Kalve S, De Vos D, Beemster GT. Leaf development: a cellular perspective. Front Plant Sci. 2014;5:362.
Article
PubMed Central
PubMed
Google Scholar
Rodriguez RE, Debernardi JM, Palatnik JF. Morphogenesis of simple leaves: regulation of leaf size and shape. Wiley Interdiscip Rev Dev Biol. 2014;3(1):41–57.
Article
PubMed
Google Scholar
Cheng Y, Dai X, Zhao Y. Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. Plant Cell. 2007;19(8):2430–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reinhardt D, Pesce ER, Stieger P, Mandel T, Baltensperger K, Bennett M, et al. Regulation of phyllotaxis by polar auxin transport. Nature. 2003;426(6964):255–60.
Article
CAS
PubMed
Google Scholar
Byrne ME, Barley R, Curtis M, Arroyo JM, Dunham M, Hudson A, Martienssen RA. Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature. 2000;408(6815):967–71.
Article
CAS
PubMed
Google Scholar
Semiarti E, Ueno Y, Tsukaya H, Iwakawa H, Machida C, Machida Y. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves. Development. 2001;128(10):1771–83.
CAS
PubMed
Google Scholar
Zadnikova P, Simon R. How boundaries control plant development. Curr Opin Plant Biol. 2014;17:116–25.
Article
PubMed
Google Scholar
Szakonyi D, Moschopoulos A, Byrne ME. Perspectives on leaf dorsoventral polarity. J Plant Res. 2010;123(3):281–90.
Article
PubMed
Google Scholar
Blomme J, Inze D, Gonzalez N. The cell-cycle interactome: a source of growth regulators? J Exp Bot. 2014;65(10):2715–30.
Article
CAS
PubMed
Google Scholar
Lau OS, Bergmann DC. Stomatal development: a plant’s perspective on cell polarity, cell fate transitions and intercellular communication. Development. 2012;139(20):3683–92.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pattanaik S, Patra B, Singh SK, Yuan L. An overview of the gene regulatory network controlling trichome development in the model plant, Arabidopsis. Front Plant Sci. 2014;5:259.
Article
PubMed Central
PubMed
Google Scholar
Gentry M, Hennig L. Remodelling chromatin to shape development of plants. Exp Cell Res. 2014;321(1):40–6.
Article
CAS
PubMed
Google Scholar
Tsukaya H, Byrne ME, Horiguchi G, Sugiyama M, Van Lijsebettens M, Lenhard M. How do ‘housekeeping’ genes control organogenesis?—Unexpected new findings on the role of housekeeping genes in cell and organ differentiation. J Plant Res. 2013;126(1):3–15.
Article
CAS
PubMed
Google Scholar
Kidner CA. The many roles of small RNAs in leaf development. J Genet Genomics. 2010;37(1):13–21.
Article
CAS
PubMed
Google Scholar
Kurepin LV, Pharis RP. Light signaling and the phytohormonal regulation of shoot growth. Plant Sci. 2014;229:280–9.
Article
CAS
PubMed
Google Scholar
Perez-Perez JM, Candela H, Robles P, Quesada V, Ponce MR, Micol JL. Lessons from a search for leaf mutants in Arabidopsis thaliana. Int J Dev Biol. 2009;53(8–10):1623–34.
Article
CAS
PubMed
Google Scholar
PHENOPSIS DB. http://bioweb.supagro.inra.fr/phenopsis/. Accessed 08 Nov 2015.
Fabre J, Dauzat M, Negre V, Wuyts N, Tireau A, Gennari E, et al. PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. BMC Plant Biol. 2011;11:77.
Article
PubMed Central
PubMed
Google Scholar
Granier C, Aguirrezabal L, Chenu K, Cookson SJ, Dauzat M, Hamard P, et al. 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 Phytol. 2006;169(3):623–35.
Article
PubMed
Google Scholar
Wilson-Sanchez D, Rubio-Diaz S, Munoz-Viana R, Perez-Perez JM, Jover-Gil S, Ponce MR, et al. Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants. Plant J. 2014;79(5):878–91.
Article
CAS
PubMed
Google Scholar
PhenoLeaf. http://genetics.umh.es/phenoleaf/index.php. Accessed 08 Nov 2015.
Das A, Bucksch A, Price CA, Weitz JS. ClearedLeavesDB: an online database of cleared plant leaf images. Plant Methods. 2014;10(1):8.
Article
PubMed Central
PubMed
Google Scholar
ClearedLeavesDB. http://clearedleavesdb.org/. Accessed 08 Nov 2015.
Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, et al. LSD: a leaf senescence database. Nucl Acids Res. 2011;39(Database issue):D1103–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li Z, Zhao Y, Liu X, Peng J, Guo H, Luo J. LSD 2.0: an update of the leaf senescence database. Nucl Acids Res. 2014;42:D1200–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Leaf Senescence Database. http://www.eplantsenescence.org/. Accessed 08 Nov 2015.
Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Buhlmann P, Hennig L, et al. Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol. 2012;8:606.
Article
PubMed Central
PubMed
Google Scholar
AGRON-OMICS data integration and data sharing portal. https://agronomics.ethz.ch/. Accessed 08 Nov 2015.
Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Sáez R, et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining. Curr Plant Biol. 2015;2015(2):1–11.
Article
Google Scholar
Ogren PV. Knowtator: a protégé plug-in for annotated corpus construction. In: Proceedings of the 2006 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology: companion volume: demonstrations; New York, New York. 1225791: Association for Computational Linguistics; 2006. p. 273–275.
Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, et al. Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genomics. 2005;6(7–8):388–97.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, et al. The BRENDA tissue ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucl Acids Res. 2011;39(Database issue):D507–13.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol. 2005;6(1):R8.
Article
PubMed Central
PubMed
Google Scholar
Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, et al. Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genomics. 2002;3(2):132–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, et al. The HUPO PSI’s molecular interaction format—a community standard for the representation of protein interaction data. Nat Biotechnol. 2004;22(2):177–83.
Article
CAS
PubMed
Google Scholar
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, et al. Gramene database in 2010: updates and extensions. Nucl Acids Res. 2011;39(Database issue):D1085–94.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucl Acids Res. 2012;40(Database issue):D1202–10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vanhaeren H, Inze D, Gonzalez N. Plant growth beyond limits. Trends Plant Sci. 2016;21(2):102–9.
Article
CAS
PubMed
Google Scholar
Krajewski P, Chen D, Cwiek H, van Dijk AD, Fiorani F, Kersey P, et al. Towards recommendations for metadata and data handling in plant phenotyping. J Exp Bot. 2015;66(18):5417–27.
Article
PubMed
Google Scholar
Miyoshi NS, Pinheiro DG, Silva WA Jr, Felipe JC. Computational framework to support integration of biomolecular and clinical data within a translational approach. BMC Bioinformatics. 2013;14:180.
Article
PubMed Central
PubMed
Google Scholar