메뉴 건너뛰기




Volumn 5, Issue , 2014, Pages

Integrated network analysis and effective tools in plant systems biology

Author keywords

Flux balance analysis; Genome scale metabolic reconstruction; Network visualization; Pathway analysis; Plant metabolism

Indexed keywords


EID: 84908641343     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2014.00598     Document Type: Review
Times cited : (44)

References (107)
  • 2
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • Altaf-Ul-Amin, M., Shinbo, Y., Mihara, K., Kurokawa, K., and Kanaya, S. (2006). Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7:207. doi: 10.1186/1471-2105-7-207
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 3
    • 84857780876 scopus 로고    scopus 로고
    • Evidence for network evolution in an Arabidopsis interactome map
    • Arabidopsis Interactome Mapping Consortium. (2011). Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601-607. doi: 10.1126/science.1203877
    • (2011) Science , vol.333 , pp. 601-607
  • 4
    • 65549085786 scopus 로고    scopus 로고
    • A pitfall of wiki solution for biological databases
    • Arita, M. (2009). A pitfall of wiki solution for biological databases. Brief. Bioinform. 10, 295-296. doi: 10.1093/bib/bbn053
    • (2009) Brief. Bioinform , vol.10 , pp. 295-296
    • Arita, M.1
  • 5
    • 84903618202 scopus 로고    scopus 로고
    • Bottom-up metabolic reconstruction of Arabidopsis and its application to determining the metabolic costs of enzyme production
    • Arnold, A., and Nikoloski, Z. (2014). Bottom-up metabolic reconstruction of Arabidopsis and its application to determining the metabolic costs of enzyme production. Plant Physiol. 165, 1380-1391. doi: 10.1104/pp.114.235358
    • (2014) Plant Physiol , vol.165 , pp. 1380-1391
    • Arnold, A.1    Nikoloski, Z.2
  • 6
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • Becker, S. A., and Palsson, B. O. (2008). Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4:e1000082. doi: 10.1371/journal.pcbi.1000082
    • (2008) PLoS Comput. Biol , vol.4
    • Becker, S.A.1    Palsson, B.O.2
  • 7
    • 42549129218 scopus 로고    scopus 로고
    • From genotype to phenotype: Systems biology meets natural variation
    • Benfey, P. N., and Mitchell-Olds, T. (2008). From genotype to phenotype: systems biology meets natural variation.Science 320, 495-497. doi: 10.1126/science.1153716
    • (2008) Science , vol.320 , pp. 495-497
    • Benfey, P.N.1    Mitchell-Olds, T.2
  • 8
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • Blazier, A. S., and Papin, J. A. (2012). Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol. 3:299. doi: 10.3389/fphys.2012.00299
    • (2012) Front. Physiol , vol.3 , pp. 299
    • Blazier, A.S.1    Papin, J.A.2
  • 9
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar, A., Monk, J. M., King, Z. A., and Palsson, B. O. (2014). Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15, 107-120. doi: 10.1038/nrg3643
    • (2014) Nat. Rev. Genet , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 10
    • 75449092046 scopus 로고    scopus 로고
    • AtPIN: Arabidopsis thaliana protein interaction network
    • Brandao, M. M., Dantas, L. L., and Silva-Filho, M. C. (2009). AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics 10:454. doi: 10.1186/1471-2105-10-454
    • (2009) BMC Bioinformatics , vol.10 , pp. 454
    • Brandao, M.M.1    Dantas, L.L.2    Silva-Filho, M.C.3
  • 11
    • 84886740491 scopus 로고    scopus 로고
    • Path2Models: Large-scale generation of computational models from biochemical pathway maps
    • Buchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., et al. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7:116. doi: 10.1186/1752-0509-7-116
    • (2013) BMC Syst. Biol , vol.7 , pp. 116
    • Buchel, F.1    Rodriguez, N.2    Swainston, N.3    Wrzodek, C.4    Czauderna, T.5    Keller, R.6
  • 12
    • 80052272064 scopus 로고    scopus 로고
    • High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions
    • Caldana, C., Degenkolbe, T., Cuadros-Inostroza, A., Klie, S., Sulpice, R., Leisse, A., et al. (2011). High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. Plant J. 67, 869-884. doi: 10.1111/j.1365-313X.2011.04640.x
    • (2011) Plant J , vol.67 , pp. 869-884
    • Caldana, C.1    Degenkolbe, T.2    Cuadros-Inostroza, A.3    Klie, S.4    Sulpice, R.5    Leisse, A.6
  • 13
    • 76249095914 scopus 로고    scopus 로고
    • Reverse-engineering the Arabidopsis thalianatranscriptional network under changing environmental conditions
    • Carrera, J., Rodrigo, G., Jaramillo, A., and Elena, S. F. (2009). Reverse-engineering the Arabidopsis thalianatranscriptional network under changing environmental conditions. Genome Biol. 10:R96. doi: 10.1186/gb-2009-10-9-r96
    • (2009) Genome Biol , vol.10
    • Carrera, J.1    Rodrigo, G.2    Jaramillo, A.3    Elena, S.F.4
  • 14
    • 84889609911 scopus 로고    scopus 로고
    • Genotype to phenotype via network analysis
    • Carter, H., Hofree, M., and Ideker, T. (2013). Genotype to phenotype via network analysis. Curr. Opin. Genet. Dev. 23, 611-621. doi: 10.1016/j.gde.2013.10.003
    • (2013) Curr. Opin. Genet. Dev , vol.23 , pp. 611-621
    • Carter, H.1    Hofree, M.2    Ideker, T.3
  • 15
    • 84860490976 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., et al. (2012). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40, D742-D753. doi: 10.1093/nar/gkr1014
    • (2012) Nucleic Acids Res , vol.40 , pp. D742-D753
    • Caspi, R.1    Altman, T.2    Dreher, K.3    Fulcher, C.A.4    Subhraveti, P.5    Keseler, I.M.6
  • 16
    • 84887634951 scopus 로고    scopus 로고
    • Tools for the functional interpretation of metabolomic experiments
    • Chagoyen, M., and Pazos, F. (2013). Tools for the functional interpretation of metabolomic experiments. Brief. Bioinform. 14, 737-744. doi: 10.1093/bib/bbs055
    • (2013) Brief. Bioinform , vol.14 , pp. 737-744
    • Chagoyen, M.1    Pazos, F.2
  • 17
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran, S., and Price, N. D. (2010). Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 107, 17845-17850. doi: 10.1073/pnas.1005139107
    • (2010) Proc. Natl. Acad. Sci. U.S.A , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 18
    • 84856433620 scopus 로고    scopus 로고
    • Metabolic network reconstruction: Advances in in silico interpretation of analytical information
    • Chen, N., Del Val, I. J., Kyriakopoulos, S., Polizzi, K. M., and Kontoravdi, C. (2012). Metabolic network reconstruction: advances in in silico interpretation of analytical information. Curr. Opin. Biotechnol. 23, 77-82. doi: 10.1016/j.copbio.2011.10.015
    • (2012) Curr. Opin. Biotechnol , vol.23 , pp. 77-82
    • Chen, N.1    Del Val, I.J.2    Kyriakopoulos, S.3    Polizzi, K.M.4    Kontoravdi, C.5
  • 19
    • 84901789998 scopus 로고    scopus 로고
    • A diel flux balance model captures interactions between light and dark metabolism during Day-Night cycles in C3 and crassulacean acid metabolism leaves
    • Cheung, C. Y., Poolman, M. G., Fell, D. A., Ratcliffe, R. G., and Sweetlove, L. J. (2014). A diel flux balance model captures interactions between light and dark metabolism during Day-Night cycles in C3 and crassulacean acid metabolism leaves. Plant Physiol. 165, 917-929. doi: 10.1104/pp.113.234468
    • (2014) Plant Physiol , vol.165 , pp. 917-929
    • Cheung, C.Y.1    Poolman, M.G.2    Fell, D.A.3    Ratcliffe, R.G.4    Sweetlove, L.J.5
  • 20
    • 84883762807 scopus 로고    scopus 로고
    • A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions
    • Cheung, C. Y., Williams, T. C., Poolman, M. G., Fell, D. A., Ratcliffe, R. G., and Sweetlove, L. J. (2013). A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions. Plant J. 75, 1050-1061. doi: 10.1111/tpj.12252
    • (2013) Plant J , vol.75 , pp. 1050-1061
    • Cheung, C.Y.1    Williams, T.C.2    Poolman, M.G.3    Fell, D.A.4    Ratcliffe, R.G.5    Sweetlove, L.J.6
  • 21
    • 70049110173 scopus 로고    scopus 로고
    • Interpreting expression data with metabolic flux models: Predicting Mycobacterium tuberculosis mycolic acid production
    • Colijn, C., Brandes, A., Zucker, J., Lun, D. S., Weiner, B., Farhat, M. R., et al. (2009). Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol. 5:e1000489. doi: 10.1371/journal.pcbi.1000489
    • (2009) PLoS Comput. Biol , vol.5
    • Colijn, C.1    Brandes, A.2    Zucker, J.3    Lun, D.S.4    Weiner, B.5    Farhat, M.R.6
  • 22
    • 84861165967 scopus 로고    scopus 로고
    • Are we ready for genome-scale modeling in plants?
    • Collakova, E., Yen, J. Y., and Senger, R. S. (2012). Are we ready for genome-scale modeling in plants? Plant Sci. 191-192, 53-70. doi: 10.1016/j.plantsci.2012.04.010
    • (2012) Plant Sci , vol.191-192 , pp. 53-70
    • Collakova, E.1    Yen, J.Y.2    Senger, R.S.3
  • 24
    • 78649796264 scopus 로고    scopus 로고
    • C4GEM, a genome-scale metabolic model to study C4 plant metabolism
    • Dal'molin, C. G., Quek, L. E., Palfreyman, R. W., Brumbley, S. M., and Nielsen, L. K. (2010). C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol. 154, 1871-1885. doi: 10.1104/pp.110.166488
    • (2010) Plant Physiol , vol.154 , pp. 1871-1885
    • Dal'molin, C.G.1    Quek, L.E.2    Palfreyman, R.W.3    Brumbley, S.M.4    Nielsen, L.K.5
  • 25
    • 77956664073 scopus 로고    scopus 로고
    • The BioPAX community standard for pathway data sharing
    • Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., et al. (2010). The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 28, 935-942. doi: 10.1038/nbt.1666
    • (2010) Nat. Biotechnol , vol.28 , pp. 935-942
    • Demir, E.1    Cary, M.P.2    Paley, S.3    Fukuda, K.4    Lemer, C.5    Vastrik, I.6
  • 26
    • 84874976941 scopus 로고    scopus 로고
    • Plant genome-scale metabolic reconstruction and modelling
    • De Oliveira Dal'molin, C. G., and Nielsen, L. K. (2013). Plant genome-scale metabolic reconstruction and modelling.Curr. Opin. Biotechnol. 24, 271-277. doi: 10.1016/j.copbio.2012.08.007
    • (2013) Curr. Opin. Biotechnol , vol.24 , pp. 271-277
    • De Oliveira Dal'molin, C.G.1    Nielsen, L.K.2
  • 27
    • 75949088191 scopus 로고    scopus 로고
    • AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis
    • De Oliveira Dal'molin, C. G., Quek, L. E., Palfreyman, R. W., Brumbley, S. M., and Nielsen, L. K. (2010). AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol. 152, 579-589. doi: 10.1104/pp.109.148817
    • (2010) Plant Physiol , vol.152 , pp. 579-589
    • De Oliveira Dal'molin, C.G.1    Quek, L.E.2    Palfreyman, R.W.3    Brumbley, S.M.4    Nielsen, L.K.5
  • 28
    • 84893401756 scopus 로고    scopus 로고
    • Cell to whole-plant phenotyping: The best is yet to come
    • Dhondt, S., Wuyts, N., and Inze, D. (2013). Cell to whole-plant phenotyping: the best is yet to come. Trends Plant Sci. 18, 428-439. doi: 10.1016/j.tplants.2013.04.008
    • (2013) Trends Plant Sci , vol.18 , pp. 428-439
    • Dhondt, S.1    Wuyts, N.2    Inze, D.3
  • 29
    • 78649592081 scopus 로고    scopus 로고
    • Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis
    • Espinoza, C., Degenkolbe, T., Caldana, C., Zuther, E., Leisse, A., Willmitzer, L., et al. (2010). Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PLoS ONE 5:e14101. doi: 10.1371/journal.pone.0014101
    • (2010) PLoS ONE , vol.5
    • Espinoza, C.1    Degenkolbe, T.2    Caldana, C.3    Zuther, E.4    Leisse, A.5    Willmitzer, L.6
  • 30
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • Feist, A. M., and Palsson, B. O. (2010). The biomass objective function. Curr. Opin. Microbiol. 13, 344-349. doi: 10.1016/j.mib.2010.03.003
    • (2010) Curr. Opin. Microbiol , vol.13 , pp. 344-349
    • Feist, A.M.1    Palsson, B.O.2
  • 31
    • 77957272033 scopus 로고    scopus 로고
    • Building and analysing genome-scale metabolic models
    • Fell, D. A., Poolman, M. G., and Gevorgyan, A. (2010). Building and analysing genome-scale metabolic models.Biochem. Soc. Trans. 38, 1197-1201. doi: 10.1042/BST0381197
    • (2010) Biochem. Soc. Trans , vol.38 , pp. 1197-1201
    • Fell, D.A.1    Poolman, M.G.2    Gevorgyan, A.3
  • 32
    • 79959621970 scopus 로고    scopus 로고
    • Predicting selective drug targets in cancer through metabolic networks
    • Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., and Shlomi, T. (2011). Predicting selective drug targets in cancer through metabolic networks. Mol. Syst. Biol. 7:501. doi: 10.1038/msb.2011.35
    • (2011) Mol. Syst. Biol , vol.7 , pp. 501
    • Folger, O.1    Jerby, L.2    Frezza, C.3    Gottlieb, E.4    Ruppin, E.5    Shlomi, T.6
  • 34
    • 47949099328 scopus 로고    scopus 로고
    • CellDesigner 3.5: A versatile modeling tool for biochemical networks
    • Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., and Kitano, H. (2008). CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc. IEEE 96, 1254-1265. doi: 10.1109/JPROC.2008.925458
    • (2008) Proc. IEEE , vol.96 , pp. 1254-1265
    • Funahashi, A.1    Matsuoka, Y.2    Jouraku, A.3    Morohashi, M.4    Kikuchi, N.5    Kitano, H.6
  • 36
    • 84885218166 scopus 로고    scopus 로고
    • Multiscale metabolic modeling: Dynamic flux balance analysis on a whole-plant scale
    • Grafahrend-Belau, E., Junker, A., Eschenroder, A., Muller, J., Schreiber, F., and Junker, B. H. (2013). Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol. 163, 637-647. doi: 10.1104/pp.113.224006
    • (2013) Plant Physiol , vol.163 , pp. 637-647
    • Grafahrend-Belau, E.1    Junker, A.2    Eschenroder, A.3    Muller, J.4    Schreiber, F.5    Junker, B.H.6
  • 37
    • 58449106341 scopus 로고    scopus 로고
    • Flux balance analysis of barley seeds: A computational approach to study systemic properties of central metabolism
    • Grafahrend-Belau, E., Schreiber, F., Koschutzki, D., and Junker, B. H. (2009). Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 149, 585-598. doi: 10.1104/pp.108.129635
    • (2009) Plant Physiol , vol.149 , pp. 585-598
    • Grafahrend-Belau, E.1    Schreiber, F.2    Koschutzki, D.3    Junker, B.H.4
  • 38
    • 84859760346 scopus 로고    scopus 로고
    • CentiLib: Comprehensive analysis and exploration of network centralities
    • Gräßler, J., Koschützki, D., and Schreiber, F. (2012). CentiLib: comprehensive analysis and exploration of network centralities. Bioinformatics 28, 1178-1179. doi: 10.1093/bioinformatics/bts106
    • (2012) Bioinformatics , vol.28 , pp. 1178-1179
    • Gräßler, J.1    Koschützki, D.2    Schreiber, F.3
  • 39
    • 84881234211 scopus 로고    scopus 로고
    • WikiPathways for plants: A community pathway curation portal and a case study in rice and arabidopsis seed development networks
    • Hanumappa, M., Preece, J., Elser, J., Nemeth, D., Bono, G., Wu, K., et al. (2013). WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice (N. Y). 6:14. doi: 10.1186/1939-8433-6-14
    • (2013) Rice (N. Y) , vol.6 , pp. 14
    • Hanumappa, M.1    Preece, J.2    Elser, J.3    Nemeth, D.4    Bono, G.5    Wu, K.6
  • 40
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Henry, C. S., Dejongh, M., Best, A. A., Frybarger, P. M., Linsay, B., and Stevens, R. L. (2010). High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 28, 977-982. doi: 10.1038/nbt.1672
    • (2010) Nat. Biotechnol , vol.28 , pp. 977-982
    • Henry, C.S.1    Dejongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 41
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. doi: 10.1093/bioinformatics/btg015
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 42
    • 84861793773 scopus 로고    scopus 로고
    • Gene set enrichment analysis: Performance evaluation and usage guidelines
    • Hung, J. H., Yang, T. H., Hu, Z., Weng, Z., and Delisi, C. (2012). Gene set enrichment analysis: performance evaluation and usage guidelines. Brief. Bioinform. 13, 281-291. doi: 10.1093/bib/bbr049
    • (2012) Brief. Bioinform , vol.13 , pp. 281-291
    • Hung, J.H.1    Yang, T.H.2    Hu, Z.3    Weng, Z.4    Delisi, C.5
  • 43
    • 84872093417 scopus 로고    scopus 로고
    • Analysis of omics data with genome-scale models of metabolism
    • Hyduke, D. R., Lewis, N. E., and Palsson, B. O. (2013). Analysis of omics data with genome-scale models of metabolism. Mol. Biosyst. 9, 167-174. doi: 10.1039/c2mb25453k
    • (2013) Mol. Biosyst , vol.9 , pp. 167-174
    • Hyduke, D.R.1    Lewis, N.E.2    Palsson, B.O.3
  • 44
    • 79951536020 scopus 로고    scopus 로고
    • Functional integration of a metabolic network model and expression data without arbitrary thresholding
    • Jensen, P. A., and Papin, J. A. (2011). Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 27, 541-547. doi: 10.1093/bioinformatics/btq702
    • (2011) Bioinformatics , vol.27 , pp. 541-547
    • Jensen, P.A.1    Papin, J.A.2
  • 45
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • Jerby, L., Shlomi, T., and Ruppin, E. (2010). Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 6:401. doi: 10.1038/msb.2010.56
    • (2010) Mol. Syst. Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 46
    • 84896731085 scopus 로고    scopus 로고
    • Flux analysis in plant metabolic networks: Increasing throughput and coverage
    • Junker, B. H. (2014). Flux analysis in plant metabolic networks: increasing throughput and coverage. Curr. Opin. Biotechnol. 26, 183-188. doi: 10.1016/j.copbio.2014.01.016
    • (2014) Curr. Opin. Biotechnol , vol.26 , pp. 183-188
    • Junker, B.H.1
  • 47
    • 84899523552 scopus 로고    scopus 로고
    • The EBI RDF platform: Linked open data for the life sciences
    • Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., et al. (2014). The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30, 1338-1339. doi: 10.1093/bioinformatics/btt765
    • (2014) Bioinformatics , vol.30 , pp. 1338-1339
    • Jupp, S.1    Malone, J.2    Bolleman, J.3    Brandizi, M.4    Davies, M.5    Garcia, L.6
  • 48
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: Back to metabolism in KEGG
    • Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M. (2014). Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205. doi: 10.1093/nar/gkt1076
    • (2014) Nucleic Acids Res , vol.42 , pp. D199-D205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Kawashima, M.4    Furumichi, M.5    Tanabe, M.6
  • 49
    • 84864258618 scopus 로고    scopus 로고
    • A whole-cell computational model predicts phenotype from genotype
    • Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B. Jr., et al. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150, 389-401. doi: 10.1016/j.cell.2012.05.044
    • (2012) Cell , vol.150 , pp. 389-401
    • Karr, J.R.1    Sanghvi, J.C.2    McKlin, D.N.3    Gutschow, M.V.4    Jacobs, J.M.5    Bolival, B.6
  • 51
    • 0036842183 scopus 로고    scopus 로고
    • Genotype-phenotype mapping: Genes as computer programs
    • Kell, D. B. (2002). Genotype-phenotype mapping: genes as computer programs. Trends Genet. 18, 555-559. doi: 10.1016/S0168-9525(02)02765-8
    • (2002) Trends Genet , vol.18 , pp. 555-559
    • Kell, D.B.1
  • 53
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: Current approaches and outstanding challenges
    • Khatri, P., Sirota, M., and Butte, A. J. (2012). Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol. 8:e1002375. doi: 10.1371/journal.pcbi.1002375
    • (2012) PLoS Comput. Biol , vol.8
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 54
    • 84864795465 scopus 로고    scopus 로고
    • Recent advances in reconstruction and applications of genome-scale metabolic models
    • Kim, T. Y., Sohn, S. B., Kim, Y. B., Kim, W. J., and Lee, S. Y. (2012). Recent advances in reconstruction and applications of genome-scale metabolic models. Curr. Opin. Biotechnol. 23, 617-623. doi: 10.1016/j.copbio.2011.10.007
    • (2012) Curr. Opin. Biotechnol , vol.23 , pp. 617-623
    • Kim, T.Y.1    Sohn, S.B.2    Kim, Y.B.3    Kim, W.J.4    Lee, S.Y.5
  • 55
    • 77955891592 scopus 로고    scopus 로고
    • Nitrate signaling: Adaptation to fluctuating environments
    • Krouk, G., Crawford, N. M., Coruzzi, G. M., and Tsay, Y. F. (2010). Nitrate signaling: adaptation to fluctuating environments. Curr. Opin. Plant Biol. 13, 266-273. doi: 10.1016/j.pbi.2009.12.003
    • (2010) Curr. Opin. Plant Biol , vol.13 , pp. 266-273
    • Krouk, G.1    Crawford, N.M.2    Coruzzi, G.M.3    Tsay, Y.F.4
  • 56
    • 84859369500 scopus 로고    scopus 로고
    • Pathways and fluxes: Exploring the plant metabolic network
    • Kruger, N. J., and Ratcliffe, R. G. (2012). Pathways and fluxes: exploring the plant metabolic network. J. Exp. Bot. 63, 2243-2246. doi: 10.1093/jxb/ers073
    • (2012) J. Exp. Bot , vol.63 , pp. 2243-2246
    • Kruger, N.J.1    Ratcliffe, R.G.2
  • 57
    • 84876896152 scopus 로고    scopus 로고
    • Current challenges and future potential of tomato breeding using omics approaches
    • Kusano, M., and Fukushima, A. (2013). Current challenges and future potential of tomato breeding using omics approaches. Breed. Sci. 63, 31-41. doi: 10.1270/jsbbs.63.31
    • (2013) Breed. Sci , vol.63 , pp. 31-41
    • Kusano, M.1    Fukushima, A.2
  • 58
    • 79960384696 scopus 로고    scopus 로고
    • Mass spectrometry strategies in metabolomics
    • Lei, Z., Huhman, D. V., and Sumner, L. W. (2011). Mass spectrometry strategies in metabolomics. J. Biol. Chem. 286, 25435-25442. doi: 10.1074/jbc.R111.238691
    • (2011) J. Biol. Chem , vol.286 , pp. 25435-25442
    • Lei, Z.1    Huhman, D.V.2    Sumner, L.W.3
  • 59
    • 84864843180 scopus 로고    scopus 로고
    • In silico method for modelling metabolism and gene product expression at genome scale
    • Lerman, J. A., Hyduke, D. R., Latif, H., Portnoy, V. A., Lewis, N. E., Orth, J. D., et al. (2012). In silico method for modelling metabolism and gene product expression at genome scale. Nat. Commun. 3:929. doi: 10.1038/ncomms1928
    • (2012) Nat. Commun , vol.3 , pp. 929
    • Lerman, J.A.1    Hyduke, D.R.2    Latif, H.3    Portnoy, V.A.4    Lewis, N.E.5    Orth, J.D.6
  • 60
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis, N. E., Nagarajan, H., and Palsson, B. O. (2012). Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 10, 291-305. doi: 10.1038/nrmicro2737
    • (2012) Nat. Rev. Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 61
    • 44949161995 scopus 로고    scopus 로고
    • Metabolic flux analysis in plants: From intelligent design to rational engineering
    • Libourel, I. G., and Shachar-Hill, Y. (2008). Metabolic flux analysis in plants: from intelligent design to rational engineering. Annu. Rev. Plant Biol. 59, 625-650. doi: 10.1146/annurev.arplant.58.032806.103822
    • (2008) Annu. Rev. Plant Biol , vol.59 , pp. 625-650
    • Libourel, I.G.1    Shachar-Hill, Y.2
  • 62
    • 79952494097 scopus 로고    scopus 로고
    • Plant systems biology: Network matters
    • Lucas, M., Laplaze, L., and Bennett, M. J. (2011). Plant systems biology: network matters. Plant Cell Environ. 34, 535-553. doi: 10.1111/j.1365-3040.2010.02273.x
    • (2011) Plant Cell Environ , vol.34 , pp. 535-553
    • Lucas, M.1    Laplaze, L.2    Bennett, M.J.3
  • 63
    • 84880199410 scopus 로고    scopus 로고
    • Pathview: An R/Bioconductor package for pathway-based data integration and visualization
    • Luo, W., and Brouwer, C. (2013). Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics 29, 1830-1831. doi: 10.1093/bioinformatics/btt285
    • (2013) Bioinformatics , vol.29 , pp. 1830-1831
    • Luo, W.1    Brouwer, C.2
  • 64
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado, D., and Herrgard, M. (2014). Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput. Biol. 10:e1003580. doi: 10.1371/journal.pcbi.1003580
    • (2014) PLoS Comput. Biol , vol.10
    • McHado, D.1    Herrgard, M.2
  • 65
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S., Heymans, K., and Kuiper, M. (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449. doi: 10.1093/bioinformatics/bti551
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 66
    • 78649775562 scopus 로고    scopus 로고
    • Enrichment map: A network-based method for gene-set enrichment visualization and interpretation
    • Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G. D. (2010). Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5:e13984. doi: 10.1371/journal.pone.0013984
    • (2010) PLoS ONE , vol.5
    • Merico, D.1    Isserlin, R.2    Stueker, O.3    Emili, A.4    Bader, G.D.5
  • 67
    • 84856015478 scopus 로고    scopus 로고
    • Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity
    • Mintz-Oron, S., Meir, S., Malitsky, S., Ruppin, E., Aharoni, A., and Shlomi, T. (2012). Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. Proc. Natl. Acad. Sci. U.S.A. 109, 339-344. doi: 10.1073/pnas.1100358109
    • (2012) Proc. Natl. Acad. Sci. U.S.A , vol.109 , pp. 339-344
    • Mintz-Oron, S.1    Meir, S.2    Malitsky, S.3    Ruppin, E.4    Aharoni, A.5    Shlomi, T.6
  • 68
    • 78149262301 scopus 로고    scopus 로고
    • GeneMANIA Cytoscape plugin: Fast gene function predictions on the desktop
    • Montojo, J., Zuberi, K., Rodriguez, H., Kazi, F., Wright, G., Donaldson, S. L., et al. (2010). GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 26, 2927-2928. doi: 10.1093/bioinformatics/btq562
    • (2010) Bioinformatics , vol.26 , pp. 2927-2928
    • Montojo, J.1    Zuberi, K.2    Rodriguez, H.3    Kazi, F.4    Wright, G.5    Donaldson, S.L.6
  • 69
    • 84908648308 scopus 로고    scopus 로고
    • GeneMANIA: Fast gene network construction and function prediction for Cytoscape
    • Montojo, J., Zuberi, K., Rodriguez, H., Bader, G. D., and Morris, Q. (2014). GeneMANIA: fast gene network construction and function prediction for Cytoscape. F1000Res 3:153. doi: 10.12688/f1000research.4572.1
    • (2014) F1000Res , vol.3 , pp. 153
    • Montojo, J.1    Zuberi, K.2    Rodriguez, H.3    Bader, G.D.4    Morris, Q.5
  • 70
    • 84901025382 scopus 로고    scopus 로고
    • A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
    • Nagele, T., and Weckwerth, W. (2013). A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Front. Plant Sci. 4:541. doi: 10.3389/fpls.2013.00541
    • (2013) Front. Plant Sci , vol.4 , pp. 541
    • Nagele, T.1    Weckwerth, W.2
  • 71
    • 84908659098 scopus 로고    scopus 로고
    • KEGGscape: A cytoscape app for pathway data integration
    • [v1; ref status: approved with reservations 2]
    • Nishida, K., Ono, K., Kanaya, S., and Takahashi, K. (2014). KEGGscape: a cytoscape app for pathway data integration [v1; ref status: approved with reservations 2, http://f1000r.es/3qe]. F1000 Research 3:144. doi: 10.12688/f1000research.4524.1
    • (2014) F1000 Research , vol.3 , pp. 144
    • Nishida, K.1    Ono, K.2    Kanaya, S.3    Takahashi, K.4
  • 72
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth, J. D., Thiele, I., and Palsson, B. O. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248. doi: 10.1038/nbt.1614
    • (2010) Nat. Biotechnol , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.O.3
  • 73
    • 70350676551 scopus 로고    scopus 로고
    • A genome-scale metabolic model of Arabidopsis and some of its properties
    • Poolman, M. G., Miguet, L., Sweetlove, L. J., and Fell, D. A. (2009). A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol. 151, 1570-1581. doi: 10.1104/pp.109.141267
    • (2009) Plant Physiol , vol.151 , pp. 1570-1581
    • Poolman, M.G.1    Miguet, L.2    Sweetlove, L.J.3    Fell, D.A.4
  • 74
    • 84880723441 scopus 로고    scopus 로고
    • Correlation networks visualization
    • Provart, N. (2012). Correlation networks visualization. Front. Plant Sci. 3:240. doi: 10.3389/fpls.2012.00240
    • (2012) Front. Plant Sci , vol.3 , pp. 240
    • Provart, N.1
  • 75
    • 77955534569 scopus 로고    scopus 로고
    • Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
    • Radrich, K., Tsuruoka, Y., Dobson, P., Gevorgyan, A., Swainston, N., Baart, G., et al. (2010). Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Syst. Biol. 4:114. doi: 10.1186/1752-0509-4-114
    • (2010) BMC Syst. Biol , vol.4 , pp. 114
    • Radrich, K.1    Tsuruoka, Y.2    Dobson, P.3    Gevorgyan, A.4    Swainston, N.5    Baart, G.6
  • 76
    • 84862499271 scopus 로고    scopus 로고
    • Pathway analysis of genomic data: Concepts, methods, and prospects for future development
    • Ramanan, V. K., Shen, L., Moore, J. H., and Saykin, A. J. (2012). Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet. 28, 323-332. doi: 10.1016/j.tig.2012.03.004
    • (2012) Trends Genet , vol.28 , pp. 323-332
    • Ramanan, V.K.1    Shen, L.2    Moore, J.H.3    Saykin, A.J.4
  • 77
    • 77951602363 scopus 로고    scopus 로고
    • Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
    • Redestig, H., Kusano, M., Fukushima, A., Matsuda, F., Saito, K., and Arita, M. (2010). Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics 11:214. doi: 10.1186/1471-2105-11-214
    • (2010) BMC Bioinformatics , vol.11 , pp. 214
    • Redestig, H.1    Kusano, M.2    Fukushima, A.3    Matsuda, F.4    Saito, K.5    Arita, M.6
  • 78
    • 84862157783 scopus 로고    scopus 로고
    • FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks
    • Rohn, H., Hartmann, A., Junker, A., Junker, B. H., and Schreiber, F. (2012a). FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks. BMC Syst. Biol. 6:33. doi: 10.1186/1752-0509-6-33
    • (2012) BMC Syst. Biol , vol.6 , pp. 33
    • Rohn, H.1    Hartmann, A.2    Junker, A.3    Junker, B.H.4    Schreiber, F.5
  • 80
    • 84895986259 scopus 로고    scopus 로고
    • Recent advances in the reconstruction of metabolic models and integration of omics data
    • Saha, R., Chowdhury, A., and Maranas, C. D. (2014). Recent advances in the reconstruction of metabolic models and integration of omics data. Curr. Opin. Biotechnol. 29C, 39-45. doi: 10.1016/j.copbio.2014.02.011
    • (2014) Curr. Opin. Biotechnol , vol.29 C , pp. 39-45
    • Saha, R.1    Chowdhury, A.2    Maranas, C.D.3
  • 81
    • 79959946634 scopus 로고    scopus 로고
    • Zea mays iRS1563: A comprehensive genome-scale metabolic reconstruction of maize metabolism
    • Saha, R., Suthers, P. F., and Maranas, C. D. (2011). Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS ONE 6:e21784. doi: 10.1371/journal.pone.0021784
    • (2011) PLoS ONE , vol.6
    • Saha, R.1    Suthers, P.F.2    Maranas, C.D.3
  • 82
    • 77951880802 scopus 로고    scopus 로고
    • Metabolomics for functional genomics, systems biology, and biotechnology
    • Saito, K., and Matsuda, F. (2010). Metabolomics for functional genomics, systems biology, and biotechnology.Annu. Rev. Plant Biol. 61, 463-489. doi: 10.1146/annurev.arplant.043008.092035
    • (2010) Annu. Rev. Plant Biol , vol.61 , pp. 463-489
    • Saito, K.1    Matsuda, F.2
  • 83
    • 78651340558 scopus 로고    scopus 로고
    • KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
    • Sakurai, N., Ara, T., Ogata, Y., Sano, R., Ohno, T., Sugiyama, K., et al. (2011). KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res. 39, D677-D684. doi: 10.1093/nar/gkq989
    • (2011) Nucleic Acids Res , vol.39 , pp. D677-D684
    • Sakurai, N.1    Ara, T.2    Ogata, Y.3    Sano, R.4    Ohno, T.5    Sugiyama, K.6
  • 84
    • 84908616695 scopus 로고    scopus 로고
    • Biological network analysis with CentiScaPe: Centralities and experimental dataset integration
    • [v1; ref status: approved with reservations 2]
    • Scardoni, G., Tosadori, G., Faizan, M., Spoto, F., Fabbri, F., and Laudanna, C. (2014). Biological network analysis with CentiScaPe: centralities and experimental dataset integration [v1; ref status: approved with reservations 2,http://f1000r.es/3p0]. F1000Res 3:139. doi: 10.12688/f1000research.4477.1
    • (2014) F1000Res , vol.3 , pp. 139
    • Scardoni, G.1    Tosadori, G.2    Faizan, M.3    Spoto, F.4    Fabbri, F.5    Laudanna, C.6
  • 85
    • 84890092837 scopus 로고    scopus 로고
    • GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data
    • Schmidt, B. J., Ebrahim, A., Metz, T. O., Adkins, J. N., Palsson, B. O., and Hyduke, D. R. (2013). GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 29, 2900-2908. doi: 10.1093/bioinformatics/btt493
    • (2013) Bioinformatics , vol.29 , pp. 2900-2908
    • Schmidt, B.J.1    Ebrahim, A.2    Metz, T.O.3    Adkins, J.N.4    Palsson, B.O.5    Hyduke, D.R.6
  • 86
    • 84903735161 scopus 로고    scopus 로고
    • High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
    • Seaver, S. M., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L. M., Zallot, R., et al. (2014). High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc. Natl. Acad. Sci. U.S.A. 111, 9645-9650. doi: 10.1073/pnas.1401329111
    • (2014) Proc. Natl. Acad. Sci. U.S.A , vol.111 , pp. 9645-9650
    • Seaver, S.M.1    Gerdes, S.2    Frelin, O.3    Lerma-Ortiz, C.4    Bradbury, L.M.5    Zallot, R.6
  • 87
    • 84859367668 scopus 로고    scopus 로고
    • Frontiers in metabolic reconstruction and modeling of plant genomes
    • Seaver, S. M., Henry, C. S., and Hanson, A. D. (2012). Frontiers in metabolic reconstruction and modeling of plant genomes. J. Exp. Bot. 63, 2247-2258. doi: 10.1093/jxb/err371
    • (2012) J. Exp. Bot , vol.63 , pp. 2247-2258
    • Seaver, S.M.1    Henry, C.S.2    Hanson, A.D.3
  • 88
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L., and Ideker, T. (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432. doi: 10.1093/bioinformatics/btq675
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 89
    • 4644268555 scopus 로고    scopus 로고
    • Mathematical models in microbial systems biology
    • Stelling, J. (2004). Mathematical models in microbial systems biology. Curr. Opin. Microbiol. 7, 513-518. doi: 10.1016/j.mib.2004.08.004
    • (2004) Curr. Opin. Microbiol , vol.7 , pp. 513-518
    • Stelling, J.1
  • 90
    • 84878983702 scopus 로고    scopus 로고
    • Systems-integration of plant metabolism: Means, motive and opportunity
    • Stitt, M. (2013). Systems-integration of plant metabolism: means, motive and opportunity. Curr. Opin. Plant Biol. 16, 381-388. doi: 10.1016/j.pbi.2013.02.012
    • (2013) Curr. Opin. Plant Biol , vol.16 , pp. 381-388
    • Stitt, M.1
  • 91
    • 28944444766 scopus 로고    scopus 로고
    • Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX
    • Strömbäck, L., and Lambrix, P. (2005). Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 21, 4401-4407. doi: 10.1093/bioinformatics/bti718
    • (2005) Bioinformatics , vol.21 , pp. 4401-4407
    • Strömbäck, L.1    Lambrix, P.2
  • 92
    • 84897461537 scopus 로고    scopus 로고
    • Systems analysis of metabolic phenotypes: What have we learnt?
    • Sweetlove, L. J., Obata, T., and Fernie, A. R. (2014). Systems analysis of metabolic phenotypes: what have we learnt? Trends Plant Sci. 19, 222-230. doi: 10.1016/j.tplants.2013.09.005
    • (2014) Trends Plant Sci , vol.19 , pp. 222-230
    • Sweetlove, L.J.1    Obata, T.2    Fernie, A.R.3
  • 93
    • 84870302280 scopus 로고    scopus 로고
    • Flux-balance modeling of plant metabolism
    • Sweetlove, L. J., and Ratcliffe, R. G. (2011). Flux-balance modeling of plant metabolism. Front. Plant Sci. 2:38. doi: 10.3389/fpls.2011.00038
    • (2011) Front. Plant Sci , vol.2 , pp. 38
    • Sweetlove, L.J.1    Ratcliffe, R.G.2
  • 94
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele, I., and Palsson, B. O. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93-121. doi: 10.1038/nprot.2009.203
    • (2010) Nat. Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 95
    • 84878263472 scopus 로고    scopus 로고
    • Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis
    • Topfer, N., Caldana, C., Grimbs, S., Willmitzer, L., Fernie, A. R., and Nikoloski, Z. (2013). Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. Plant Cell 25, 1197-1211. doi: 10.1105/tpc.112.108852
    • (2013) Plant Cell , vol.25 , pp. 1197-1211
    • Topfer, N.1    Caldana, C.2    Grimbs, S.3    Willmitzer, L.4    Fernie, A.R.5    Nikoloski, Z.6
  • 96
    • 84871689511 scopus 로고    scopus 로고
    • Network analysis: Tackling complex data to study plant metabolism
    • Toubiana, D., Fernie, A. R., Nikoloski, Z., and Fait, A. (2013). Network analysis: tackling complex data to study plant metabolism. Trends Biotechnol. 31, 29-36. doi: 10.1016/j.tibtech.2012.10.011
    • (2013) Trends Biotechnol , vol.31 , pp. 29-36
    • Toubiana, D.1    Fernie, A.R.2    Nikoloski, Z.3    Fait, A.4
  • 97
    • 57749114788 scopus 로고    scopus 로고
    • Arabidopsis reactome: A foundation knowledgebase for plant systems biology
    • Tsesmetzis, N., Couchman, M., Higgins, J., Smith, A., Doonan, J. H., Seifert, G. J., et al. (2008). Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell 20, 1426-1436. doi: 10.1105/tpc.108.057976
    • (2008) Plant Cell , vol.20 , pp. 1426-1436
    • Tsesmetzis, N.1    Couchman, M.2    Higgins, J.3    Smith, A.4    Doonan, J.H.5    Seifert, G.J.6
  • 98
    • 27244453164 scopus 로고    scopus 로고
    • Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses
    • Usadel, B., Nagel, A., Thimm, O., Redestig, H., Blaesing, O. E., Palacios-Rojas, N., et al. (2005). Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 138, 1195-1204. doi: 10.1104/pp.105.060459
    • (2005) Plant Physiol , vol.138 , pp. 1195-1204
    • Usadel, B.1    Nagel, A.2    Thimm, O.3    Redestig, H.4    Blaesing, O.E.5    Palacios-Rojas, N.6
  • 101
    • 84858718127 scopus 로고    scopus 로고
    • Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology
    • Weckwerth, W. (2011). Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J. Proteomics 75, 284-305. doi: 10.1016/j.jprot.2011.07.010
    • (2011) J. Proteomics , vol.75 , pp. 284-305
    • Weckwerth, W.1
  • 102
    • 77954256613 scopus 로고    scopus 로고
    • MSEA: A web-based tool to identify biologically meaningful patterns in quantitative metabolomic data
    • Xia, J., and Wishart, D. S. (2010). MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res. 38, W71-W77. doi: 10.1093/nar/gkq329
    • (2010) Nucleic Acids Res , vol.38 , pp. W71-W77
    • Xia, J.1    Wishart, D.S.2
  • 104
    • 77954197778 scopus 로고    scopus 로고
    • Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
    • Yizhak, K., Benyamini, T., Liebermeister, W., Ruppin, E., and Shlomi, T. (2010). Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics 26, i255-i260. doi: 10.1093/bioinformatics/btq183
    • (2010) Bioinformatics , vol.26 , pp. i255-i260
    • Yizhak, K.1    Benyamini, T.2    Liebermeister, W.3    Ruppin, E.4    Shlomi, T.5
  • 105
    • 84979561805 scopus 로고    scopus 로고
    • Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana
    • Yu, X., Zheng, G., Shan, L., Meng, G., Vingron, M., Liu, Q., et al. (2014). Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Front. Plant Sci. 5:273. doi: 10.3389/fpls.2014.00273
    • (2014) Front. Plant Sci , vol.5 , pp. 273
    • Yu, X.1    Zheng, G.2    Shan, L.3    Meng, G.4    Vingron, M.5    Liu, Q.6
  • 106
    • 27244443126 scopus 로고    scopus 로고
    • MetaCyc and AraCyc. Metabolic pathway databases for plant research
    • Zhang, P., Foerster, H., Tissier, C. P., Mueller, L., Paley, S., Karp, P. D., et al. (2005). MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol. 138, 27-37. doi: 10.1104/pp.105.060376
    • (2005) Plant Physiol , vol.138 , pp. 27-37
    • Zhang, P.1    Foerster, H.2    Tissier, C.P.3    Mueller, L.4    Paley, S.5    Karp, P.D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.