References

      Articles of interest suggested by project partners  NEW!

• Bensmihen S, Hanna AI, Langlade NB, Miocl JL, Bangham A, Coen ES (2008) Mutational spaces for leaf shape and size. HSFP Journal. DOI: 10.2976/1.2836738
• Weight C, Parnham D, Waites R (2007) LeafAnalyser: a computational method for rapid and large-scale analyses of leaf shape variation. Plant J 53(3):578-86 PMID: 18028263

      Workshop on "Ontologies, Standards and Best Practice", Gent, May 2007: suggested readings

• Aitken S, Korf R, Webber B, Bard J (2005) COBrA: a bio-ontology editor. Bioinformatics 21: 825-826. PMID: 15513995
• Bard JB, Rhee SY (2004) Ontologies in biology: design, applications and future challenges. Nat Rev Genet 5(3):213-22 PMID: 14970823
• Blake JA, Bult CJ (2006) Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 39: 314-320 PMID: 16564748
• Brazma A, Krestyaninova M, Sarkans U (2006) Standards for systems biology. Nature Rev Genet 7(8):593-605 PMID: 16847461
• Chandrasekaran, Josephson JR, Benjamins VR (1999) What are ontologies, and why do we need them? IEEE Intelligent Systems, 14: 20-26
• Cote RG, Jones P, Apweiler R, Hermjakob H (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics. 28;7:97. PMID: 16507094
• Day-Richter J, Harris MA, Haendel M, Lewis S (2007) OBO-Edit - An Ontology Editor for Biologists. Bioinformatics. 2007 Jun 1; [Epub ahead of print] PMID: 17545183
• Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J-H, Hunter PJ, Juty ES, Kasberger JL, A. Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD Stelling J, Takahashi K, Tomita M, Wagner J, Wang J(2003) The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531.
• Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 143(2):587-99. PMID: 17142475
• Kawas E, Senger M, Wilkinson MD (2006) BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics. 30;7:523. PMID: 17137515
• Kersey P, Apweiler R (2006) Linking publication, gene and protein data. Nature Cell Biol 8(11):1183-1189 PMID: 17060904
• Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A (2007) ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35:D747-50. PMID: 17132828
• Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, McCouch S (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol. 142(2):414-28 PMID: 16905665
• Rhee SY, Dickerson J, Xu D (2006) Bioinformatics and its applications in plant biology, Annu Rev Plant Biol 57:335-360 PMID: 16669765
• Rosse C, Mejino JL Jr (2003) A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 36(6):478-500 PMID: 14759820
• Schulz S, Kumar A, Bittner T (2006) Biomedical ontologies: what part-of is and isn't. J Biomed Inform. 39(3):350-61 PMID: 16442850
• Soldatova LN, King RD (2005) Are the current ontologies in biology good ontologies? Nat Biotechnol. 23(9):1095-8. PMID: 16151402
• Spear AD Ontology for the twenty first century: An introduction with recommendations. http://www.ifomis.uni-saarland.de/bfo/manual/manual.pdf
• Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37(6):914-39. PMID: 14996223
• Usadel B, Nagel A, Steinhauser D, Gibon Y, Blasing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M. (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 18;7: 535. PMID: 17176458
• Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007;8(3):R39. PMID: 17367534
• Wilkinson M, Schoof H, Ernst R, Haase D (2005) BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case. Plant Physiol. 2005 138(1):5-17 PMID: 15888673
• Yu AC (2006) Methods in biomedical ontology. J Biomed Inform. 39(3):252-66. PMID: 16387553
• Zimmermann P, Hennig L, Gruissem W (2005) Gene-expression analysis and network discovery using Genevestigator. Trends Plant Sci 10: 407–409

      Workshop on "Plant Growth Phenotyping", Montpellier, July 2007: suggested readings

• Aguirrezabal L, Bouchier-Combaud S, Radziejwoski A, Dauzat M, Cookson SJ, Granier C (2006) Plasticity to soil water deficit in Arabidopsis thaliana: dissection of leaf development into  underlying growth dynamic and cellular variables reveals invisible phenotypes. Plant, Cell and Environment, 29: 2216-2227.
• Granier C, Aguirrezabal L, Chenu K, Cookson SJ, Dauzat M, Hamard P, Thioux JJ, Rolland G, Bouchier-Combaud S, Lebaudy A, Muller B, Simonneau T & Tardieu F. (2006). PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytologist 169 (3): 623-635.
• Gutiérrez RA, Shasha DE, Coruzzi GM (2005) Systems biology for the virtual plant. Plant Physiol. 2005 Jun;138(2):550-4.
• Kavanova M, Lattanzi FA, Grimoldi AA, Schnyder H (2006) Phosphorus deficiency decreases cell division and elongation in grass leaves. Plant Physiol. 141: 766-775
• Laufs P, Grandjean O, Jonak C, Kiêu K, Traas J. (1998) Cellular parameters of the shoot apical meristem in Arabidopsis. The Plant Cell 10(8):1375-90.
• Lee K, Avondo J, Morrison H, Blot L, Stark M, Sharpe J, Bangham A, Coen E (2006) Visualizing plant development and gene expression in three dimensions using optical projection tomography. The Plant Cell 18:2145-2156.
• Poorter H (2002) Plant growth and carbon economy. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [doi: 10.1038/npg.els.0003200]
• Merks RMH, Van de Peer Y, Inzé D, Beemster GTS (2007) Canalization without flux sensors: a traveling-wave hypothesis. Trends in Plant Science 12:384-390.
• Reddy GV, Gordon SP, Meyerowitz EM (2007) Unravelling developmental dynamics: transient intervention and live imaging in plants. Nature Rev. Mol. Cell. Biol. 8(6):491-501.
• Sadok W, Naudin Ph, Boussuge B, Muller B, Welcker C, Tardieu F (2007) Leaf growth rate per unit thermal time follows QTL-dependent daily patterns in hundreds of maize lines under naturally fluctuating conditions. Plant Cell and Environment 30, 135–146.
• Schmundt D, Stitt M, Jähne B, Schurr U (1998) Quantitative analysis of the local rates of growth of dicot leaves at a high temporal and spatial resolution, using image sequence analysis. The Plant Journal 16 (4), 505–514.
  
• Walter A, Scharr H, Gilmer F, Zierer R, Nagel KA, Ernst M, Wiese A, Virnich O, Christ MM, Uhlig B, Jünger S, Schurr U (2006) Dynamics of seedling growth acclimation towards altered light conditions can be quantified via GROWSCREEN: a setup and procedure designed for rapid optical phenotyping of different plant species. New Phytologist 174: 447-455.
• Wiese, A, Christ, MM, Virnich O, Schurr U, Walter A (2007) Spatio-temporal leaf growth patterns of Arabidopsis thaliana and evidence for sugar control of the diel leaf growth cycle. New Phytologist 174 (2007), 752 – 761.
• Wyrzykowska J, Pien S, Shen WH, Fleming AJ (2002) Manipulation of leaf shape by modulation of cell division. Development 129: 957-964