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References
Albert R, Barabási AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 74: 47–97
Aldana M (2003) Boolean dynamics of networks with scale-free topology. Physica D 185: 45–66
Aldana M, Coppersmith S, Kadanoff LP (2003) Boolean dynamics with random couplings. In: Kaplan E, Marsden JE, Sreenivasan KR (eds) Perspectives and problems in nonlinear science. Springer, Berlin Heidelberg New York
Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839–843
Amit DJ (1989) Modeling brain function: the world of attractor neural networks. Cambridge University Press, Cambridge
Antogoni F, Fornale S, Grimmer C, Komor E, Bagni N (1998) Long-distance translocation of polyamines in phloem and xylem of Ricinus communis L. plants. Planta 204: 520–527
Baier G, Sahle S (1998) Homogeneous and spatio-temporal chaos in biochemical reactions with feedback inhibition. J Theor Biol 193: 233–242
Barabási AL (2002) Linked: the new science of networks. Perseus, London
Barabási AL, Albert R (1999) Emergence of scaling in random networks. Science 286: 509–512
Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5: 101–113
Barak S, Tobin EM, Andronis C, Sugano S, Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends Plant Sci 5: 517–522
Bassingthwaighte JB, Liebovitch LS, West BJ (1994) Fractal physiology. Oxford University Press, Oxford
Basu U, Good AG, Taylor GJ (2001) Transgenic Brassica napus plants overexpressing aluminium-induced mitochondrial manganese superoxide dismutase cDNA are resistant to aluminium. Plant Cell Environ 24: 1269–1278
Baxter I, Tchieu J, Sussman MR, Boutry M, Palmgren MG, Gribskov M, Harper JF, Axelsen KB (2003) Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol 132: 618–628
Beck F, Blasius B, Lüttge U, Neff R, Rascher U (2001) Stochastic noise interferes coherently with a model biological clock and produces specific dynamic behaviour. Proc R Soc B 268: 1307–1313
Beligni MV, Lamattina L (2000) Nitric oxide stimulates seed germination and de-etiolation, and inhibits hypocotyl elongation, three light-inducible responses in plants. Planta 210: 215–221
Beligni MV, Lamattina L (2001) Nitric oxide in plants: the history is just beginning. Plant Cell Environ 24: 267–278
Blázquez MA, Weigel D (2000) Integration of floral inductive signals in Arabidopsis. Nature 404: 889–892
Bornholdt S (2001) Modelling genetic networks and their evolution: a complex dynamical systems perspective. Biol Chem 382: 1289–1299
Bornholdt S, Sneppen K (1998) Neutral mutations and punctuated equilibrium in evolving genetic networks. Phys Rev Lett 81: 236–239
Bowler C, Fluhr R (2000) The role of calcium and activated oxygen as signals for controlling cross tolerance. Trends Plant Sci 5: 241–246
Cheng N-H, Pittman JK, Barkla BJ, Shigaki T, Hirschi KD (2003) The Arabidopsis cax1 mutant exhibits impaired ion homeostasis, development, and hormonal responses and reveals interplay among vacuolar transporters. Plant Cell 15: 347–364
Chinnusamy V, Schumaker K, Zhu JK (2004) Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J Exp Bot 55: 225–236
Cockburn W, Patel K (2001) Control of internal carbon dioxide concentration during decarboxylation in CAM plants. In: Holtum JAM (ed) Proc CAM 2001, School of Tropical Biology, James Cook University, Townsville, p 213
Crawford NM (1997) Nitrate: nutrient and signal for plant growth. Plant Cell 7: 859–868
De Perlinghi J (2003) Isabelle Stengers: ‘Et si un jour les sciences devenaient civilisée...’. La Recherche 367: 67–70
Devlin PF, Kay SA (2000) Flower arranging in Arabidopsis. Science 288: 1600–1602
Drossel B, Schwabl F (1992) Self-organized critical forest-fire model. Phys Rev Lett 69: 1629–1632
Erdös P, Rényi A (1960) On the evolution of random graphs. Publ Math Inst Hung Acad Sci 5: 17–61
Erwin TL (1982) Tropical forests: their richness in coleoptera and other arthropod species. Coleopt Bull 36: 74–75
Erwin TL (1995) Measuring arthropod diversity in the tropical forest canopy. In: Lowman MD, Nadkarni NM (eds) Forest canopies. Academic Press, San Diego, pp 109–127
Farkas IJ, Derényi I, Jeong H, Neda Z, Oltvai ZN, Ravasz E, Schurbert A, Barabási AL (2003) The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae. Physica A381: 601–612
Fell DA, Wagner A (2000) The small world of metabolism. Nat Biotechnol 18: 1121–1122
Felle HH (2001) pH: signal and messenger in plant cells. Plant Biol 3: 577–591
Fox JJ, Hill CC (2001) From topology to dynamics in biochemical networks. Chaos 11: 809–815
Foyer CH, Lopez-Delgado L, Dat JF, Scott IM (1997) Hydrogen peroxide and glutathione associated mechanism of acclimatory stress tolerance and signaling. Physiol Plant 100: 241–254
Furuichi T, Mori IC, Takahashi K, Muto S (2001) Sugar-induced increase in cytosolic Ca2+ in Arabidopsis thaliana whole plants. Plant Cell Physiol 42: 1149–1155
Gibson SI (2000) Plant sugar-response-pathways. Part of a complex regulatory web. Plant Physiol 124: 1532–1539
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li YL, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM (2003) A protein interaction map of Drosophila melanogaster. Science 3025: 1727–1736
Girke T, Ozkan M, Carter D, Raikhel NV (2003) Towards a modeling infrastructure for studying plant cells. Plant Physiol 132: 410–414
Golden SS, Strayer C (2001) Time for plants. Progress in plant chronobiology. Plant Physiol 125: 98–101
Graham I, Matthai CC (2003) Investigation of the forest-fire model on a small-world network. Phys Rev E 68:036109
Guardiola X, Diaz-Guilera A, Lilas M, Pérez CJ (2000) Synchronization, diversity and topology of networks of integrate and fire oscillators. Phys Rev E 62: 5565–5570
Guare J (1990) Six degrees of separation: a play. Vintage Books, New York
Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110–2113
Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47–C52
Heldt HW (1976a) Metabolite carriers of chloroplasts. In: Stocking CR, Heber U (eds) Transport in plants III. Intracellular interactions and transport processes. Encyclopedia of plant physiology new series, vol 3. Springer, Berlin Heidelberg New York, pp 137–143
Heldt HW (1976b) Transport of metabolites between cytoplasm and the mitochondrial matrix. In: Stocking CR, Heber U (eds) Transport in plants III. Intracellular interactions and transport processes. Encyclopedia of plant physiology new series, vol 3. Springer, Berlin Heidelberg New York, pp 235–254
Hütt MT (2001) Datenanalyse in der Biologie. Springer, Berlin Heidelberg New York
Hütt MT, Lüttge U (2002) Nonlinear dynamics as a tool for data analysis and modeling in plant physiology. Plant Biol 4: 281–297
Hütt MT, Neff R, Busch H, Kaiser F (2002) A method for detecting the signature of spatiotemporal stochastic resonance. Phys Rev E 66: 026117
Hütt MT, Busch H, Kaiser F (2003) The effect of biological variability on spatiotemporal patterns: model simulations for a network of biochemical oscillators. Nova Acta Leopoldina 332: 381–404
Hunt L, Mills LN, Pical C, Leckie CP, Aitken FL, Kopka J, Mueller-Roeber B, McAinsh MR, Hetherington AM, Gray JE (2003) Phospholipase Cis required for the control of stomatal aperture by ABA. Plant Cell 34: 47–55
Ishiura M, Kutsuna S, Aoki S, Iwasaki H, Andersson CR, Tanabe A, Golden SS, Johnson CH, Kondo T (1998) Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281: 1519–1523
Iwasaki H, Kondo T (2000) The current state and problems of circadian clock studies in cyanobacteria. Plant Cell Physiol 41: 1013–1020
Jensen HJ (1998) Self-organized criticality. Cambridge University Press, Cambridge
Jeong H, Tombor B, Albert R, Oltavi ZN, Barabási A-L (2000) The large scale organization of metabolic networks. Nature 407: 651–654
Jeong H, Mason SP, Barabási A-L, Ottavi ZN (2001) Lethality and centrality in protein networks. Nature 411: 41–42
Kanz KT (2003) Christian Gottfried Nees von Esenbeck. Briefwechsel mit Johann Wolfgang von Goethe nebst ergänzenden Schriften. Acta Historica Leopoldina, no. 40. Deutsche Akademie der Naturforscher Leopoldina, Halle and Wissenschaftliche Verlagsgesellschaft, Stuttgart
Katayama M, Tsinoremas NF, Kondo T, Golden SS (1999) cpmA, a gene involved in an output pathway of the cyanobacterial circadian system. J Bacteriol 181: 3516–3524
Kauffman S (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22: 437–467
Kauffman S, Peterson C, Samuelsson B, Troein C (2003) Random Boolean network models and the yeast transcriptional network. Proc Natl Acad Sci USA 100: 14796–14799
Klingenberg M (1970) Metabolite transport in mitochondria: an example of intracellular membrane function. Essays Biochem 6: 119–159
Koch KE (1996) Carbohydrate-modulated gene expression in plants. Annu Rev Plant Physiol Plant Mol Biol 47: 509–540
Koorneef M, Alonso-Blanco C, Peeters AJM, Soppe W (1998) Genetic control of flowering in Arabidopsis. Annu Rev Plant Physiol Plant Mol Biol 49: 345–370
Kratochwil A (1998) Biodiversity in ecosystems. Atti Convegni Lincei 145: 23–62
Kuno N, Moller SG, Shinomura T, Xu XM, Chua NH, Furuya M (2003) The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE 1 is a component of a slave circadian oscillator in Arabidopsis. Plant Cell 15: 2476–2483
Kuramoto Y (1984) Chemical oscillations, waves, and turbulence. Springer, Berlin Heidelberg New York
Laby RJ, Kincaid S, Kim D, Gibson SI (2000) The Arabidopsis sugar-insensitive mutants sis4 and sis5 are defective in abscisic acid synthesis and response. Plant J 23: 587–596
Lalonde S, Boles E, Hellmann H, Barker L, Patrick JW, Frommer WB, Ward JM (1999) The dual function of sugar carriers: transport and sugar sensing. Plant Cell 11: 707–726
Lamattina L, García-Mata C, Graziano M, Pagnussat G (2003) Nitric oxide: the versatility of an extensive signal molecule. Annu Rev Plant Biol 54: 109–136
Lehle L (1990) Phosphatidyl inositol metabolism and its role in signal transduction in growing plants. Plant Mol Biol 15: 647–658
Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JDJ, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A (2004) A map of the interactome network of the Metazoan C. elegans. Science 303: 540–543
Linsenmair KE (1995) Biologische Vielfalt und ökologische Stabilität. In: Markl H, Geiler G, Großmann S, Oesterhelt D, Schmidbaur H, Quadbeck-Seeger H-J, Truscheit E (eds) Wissenschaft in der globalen Herausforderung. Edition Universitas. Hirzel Wissenschaftliche Verlagsgesellschaft, Stuttgart, pp 267–295
Lüttge U (1974) Co-operation of organs in intact higher plants: a review. In: Zimmermann U, Dainty J (eds) Membrane transport in plants. Springer, Berlin Heidelberg New York, pp 353–362
Lüttge U (2002a) CO2-concentrating: consequences in Crassulacean acid metabolism. J Exp Bot 53: 2131–2142
Lüttge U (2002b) Circadian rhythmicity: is the ‘biological clock’ hardware or software? Progress in Botany, vol 64. Springer, Berlin Heidelberg New York, pp 277–319
Lüttge U (2003) Circadian rhythms. In: Thomas B, Murphy DJ, Murray BG (eds) Encyclopedia of applied plant sciences. Elsevier, Academic Press, Amsterdam, pp 1084–1096
Lüttge U (2004) Ecophysiology of Crassulacean acid metabolism (CAM). Ann Bot 93: 629–652
Maathuis FMJ, Filatov V, Herzyk P et al. (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. Plant J 35: 675–692
Mandava NB (1988) Plant growth-promoting brassinosteroids. Annu Rev Plant Physiol 39: 23–52
Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910–913
Mata CG, Lamattina L (2001) Nitric oxide induces stomatal closure and enhances the adaptive plant responses against drought stress. Plant Physiol 126: 1196–1204
Maxwell BB, Andersson CR, Poole DS, Kay SA, Chory J (2003) HY5, circadian clock-associated 1, and a cis-element, DET 1 dark response element, mediate DET1 regulation of chlorophyll a/b-binding protein 2 expression. Plant Physiol 133: 1565–1577
May RM (1988) How many species are there on earth? Science 241: 1441–1449
McClung CR (2000) Circadian rhythms in plants: a millennial view. Physiol Plant 109: 359–371
Milgram S (1967) The small world problem. Psychol Today 2: 60–67
Millar AJ (1999) Biological clocks in Arabidopsis thaliana. New Phytol 141: 175–197
Minorsky PV (2003) Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol 132: 404–409
Morcuende R, Krapp A, Hurry V, Stitt M (1998) Sucrose-feeding leads to increased rates of nitrate assimilation, increased rates of α-oxoglutarate synthesis, and increased synthesis of a wide spectrum of amino acids in tobacco leaves. Planta 206: 394–409
Neill SJ, Desikan R, Hancock JT (2003) Nitric oxide signalling in plants. New Phytol 159: 11–35
Newman MEJ (2001) The structure of scientific collaboration networks. Proc Natl Acad Sci USA 98: 404–409
Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45: 167–256
Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Hoefgen R (2003) Transcriptome analysis of sulphur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J 33: 633–650
Pikovsky A, Rosenblum M, Kurths J (2001) Synchronization. A universal concept in nonlinear sciences. Cambridge University Press, Cambridge
Pitman MG (1972) Uptake and transport of ions in barley seedlings. III. Correlation of potassium transport to the shoot with plant growth. Aust J Biol Sci 25: 905–919
Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high salinity stresses and abscisic acid and application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133: 1755–1767
Raikhel NV, Coruzzi GM (2003) Plant systems biology. Plant Physiol 132: 403
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barábasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551–1555
Rengel Z, Zhang W-H (2003) Role of dynamics of intracellular calciumin aluminum-toxicity syndrome. Plant Physiol 159: 295–314
Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANs target genes in reproductive development of Arabidopsis. Science 288: 1613–1616
Scheible W-R, Gonzales-Fontes A, Lauerer M, Müller-Röber B, Caboche M, Stitt M (1997) Nitrate acts as a signal to induce organic acid metabolism and repress starch metabolism in tobacco. Plant Cell 9: 783–798
Schimper AFW (1883) Über die Entwicklung der Chloröphyllkörner und Farbkörner. Bot Zeit 41: 105–114
Schmitz O, Katayama M, Williams SB, Kondo T, Golden SS (2000) CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock. Science 289: 765–768
Schnepf E (1966) Organellen-Reduplikation und Zellkompartimentierung. In: Sitte P (ed) Probleme der biologischen Reduplikation, 3.Wiss Konf Ges Dt Naturf Ärzte, Semmering 1965. Springer, Berlin Heidelberg New York, pp 371–393
Sheen J, Zhou L, Jang J-C (1999) Sugars as signaling molecules. Curr Opin Plant Biol 2: 410–418
Simpson GG, Gendall AR, Dean C (1998) The control of flowering time and floral identity in Arabidopsis. Plant Physiol 117: 1–8
Smeekens S (2000) Sugar-induced signal transduction in plants. Annu Rev Plant Physiol Plant Mol Biol 51: 49–81
Solé RV, Manrubia SC, Luque B, Delgado J, Bascompte J (1996) Phase transitions and complex systems. Complexity 2: 13
Somers DE (1999) The physiology and molecular bases of the plant circadian clock. Plant Physiol 121: 9–19
Staiger D (2000) Biologische Zeitmessung bei Pflanzen. Biol Unserer Zeit 30: 76–79
Stocking CR, Heber U (eds) (1976) Transport in plants III. Intracellular interactions and transport processes. Encyclopedia of plant physiology new series, vol 3. Springer, Berlin Heidelberg New York
Stöhr C (1999) Relationship of nitrate supply with growth rate, plasma membrane-bound and cytosolic nitrate reductase, and tissue nitrate content in tobacco plants. Plant Cell Environ 2: 169–177
Stöhr C, Strube F, Marx G, Ullrich W, Rockel P (2001) A plasma membrane-bound enzyme of tobacco roots catalyses the formation of nitric oxide from nitrite. Planta 212: 835–841
Strogatz SH (2001) Exploring complex networks. Nature 410: 268–276
Sweetlove LJ, Last RL, Fernia AR (2003) Predictive metabolic engineering: a goal for systems biology. Plant Physiol 132: 420–425
Taylor JE, McAinsh MR (2004) Signalling crosstalk in plants: emerging issues. J Exp Bot 55: 147–149
Theißen G, Saedler H (1997) Molecular architects of plant body plans. Prog Bot 59: 227–256
Thron CD (1991) Biochemical oscillations. Bull Math Biol 53: 383
Tong AHY, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen YQ, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C (2004) Global mapping of the yeast genetic interaction network. Science 303: 808–813
Wagner A, Fell DA (2001) The small world inside large metabolic networks. Proc R Soc Lond B 268: 1803–1810
Walden R, Cordeiro A, Triburcio AF (1997) Polyamines: small molecules triggering pathways in plant growth and development. Plant Physiol 113: 1009–1013
Wang R, Okamoto M, Xing X, Crawford NM (2003) Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron and sulphate metabolism. Plant Physiol 132: 556–567
Watts DJ (1999) Small worlds: the dynamics of networks between order and randomness. Princeton University Press, Princeton
Watts DJ, Strogatz SH (1998) Collective dynamics of ’small-world’ networks. Nature 393: 440–442
Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54: 669–689
Wu P, Ma L, Hou X, Wang M, Wu Y, Liu F, Deng XW (2003) Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol 132: 1260–1271
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Hütt, MT., Lüttge, U. (2005). Network Dynamics in Plant Biology: Current Progress in Historical Perspective. In: Esser, K., Lüttge, U., Beyschlag, W., Murata, J. (eds) Progress in Botany. Progress in Botany, vol 66. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-27043-4_12
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