Zoran Nikoloski, Ph.D. - Publications

Affiliations: 
2005 University of Central Florida, Orlando, FL, United States 
Area:
Computer Science

104 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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 and Environment. 38: 1457-1470. DOI: 10.1111/pce.12517  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2013 Sajitz-Hermstein M, Nikoloski Z. Structural control of metabolic flux. Plos Computational Biology. 9: e1003368. PMID 24367246 DOI: 10.1371/journal.pcbi.1003368  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2013 Zakharova A, Nikoloski Z, Koseska A. Dimensionality Reduction of Bistable Biological Systems Bulletin of Mathematical Biology. 75: 373-392. PMID 23392578 DOI: 10.1007/s11538-013-9807-8  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2013 Khalid F, Nikoloski Z, Tröger P, Polze A. Heterogeneous combinatorial candidate generation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8097: 751-762. DOI: 10.1007/978-3-642-40047-6_75  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2011 Nikoloski Z, van Dongen JT. Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions. The New Phytologist. 190: 273-6; author reply . PMID 21348875 DOI: 10.1111/j.1469-8137.2011.03674.x  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2009 Childs L, Nikoloski Z, May P, Walther D. Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Research. 37: e66. PMID 19339518 DOI: 10.1093/nar/gkp206  0.56
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  0.56
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  0.56
2008 Brandes U, Delling D, Gaertler M, Görke R, Hoefer M, Nikoloski Z, Wagner D. On modularity clustering Ieee Transactions On Knowledge and Data Engineering. 20: 172-188. DOI: 10.1109/TKDE.2007.190689  0.56
2008 Kejžar N, Nikoloski Z, Batagelj V. Probabilistic inductive classes of graphs Journal of Mathematical Sociology. 32: 85-109. DOI: 10.1080/00222500801931586  0.56
2008 Nikoloski Z, Grimbs S, Selbig J, Ebenhöh O. Hardness and approximability of the inverse scope problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 99-112. DOI: 10.1007/978-3-540-87361-7_9  0.56
2007 Brandes U, Delling D, Gaertler M, Görke R, Hoefer M, Nikoloski Z, Wagner D. On finding graph clusterings with maximum modularity Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4769: 121-132.  0.56
2006 Nikoloski Z, Deo N, Kucera L. Correlation model of worm propagation on scale-free networks Complexus. 3: 169-182. DOI: 10.1159/000094198  0.56
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