloski Z. A quantitative comparison of Calvin-Benson cycle models. Trends in Plant Science. 16: 676-83. PMID 22001849 DOI: 10.1016/J.Tplants.2011.09.004 |
0.436 |
|
| 2011 |
Basler G, Nikoloski Z. JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics (Oxford, England). 27: 2761-2. PMID 21803803 DOI: 10.1093/Bioinformatics/Btr448 |
0.44 |
|
| 2011 |
Hempel S, Koseska A, Nikoloski Z, Kurths J. Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. Bmc Bioinformatics. 12: 292. PMID 21771321 DOI: 10.1186/1471-2105-12-292 |
0.35 |
|
| 2011 |
Larhlimi A, Blachon S, Selbig J, Nikoloski Z. Robustness of metabolic networks: a review of existing definitions. Bio Systems. 106: 1-8. PMID 21708222 DOI: 10.1016/J.Biosystems.2011.06.002 |
0.41 |
|
| 2011 |
Lisec J, Römisch-Margl L, Nikoloski Z, Piepho HP, Giavalisco P, Selbig J, Gierl A, Willmitzer L. Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns. The Plant Journal : For Cell and Molecular Biology. 68: 326-36. PMID 21707803 DOI: 10.1111/J.1365-313X.2011.04689.X |
0.397 |
|
| 2011 |
Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S. PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. The Plant Cell. 23: 895-910. PMID 21441431 DOI: 10.1105/Tpc.111.083667 |
0.404 |
|
| 2011 |
Basler G, Ebenhöh O, Selbig J, Nikoloski Z. Mass-balanced randomization of metabolic networks. Bioinformatics (Oxford, England). 27: 1397-403. PMID 21436128 DOI: 10.1093/Bioinformatics/Btr145 |
0.408 |
|
| 2011 |
Nikoloski Z, Grimbs S, Klie S, Selbig J. Complexity of automated gene annotation. Bio Systems. 104: 1-8. PMID 21219964 DOI: 10.1016/J.Biosystems.2010.12.003 |
0.32 |
|
| 2011 |
Grimbs S, Arnold A, Koseska A, Kurths J, Selbig J, Nikoloski Z. Spatiotemporal dynamics of the Calvin cycle: multistationarity and symmetry breaking instabilities. Bio Systems. 103: 212-23. PMID 21075168 DOI: 10.1016/J.Biosystems.2010.10.015 |
0.342 |
|
| 2011 |
Hempel S, Koseska A, Kurths J, Nikoloski Z. Inner composition alignment for inferring directed networks from short time series Physical Review Letters. 107. DOI: 10.1103/Physrevlett.107.054101 |
0.36 |
|
| 2011 |
Redestig H, Szymanski J, Hirai MY, Selbig J, Willmitzer L, Nikoloski Z, Saito K. Data Integration, Metabolic Networks and Systems Biology Annual Plant Reviews Volume 43: Biology of Plant Metabolomics. 43: 261-316. DOI: 10.1002/9781444339956.ch9 |
0.332 |
|
| 2010 |
Sajitz-Hermstein M, Nikoloski Z. A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana. Bioinformatics (Oxford, England). 26: i582-8. PMID 20823325 DOI: 10.1093/Bioinformatics/Btq390 |
0.309 |
|
| 2010 |
Nikoloski Z, May P, Selbig J. Algebraic connectivity may explain the evolution of gene regulatory networks. Journal of Theoretical Biology. 267: 7-14. PMID 20682325 DOI: 10.1016/J.Jtbi.2010.07.028 |
0.395 |
|
| 2009 |
Szymanski J, Jozefczuk S, Nikoloski Z, Selbig J, Nikiforova V, Catchpole G, Willmitzer L. Stability of metabolic correlations under changing environmental conditions in Escherichia coli--a systems approach. Plos One. 4: e7441. PMID 19829699 DOI: 10.1371/Journal.Pone.0007441 |
0.437 |
|
| 2009 |
Nikoloski Z, May P, Selbig J. A new network model explains the evolution of plant-specific metabolic networks Comparative Biochemistry and Physiology Part a: Molecular & Integrative Physiology. 153: S227. DOI: 10.1016/J.Cbpa.2009.04.567 |
0.456 |
|
| 2008 |
Basler G, Nikoloski Z, Ebenhöh O, Handorf T. Biosynthetic potentials from species-specific metabolic networks. Genome Informatics. International Conference On Genome Informatics. 20: 135-48. PMID 19425129 DOI: 10.1142/9781848163003_0012 |
0.439 |
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| 2008 |
Nikoloski Z, Grimbs S, May P, Selbig J. Metabolic networks are NP-hard to reconstruct. Journal of Theoretical Biology. 254: 807-16. PMID 18682254 DOI: 10.1016/J.Jtbi.2008.07.015 |
0.461 |
|
| 2008 |
Kejžar N, Nikoloski Z, Batagelj V. Probabilistic inductive classes of graphs Journal of Mathematical Sociology. 32: 85-109. DOI: 10.1080/00222500801931586 |
0.301 |
|
| 2006 |
Nikoloski Z, Deo N, Kucera L. Correlation model of worm propagation on scale-free networks Complexus. 3: 169-182. DOI: 10.1159/000094198 |
0.579 |
|
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