From systems biology to photosynthesis and whole-plant physiology: A conceptual model for integrating multi-scale networks

Plant Signaling and Behavior

Volumn 7, Issue 2, 2012, Pages

  Weston, David J ^a   Hanson, Paul J ^a,b   Norby, Richard J ^a,b   Tuskan, Gerald A ^a   Wullschleger, Stan D ^a,b  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Ecology; Modeling; Molecular biology; Networks; Photosynthesis; Transcriptomics

Indexed keywords

ALGORITHM; ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; HEAT; METHODOLOGY; PHOTOSYNTHESIS; PHYSIOLOGY; POPULUS; SOYBEAN; SYSTEMS BIOLOGY;

ALGORITHMS; ARABIDOPSIS; HOT TEMPERATURE; MODELS, BIOLOGICAL; PHOTOSYNTHESIS; POPULUS; SOYBEANS; SYSTEMS BIOLOGY;

EID: 84860995838     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: None     Document Type: Article

References (14)

1. Bennett M, Monk N. The flowering of systems approaches in plant and crop biology. New Phytol 2008; 179:567-8; PMID:18715319; http://dx.doi.org/10.1111/j.1469-8137.2008.02565.x
2. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, et al. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 2007; 50:347-63; PMID:17376166; http://dx.doi.org/10.1111/j.1365-313X.2007.03052.x
3. Weston DJ, Gunter LE, Rogers A, Wullschleger SD. Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Syst Biol 2008; 2:16; PMID:18248680; http://dx.doi.org/10.1186/1752-0509-2-16
4. Teusink B, Westerhoff HV, Bruggeman FJ. Comparative systems biology: from bacteria to man. Wiley Interdiscip Rev Syst Biol Med 2010; 2:518-32; PMID:20836045
5. Weston DJ, Karve AA, Gunter LE, Jawdy SS, Yang X, Allen SM, et al. Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max. Plant Cell Environ 2011; 34:1488-506; PMID:21554326; http://dx.doi.org/10.1111/j.1365-3040.2011.02347.x
6. Dong J, Horvath S. Understanding network concepts in modules. BMC Syst Biol 2007; 1:24; PMID: 17547772; http://dx.doi.org/10.1186/1752-0509-1-24
7. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005; 4:e17; PMID:16646834; http://dx.doi.org/10.2202/1544-6115.1128
8. Lucas M, Laplaze L, Bennett MJ. Plant systems biology: network matters. Plant Cell Environ 2011; 34: 535-53; PMID:21309807; http://dx.doi.org/10.1111/j.1365-3040.2010.02273.x
9. Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 2007; 8:R7; PMID:17217541; http://dx.doi.org/10.1186/gb-2007-8-1-r7
10. Bohnert HJ, Gong Q, Li P, Ma S. Unraveling abiotic stress tolerance mechanisms-getting genomics going. Curr Opin Plant Biol 2006; 9:180-8; PMID:16458043; http://dx.doi.org/10.1016/j.pbi.2006.01.003
11. van Hulten M, Pelser M, van Loon LC, Pieterse CML, Ton J. Costs and benefits of priming for defense in Arabidopsis. Proc Natl Acad Sci U S A 2006; 103: 5602-7; PMID:16565218; http://dx.doi.org/10.1073/pnas.0510213103
12. Yang ZJ, Midmore DJ. Modelling plant resource allocation and growth partitioning in response to environmental heterogeneity. Ecol Modell 2005; 181: 59-77; http://dx.doi.org/10.1016/j.ecolmodel.2004.06.023
13. Norby RJ, Zak DR. Ecological lessons from free-air CO2 enrichment (FACE) experiments. Annu Rev Ecol Evol Syst 2011; 42:181-203; http://dx.doi.org/10.1146/annurev-ecolsys-102209-144647
14. Litton CM, Raich JW, Ryan MG. Carbon allocation in forest ecosystems. Glob Change Biol 2007; 13: 2089-109; http://dx.doi.org/10.1111/j.1365-2486.2007.01420.x