Abstract
In order to study the complex biology of plants, systems biology focuses on every aspect of the highly interacting components (adjustment of metabolism in response to stresses, different physiological properties due to mutation and epigenetic effects, etc.) by the development of high-throughput data generation technologies, i.e. ‘omics’, massive databases, employment of specialised bioinformatics tools and algorithms. Mathematical models are also used to study the structure and dynamics of interacting networks. This approach is essential for understanding how a plant system works which is advantageous for further research.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abdi H, Williams LJ, Valentin D, Bennani-Dosse M (2012) STASIS and DISTATIS: optimum multi-table principal component analysis and three way metric multidimensional scaling. Wiley Interdiscip Rev Comput Stat 4:124–167
Abdul RW, Paulraj MG, Ahmad T, Buhroo AA, Hussain B, Ignacimuthu S, Sharma HC (2012) Mechanisms of plant defense against insect herbivores. Plant Signal Behav 7(10):1306–1320
Abumhadi N, Kamenarova K, Gecheff K, Atanassov A (2005) Molecular farming in plants: an approach of agricultural biotechnology. J Cell Mol Biol 4:77–86
Agrawal AA, Fishbein M, Jetter R, Salminen JP, Goldstein JB, Freitag AE et al (2009) Phylogenetic ecology of leaf surface traits in the milkweeds (Asclepias spp.): chemistry, ecophysiology, and insect behavior. New Phytol 183:848–867
Albert R (2007) Network inference, analysis, and modeling in systems biology. Plant Cell 19(11):3327–3338
Albert R, Wang RS (2009) Discrete dynamic modeling of cellular signaling networks. Methods Enzymol 467:281–306
Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK (2006) Physicochemical modelling of cell signalling pathways. Nat Cell Biol 8(11):1195–1203
Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA (2009) Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol 5:e1000340
Alistair M, Middleton EF, Markus RO, Teva V (2012) Modeling regulatory networks to understand plant development: small is beautiful. Plant Cell 24:3876–3891
Al-Shahrour F, Minguez P, Tarraga J et al (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34:W472–W476
Arimura GI, Matsui K, Takabayashi J (2009) Chemical and molecular ecology of herbivore-induced plant volatiles: proximate factors and their ultimate functions. Plant Cell Physiol 50:911–923
Assmann SM, Albert R (2009) Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information. Methods Mol Biol 553:207–225
Banga JR, Balsa-Canto E (2008) Parameter estimation and optimal experimental design. Essays Biochem 45:195–210
Bennett RN, Wallsgrove RM (1994) Secondary metabolites in plant defence mechanisms. New Phytol 127:617–633. Biophys J 88: 1616–1625
Blais A, Dynlacht BD (2005) Constructing transcriptional regulatory networks. Genes Dev 19(13):1499–1511
Blakes J, Twycross J, Romero FJ et al (2011) The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. Bioinformatics 27(23):3323–3324
Blasing OE et al (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17(12):3257–3281
Bonneau R et al (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 7:R36
Breitkreutz BJ, Stark C, Tyers M (2003) Osprey: a network visualization system. Genome Biol 4(3):R22
Carrari F et al (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142:1380–1396
Carrera J, Rodrigo G, Jaramillo A, Elena SF (2009) Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol 10(9):R96
Caspi R, Altman T, Dale JM et al (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38(1):473–479
Causier B (2004) Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom Rev 23:350–367
Chamarthi SK, Sharma HC, Sahrawat KL, Narasu LM, Dhillon MK (2010) Physico-chemical mechanisms of resistance to shoot fly, Atherigona soccata in sorghum, Sorghum bicolor. J Appl Entomol 135:446–455
Chaouiya C (2007) Petri net modelling of biological networks. Brief Bioinform 8:210–219
Chapple C (2000) Molecular ‘pharming’ with plant P450s. Trends Plant Sci 5(7):271–272
Chis O, Banga JR, Canto EV (2011) Structural identifiability of systems biology models: a critical comparison of methods. PLoS ONE 6(11):e27755
Choi H, Pavelka N (2011) When one and one gives more than two: challenges and opportunities of integrative omics. Front Genet 2:105
Cook D, Fowler S, Fiehn O, Thomashow MF (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci U S A 101(42):15243–15248
Coruzzi G, Gutierrez R (2009) Plant system biology. Annu Plant Rev 35
Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163
Cusick ME, Klitgord ME, Vidal M, Hill DE (2005) Interactome: gateway into systems biology. Hum Mol Genet 14:R171–R181
de Ruiter PC et al (2005) Ecology. Food web ecology: playing Jenga and beyond. Science 309:68–71
Davidich M, Bornholdt S (2008) The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model. J Theor Biol 255:269–277
Davidson EH et al (2002) A genomic regulatory network for development. Science 295:1669–1678
Davies PJ (ed) (2010) Plant hormones: biosynthesis, signal transduction, action. Plant Hormones. Springer, pp. 1–15
De Las Rivas J et al (2004) Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins. Trends Plant Sci 9:18–25
Dixon RA, Paiva N (1995) Stressed induced phenylpropanoid metabolism. Plant Cell 7:1085–1097
Edwards D, Batley J (2004) Plant bioinformatics: from genome to phenome. Trends Biotechnol 22(5):232–237
Evers JB et al (2010) Simulation of wheat growth and development based on organ-level photosynthesis and assimilate allocation. J Exp Bot 61:2203–2216
Famili I, Mahadevan R, Palsson BØ (2005) k-cone analysis: determining all candidate values for kinetic parameters on a network scale Biophys J 88(3):1616–1625
Fell D (1997) Understanding the control of metabolism. Ashgate Publishing, London, 300 p
Fiehn O (2002) Metabolomics–the link between genotypes and phenotypes. Plant Mol Biol 48(1–2):155–171
Field S, Song OK (1989) A novel genetic system to detect protein–protein interactions. Nature 340:245–246
Fisher J, Henzinger TA (2007) Formal Methods in Systems Biology Executable cell biology. Nat Biotechnol 25:1239–1249
Forrester JW (1958) Industrial dynamics: A major breakthrough for decision makers. Harv Bus Rev 36(4):37–66
Fukusaki E, Kobayashi A (2005) Plant metabolomics: potential for practical operation. J Biosci Bioeng 100:347–354
Ghaemmaghami S, Huh W-K, Bower K, Howson RW, Belle A, Dephoure N, O’Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–741
Gomez-Roldan V, Fermas S, Brewer PB et al (2008) Strigolactone inhibition of shoot branching. Nature 455(7210):189–194
Goossens A et al (2003) A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sci U S A 100:8595–8600
Goymer P (2008) Network biology: why do we need hubs? Nat Rev Genet 9:650–651
Grant RC, Kaoru U, Serge D, Mario P, Kazuo SC et al (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 2011(11):163
Gulsen O, Eickhoff T, Heng-Moss T, Shearman R, Baxendale F, Sarath G et al (2010) Characterization of peroxidase changes in resistant and susceptible warm-season turfgrasses challenged by Blissus occiduus. Arthropod-Plant Interact 4:45–55
Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP (2004) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput 3(10):e189
Hallikas O, Taipale J (2006) High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nat Protoc 1:215–222
Hammer GL, Sinclair TR, Chapman SC, Oosterom EV (2004) On systems thinking, systems biology, and the in silico plant. Plant Physiol V 134:909–911
Handley R, Ekbom B, Agren J (2005) Variation in trichome density and resistance against a specialist insect herbivore in natural populations of Arabidopsis thaliana. Ecol Entomol 30:284–292
Hanley ME, Lamont BB, Fairbanks MM, Rafferty CM (2007) Plant structural traits and their role in antiherbivore defense. Perspect Plant Ecol Evol Syst 8:157–178
Harel D (2003) A grand challenge for computing: full reactive modeling of a multi-cellular animal. Verification, model checking, and abstract interpretation. Lect Notes Comput Sci 2937:323–324
Harel D, Pnueli A (1985) On the development of reactive systems. Logics Model Concurr Syst 13:477–498
He J, Chen F, Chen S, Lv G, Deng Y, Fang W et al (2011) Chrysanthemum leaf epidermal surface morphology and antioxidant and defense enzyme activity in response to aphid infestation. J Plant Physiol 168:687–693
Heinrich R, Schuster S (1996) The regulation of cellular systems. Chapman & Hall, London
Hesse H, Hoefgen R (2006) On the way to understand biological complexity in plants: S-nutrition as a case study for systems biology. Cell Mol Biol Lett 11:37–56
Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A 101(27):10205–10210
Hirai MY et al (2005) Elucidation of gene-to-gene and metabolite-togene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280:25590–25595
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183
Hood EE, Witcher DR, Maddock S, Meyer T, Baszczynski C, Bailey M, Flynn P, Register J, Marshall L, Bond D, Kulisek E, Kusnadi A, Evangelista R, Nikolov Z, Wooge C, Mehigh RJ, Hernan R, Kappel WK, Ritland D, Li CP, Howard JA (1997) Commercial production of avidin from transgenic maize: characterization of transformant, production, processing, extraction and purification. Mol Breed 3:291–306
Hoops S, Sahle S, Gauges R et al (2006) COPASI—a complex pathway simulator. Bioinformatics 22(24):3067–3074
Horn ME, Woodard SL, Howard JA (2004) Plant molecular farming: systems and products. Plant Cell Rep 22:711–720
Houtman JCD, Barda-Saad M, Samelson LE (2005) Examining multiprotein signaling complexes from all angles. FEBS J 272:5426–5435
Howe GA, Jander G (2008) Plant immunity to insect herbivores. Annu Rev Plant Biol 59:41–66
Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A. 103(35):12987–12992
Ingram PJ, Stumpf MPH, Stark J (2006) Network motifs: structure does not structure does not determine function. BMC Genomics 5(7):108
Ivanov VV, Ivanova NV (2006) Mathematical models of the cells and cell-associated objects. In: Chui CK (ed) Mathematics in science and engineering. Elsevier, 206 p
Jacob F (1974) The logic of living systems. Plant Cell 18:2420–2430
Janes K, Lauffenburger D A(2006) A biological approach to computational models of proteomic networks. Curr Opin Chem Biol 10:73–80. http://www.cdpcenter.org/files/pubs/janes_biological.pdf
Jones JW et al (2003) The DSSAT cropping system model. Eur J Agron 18:235–265
Jordan MI (1999) Learning in graphical models. Adaptive Computation and Machine Learning series, MIT Press, Cambridge
Joyce AR, Palsson BO (2006) The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 7:198–210
Kahlem P, Birney E (2006) Dry work in a wet world: computation in systems biology. Mol Syst Biol 2:40
Kainulainen P, Holopainen JK, Holopainen T (1998) The influence of elevated CO2 and O3 concentrations on Scots pine needles: changes in starch and secondary metabolites over three exposure years. Oecologia 114:45560
Kamlage B, Poorter H, Stitt M (2008) Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range. Plant Cell Environ 31(4):518–547
Kanehisa M, Goto S, Sato Y et al (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(D1):109–114
Karlebach G, Shamir R (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9:770–780
Karp PD (1996) A strategy for database interoperation. J Comput Biol 2(4):573–583
Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467
Kaufmann K, Smaczniak C, de Vries S, Angenent GC, Karlova R (2011) Proteomics insights into plant signaling and development. Proteomics 11(4):744–755
Keasling DJ (2010) Advanced biofuel production in microbes. Biotechnol J 5:147–162
Kefi S et al (2007) Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems. Nature 449:213–217
Keurentjes JJB et al (2007) Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 104:1708–1713
Keurentjes JJ, Angenent GC, Dicke M, Vı´tor AP, Santos MD, Olenaar JM, Wim H (2012) Redefining plant systems biology: from cell to ecosystem. Trends Plant Sci 16:4
Kitano H (2002) Computational systems biology. Nature 420:206–210
Klie S, Caldana C, Nikoloski Z (2012) Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions. Front Plant Sci 3:249
Koffas M, Roberge C, Lee K, Stephanopoulos G (1999) Metabolic engineering. Annu Rev Biomed Eng 1:535–557
Kuhn C et al (1997) Macromolecular trafficking indicated by localization and turnover of sucrose transporters in enucleate sieve elements. Science 275:1298–1300
Kusano M, Tohge T, Fukushima A, Kobayashi M, Hayashi N, Otsuki H, Kondou Y, Goto H, Kawashima M, Matsuda F, Niida R, Matsui M, Saito K, Fernie AR (2011) Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light. Plant J 67(2):354–369
Kohn KW (1999) Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell 10:2703–2734
Laakso M, Hautaniemi S (2010) Integrative platform to translate gene sets to networks. Bioinformatics 26(14):1802–1803
Lamphear BJ, Jilka JM, Kesl L, Welter M, Howard JA, Streatfield SJ (2004) A corn-based delivery system for animal vaccines: an oral transmissible gastroenteritis virus vaccine boosts lactogenic immunity in swine. Vaccine 22(19):2420–2424
Langebartels C, Gruissem W, Inze D, Van BF (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 139(2):806–821
Le Novere N, Bornstein B, Broicher A et al (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34(1):689–691
Lee WP, Tzou WS (2009) Computational methods for discovering gene networks from expression data. Brief Bioinform 10:408–423
Lee TI et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799–804
Lenz T, Fischer JJ, Dreger M (2011) Probing small molecule-protein interactions: a new perspective for functional proteomics. J Proteomics 75(1):100–115
Li S, Assmann SM, Albert R (2006) Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol 4:e312
Locke JCW, Southern MM, Kozma-Bognr L, Hibberd V, Brown PE et al (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 1:0013
Loew LM, Schaff JC (2001) The virtual cell: a software environment for computational cell biology. Trends Biotechnol 10:401–406
Loew LM, Schaff JC (2011) Virtual Cell; a software environment for computational cell biology. Trends Biotechnol 19(10):401–406
Lorenz WW, Alba R, Yu YS, Bordeaux JM, Simoes M, Dean JF (2011) Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.). BMC Genomics 24(12):264
Lavit C, Escoufier Y, Sabatier R, Traissac P (1994) The, ACT (STASIS method). Computational 18:97–119
Lu Y, Hong S, Tjonahen E, Serhan CN (2005) Mediator lipidomics: databases and search algorithms for PUFA-derived Mediators. J Lipid Res 46:790–802
Ma JK-C, Drake PMW, Christou P (2003) The production of recombinant pharmaceutical proteins in plants. Genetics 4:794–805
Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315(5809):233–237
Makkar HPS, Francis G, Becker K (2007) Bioactivity of phytochemicals in some lesser-known plants and their effects and potential applications in livestock and aquaculture production systems. Animal 1:1371–1391
Marbach D et al (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A 107:6286–6291
Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, Fujita M, Yoshiwara K, Matsukura S, Morishita Y, Sasaki R, Suzuki H, Saito K, Shibata D, Shinozaki K, Yamaguchi-Shinozaki K (2009) Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol 150(4):1972–1980
Mattheij RMM, Molenaar J (2002) Ordinary differential equations in theory and practice. SIAM classics in Applied Mathematics 43. SIAM, Philadelphia
Mayer BJ (1999) Protein–protein interactions in signaling cascades. Mol Biotechnol 13:201–213
Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cisregulatory input function of a gene. PLoS Biol 4:e45
Mendes P (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi. Trends Biochem Sci 22:361–363
Middleton AM, Úbeda-Tomás S, Griffiths J, Holman T, Hedden P, Thomas SG, Phillips AL, Holdsworth MJ, Bennett MJ, King JR, Owen MR (2012) Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Proc Natl Acad Sci U S A 109:7571–7576
Miller HI (2003) Will we reap what biopharming sows? Nat Biotechnol 21(5):480–481
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276:10577–10580
Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti VB, Vandepoele K, Gollery M, Shulaev V, Van BF (2011) ROS signaling: the new wave? Trends Plant Sci 16(6):300–309
Molassiotis A, Fotopoulos V (2011) Oxidative and nitrosative signaling in plants: two branches in the same tree? Plant Signal Behav 6(2):210–214
Morgan PW, Drew MC (1997) Ethylene and plant responses to stress. Physiology 100:620–630
Morison JIL, Lawlor DW (1999) Interactions between increasing CO2 concentration and temperature on plant growth. Plant Cell Environ 22:659–682
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA (2011) Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol 7:e1001099
Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132(2):453–460
Nagasaki M, Saito A, Jeong E et al (2010) Cell Illustrator 4.0: a computational platform for systems biology. Silico Biol 10(1):5–26
Neapolitan RE (2004) Learning Bayesian networks. Prentice Hall, Upper Saddle River, NJ
Neutel AM et al (2002) Stability in real food webs: weak links in long loops. Science 296:1120–1123
Nikiforova VJ et al (2005) Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J Exp Bot 56:1887–1896
Nishimura D (2001) BioCarta. Biotech Softw Internet Rep 2:117–120
Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20:2143–2144
Pabinger S, Rader R, Agren R et al (2011) MEMOSys: bioinformatics platform for genome-scale metabolic models. BMC Syst Biol 5(1):20
Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6:99–111
Polynikis A et al (2009) Comparing different ODE modelling approaches for gene regulatory networks. J Theor Biol 261:511–530
Press W, Teukolsky S, Flannery B, Vetterling W (1990) Numerical recipes: FORTRAN. Cambridge University Press, Cambridge
Puchalka J et al (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4:e1000210
Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Bragado-Nilsson E, Wilm M, Seraphin B (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218–229
Rastogi SC, Rastogi P, Mendiratta N (2012) Bioinformatics methods and applications: genomics proteomics and drug discovery ed. (3). PHI Learning Private Limited, Delhi
Raue A, Schilling M, Bachmann J, Matteson A, Schelke M, Kaschek D, Hug S, Kreutz C, Brian DH, Fabian JT, Ursula K, Jens T (2013) Lessons learned from quantitative dynamical modeling in systems biology. PLoS ONE 8(9):e74335
Ravishankar GA, Rao SR (2000) Biotechnological production of phytopharmaceuticals. J Biochem Mol Biol Biophys 4:73–102
Ravishankar GA, Venkataraman LV (1990) Food applications of plant cell cultures. Curr Sci 57:381–383
Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030–1032
Rischer H et al (2006) Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proc Natl Acad Sci U S A 103:5614–5619
Rosemann D, Heller W, Sandermann H (1991) Biochemical plant responses to ozone. II. Induction of stilbene biosynthesis in Scots pine (Pinus sylvestris L.) seedlings. Plant Physiol 97:1280–1286
Ruths D, Muller M, Tseng JT, Nakhleh L, Ram PT (2008) The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PLoS Comput Biol 298:799–804
Sachs K, Perez O, Pe’er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308:523–529
Sadot A, Sarbu S, Kesseli J, Amir-Kroll H, Zhang W, Nykter M, Shmulevich I (2013) Information-theoretic analysis of the dynamics of an executable biological model. PLoS One 8(3):e59303
Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK (2009) Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol 5:331
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK (2011) Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res 71:5400–5411
Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci U S A 104(15):6478–6483
Sauro HM, Hucka M, Finney A et al (2003) Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. Omics 7(4):355–372
Schaefer CF, Anthony K, Krupa S et al (2009) PID: the pathway interaction database. Nucleic Acids Res 37(1):674–679
Scheible WR et al (2004) Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol 136:2483–2499
Schillberg S, Fischer R, Emans N (2003) Molecular farming of antibodies in plants. Naturwissenschften 90:145–155
Shaitan KV, Tourleigh Ye V, Golik DN, Tereshkina KV, Levtsova OV, Fedik IV, Shaitan AK, Li A, Kirpichnikov MP (2006) Dynamics and molecular design of bio- and nanostructures. Ros Khim Zh 50:53–65
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
Shmulevich I, Dougherty ER, Kim S, Zhang W (2002) Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18:261–274
Simpson SJ et al (2010) Modelling nutritional interactions: from individuals to communities. Trends Ecol Evol 25:53–60
Sobie EA, Lee YS, Jenkins SL, Iyengar R (2011) Systems biology—biomedical modeling. Sci Signal 4(190):2
Srivastava A, Somvanshi P, Mishra BN (2013) Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. Syst Synth Biol 7(7):22
Staab PR, Walossek J, Nellessen D, Grünberg R, Arndt KM, Müller KM (2010) SynBioWave–a real-time communication platform for molecular and synthetic biology. Bioinformatics 26(21):2782–2783
Stepanova AN, Alonso JM (2009) Ethylene signaling and response: where different regulatory modules meet. Curr Opin Plant Biol 12(5):548–555
Stephanopoulos G (1999) Metabolic fluxes and metabolic engineering. Metab Eng 1:11
Stephens DJ, Banting G (2000) The use of yeast two-hybrid screens in studies of protein: protein interactions involved in trafficking. Traffic 1:763–768
Steppuhn A, Baldwin IT (2007) Resistance management in a native plant: nicotine prevents herbivores from compensating for plant protease inhibitors. Ecol Lett 10:499–511
Stöger E, Vaquero C, Torres E, Sack M, Nicholson L, Drossard J, Williams S, Keen D, Perrin Y, Christou P, Fischer R (2000) Cereal crops as viable production and storage systems for pharmaceutical scFv antibodies. Plant Mol Biol 42(4):583–590
Stumpf MPH, Thorne T, de Silva E, Stewart R, An HJ, Lapper M, Wiuf C (2008) Estimating the size of the human interactome. Proc Natl Acad Sci U S A 105:6959–6964
Sucaet Y, Wang Y, Li J et al (2012) MetNet Online: a novel integrated resource for plant systems biology. BMC Bioinforma 13(1):267
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270:467–470
Strogatz SH (2001) Exploring complex networks. Nature 410:268–276
Takahashi S, Seki M, Ishida J, Satou M, Sakurai T, Narusaka M, Kamiya A, Nakajima M, Enju A, Akiyama K, Yamaguchi-Shinozaki K, Shinozaki K (2004) Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray. Plant Mol Biol 56(1):29–55
Ter Braak CJF, Prentice IC (2004) A theory of gradient analysis. Adv Ecol Res 34:235–282
Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC et al (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267:5313–5329
Thakar J, Albert R (2010) Boolean models of within-host immune interactions. Curr Opin Microbiol 13:377–381
Thomas R (1973) Boolean formalization of genetic control circuits. J Theor Biol 42:563–585
Thomas R, D’Ari R (1990) Biological feedback. CRC Press, Boca Raton
Thomas B, Van Deynze A, Bradford K (2002) Production of therapeutic proteins in plants. Agricultural Biotechnology in California Series. Division of Agriculture and Natural resources, University of California Pub 8078
Tohge T et al (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J 42:218–235
Tomita M, Hashimoto K, Takahashi K et al (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1):72–84
Tong AH et al (2004) Global mapping of the yeast genetic interaction network. Science 303:808–813
Trewavas A (2006) A brief history of systems biology. ‘Every object that biology studies are a system of systems.’ Francois Jacob (1974). Plant Cell 18:2420–2430
Turenne N (2011) Role of a web-based software platform for systems biology. J Comput Sci Syst Biol 4:035–041
Tuteja N, Mahajan S (2007) Calcium signaling network in plants: an overview. Plant Signal Behav 2:79–85
Terentiev AA, Moldogazieva NT, Shaitan KV (2009) Dynamic proteomics in modeling of the living cell. Protein–protein interactions. Biochemistry 74(13):1587–1607
Umehara M, Hanada A, Yoshida S et al (2008) Inhibition of shoot branching by new terpenoid plant hormones. Nature 455(7210):195–200
Urano K, Maruyama K, Ogata Y, Morishita Y, Takeda M, Sakurai N, Suzuki H, Saito K, Shibata D, Kobayashi M, Yamaguchi-Shinozaki K, Shinozaki K (2009) Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant J 57(6):1065–1078
Usadel B 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
Usadel B, Fernie AR (2013) The plant transcriptome-from integrating observations to models. Front Plant Sci 4:48. doi:10.3389/fpls.2013.00048
Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32(12):1633–1651
Usha Rani P, Jyothsna Y (2010) Biochemical and enzymatic changes in rice as a mechanism of defense. Acta Physiol Plant 32:695–701
Van der Putten WH (2009) A multitrophic perspective on functioning and evolution of facilitation in plant communities. J Ecol 97:1131–1138
Van der Putten WH et al (2001) Linking above- and below ground multitrophic interactions of plants, herbivores, pathogens and their antagonists. Trends Ecol Evol 16:547–554
Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inzé D, Van Breusegem F (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 139(2):806–821
Vemuri GM, Aristidou AA (2005) Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev 69:197–216
Voit EO (2000) Computational analysis of biochemical systems: a practical guide for biochemists and molecular biologists. Cambridge University Press, Cambridge
Voit E, Neves AR, Santos H (2006) The intricate side of systems biology. Proc Natl Acad Sci U S A 103(25):9452–9457
Vrugt JA et al (2009) Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling. Int J Nonlinear Sci Numer Simul 10:273–290
Wang G et al (2012) Process-driven inference of biological network structure: feasibility, minimality, and multiplicity. PLoS One 7:e40330
Walter M, Chaban C, Schütze K, Batistic O, Weckermann K, Na¨ ke C, Blazevic D, Grefen C, Schumacher K, Oecking C, Harter K, Jo¨ rg K (2004) Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J 40:428–438
War AR, Paulraj MG, Ahmad T, Buhroo AA, Hussain B, Ignacimuthu S, Sharma HC (2012) Mechanisms of plant fefense against insect herbivores. Plant Signal Behav 7(10):1306–1320
Wardle DA et al (2004) Ecological linkages between aboveground and belowground biota. Science 304:1629–1633
Weiss P (1973) The science of life. Futura Publishing, New York
Welti R, Shah J, Li W et al (2007) Plant lipidomics: discerning biological function by profiling plant complex lipids using mass spectrometry. Front Biosci 12:2494–2506
Weston DJ, Gunter LE, Rogers A, Wullschleger SD (2008) Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Syst Biol 2:16
Wiback S, Famili I, Greenberg HJ, Palsson BØ (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol 228:437–447
Wilkinson S, Davies WJ (2009) Drought, ozone, ABA and ethylene: new insights from cell to plant to community. Plant Cell Environ 33(4):510–525
Williams RJ (1956) Biochemical individuality. The key for the genetotrophic concept. Wiley, New York
Williams TC et al (2010) A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol 154:311–323
Winter D, Vinegar B, Nahal H et al (2007) An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2(8):e718
Wolkenhauer O (2008) Systems biology. Portland Press, London
Wolkenhauer O, Ullah M, Kolch W, Cho KH (2004) Modelling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobioscience 3(3):200–207
Wiener N (1948) Cybernetics, or control and communication in the animal and the machine. The Technology Press/Wiley, Cambridge/New York
Yang YT, Bennet GN, San KY (1998) Genetic and metabolic engineering. EJB Electron J Biotechnol 1(3):134–141
You L (2004) Toward computational systems biology. Cell Biochem Biophys 40:167–184
Yuan JS, Galbraith DW, Dai SY et al (2008) Plant systems biology comes of age. Trends Plant Sci 13(4):165–171
Zulak KG et al (2007) Gene transcript and metabolite profiling of elicitor-induced opium poppy cell cultures reveals the coordinate regulation of primary and secondary metabolism. Planta 225:1085–1106
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer India
About this chapter
Cite this chapter
Bhardwaj, T., Somvanshi, P. (2015). Plant Systems Biology: Insights and Advancements. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_28
Download citation
DOI: https://doi.org/10.1007/978-81-322-2172-2_28
Published:
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2171-5
Online ISBN: 978-81-322-2172-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)