Publications

Jackson MDB, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017) Topological analysis  of multicellular complexity in the plant hypocotyl. eLife link

Topham AT, Taylor RE, Yan D, Nambara E, Bassel GW (2017) Temperature variability is integrated by a spatially-embedded decision-making center to break dormancy in Arabidopsis seeds. Proceedings of the National Academy of Sciences USA. link

F1000 Recommendation, Editor’s Choice in Science

Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. Journal of Experimental Botany 68 (7): 1531-1537. link

Stamm P, Topham AT, Mukhtar NK, Jackson MDB, Tome DA, Beynon JL, Bassel GW (2017) The transcription factor ATHB5 affects GA-mediated plasticity in hypocotyl cell growth during seed germination. Plant Physiology link

Stamm P, Strauss S, Montenegro-Johnson T, Smith RS, Bassel GW (2017) In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas. Plant Hormones: Methods in Molecular Biology link

Mitchell J, Johnston IG, Bassel GW (2016) Variability in seeds: biological, ecological, and agricultural implications. Journal of Experimental Botany link

Nieuwland J, Stamm P, Wen B, Randall R, Murray JAH, Bassel GW (2016) Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6. Scientific Reports 6:23586 link

Bassel GW (2016) To grow, or not to grow? Trends in Plant Science 21(6): 498–505 link

Hossain MR, Bassel GW, Pritchard JR, Sharma GP, Ford-Lloyd BV (2016) Trait specific expression profiling of salt stress responsive genes in diverse rice genotypes as determined by modified Significance Analysis of Microarrays. Frontiers in Plant Science 7: 567 link

Bassel GW, Smith RS (2016) Quantifying morphogenesis in plants in 4D. Current Opinion in Plant Biology 29: 87–94 link

Vesty EF, Saidi Y, Moody LA, Holloway D, Whitbread A, Needs S, Choudhary A, Burns B, McLeod D, Bradshaw SJ, Bae H, King BC, Bassel GW, Simonsen HT, Coates JC (2016) The decision to germinate is regulated by divergent molecular networks in spores and seeds. New Phytologist link

Finch-Savage WE, Bassel GW (2015) Seed vigour and crop establishment: extending performance beyond adaptation. Journal of Experimental Botany link

Abbas M, Berckhan S, Rooney D, Gibbs DJ, Vicente Conde J, Sousa Correia C, Bassel GW, Marin-de la Rosa N, León J, Alabadí D, Blázquez MA, Holdsworth MJ. (2015) Oxygen sensing coordinates photomorphogenesis to facilitate seedling survival. Current Biology 25(11), 1483–1488 link

Barbier de Reulle P, Routier-Kierzkowska A-L, Kierzkowski D, Bassel GW, Schupbach T, Tauriello G, Bajpai N, Strauss S, Weber A, Kiss A, Burian A, Hofthuis H, Sapala A, Lipowczan M, Heimlicher MB, Robinson S, Bayer EM, Basler K, Koumoutsakos P, Roeder AHK, Aegerter-Wilmsen T, Nakayama N, Tsiantis M, Hay A, Kwiatkowska D, Xenarios I, Kuhlmeier C, Smith RS (2015) MorphoGraphX: A platform for quantifying morphogenesis in 4D.  eLife 4, e05864 link

Montenegro-Johnson TD, Stamm P, Strauss S, Topham AT, Tsagris M, Wood ATA, Smith RS, Bassel GW (2015) Digital single cell analyses of plant organ development using 3DCellAtlas. The Plant Cell 27 (4), 1018-1033 link

F1000 Recommendation

Bassel GW (2015) Accuracy in Quantitative 3D Image Analysis. The Plant Cell 27 (4), 950-953 link

Bassel GW, Stamm P, Mosca G, Barbier de Reuille P, Gibbs DJ, Winter R, Janka A, Holdsworth MJ, Smith RS (2014) Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo.Proc Natl Acad Sci U S A. 111(23):8685-90 link

Gibbs DJ, Voß U, Harding SA, Fannon J, Moody LA, Yamada E, Swarup K, Nibau C, Bassel GW, Choudhary A, Lavenus J, Bradshaw SJ, Stekel DJ, Bennett MJ, Coates JC. (2014) AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis. New Phytologist.203 (4), 1194-1207 link

Yoshida S, Barbier de Reuille P, Lane B, Bassel GW, Prusinkiewicz P, Smith RS, Weijers D. (2014) Genetic Control of Plant Development by Overriding a Geometric Division Rule. Developmental Cell 29 (1): 75-87 link

Gibbs DJ, Md Isa N, Movahedi M, Lozano-Juste J, Mendiondo GM, Berckhan S, Marín-de la Rosa N, Vicente Conde J, Sousa Correia C, Pearce SP, Bassel GW, Hamali B, Talloji P, Tomé DF, Coego A, Beynon J, Alabadí D, Bachmair A, León J, Gray JE, Theodoulou FL, Holdsworth MJ (2014) Nitric Oxide Sensing in Plants Is Mediated by Proteolytic Control of Group VII ERF Transcription Factors. Molecular Cell 6;53(3):369-79 link

Dekkers BJ, Pearce S, van Bolderen-Veldkamp RP, Marshall A, Widera P, Gilbert J, Drost HG, Bassel GW, Müller K, King JR, Wood AT, Grosse I, Quint M, Krasnogor N, Leubner-Metzger G, Holdsworth MJ, Bentsink L. (2013) Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant Physiology 2013 163(1):205-15 link

Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I (2012) Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks. The Plant Cell 24 (10), 3859-3875 link

Gonzalez-Guzman M, Pizzio GA, Antoni R, Vera-Sirera F, Merilo E, Bassel GW, Fernández MA, Holdsworth MJ, Perez-Amador MA, Kollist H, Rodriguez PL. (2012) Arabidopsis PYR/PYL/RCAR Receptors Play a Major Role in Quantitative Regulation of Stomatal Aperture and Transcriptional Response to Abscisic Acid. The Plant Cell 24 (6), 2483-2496 link

Martínez-Andújar C, Pluskota WE, Bassel GW, Asahina M, Pupel P, Nguyen TT, Takeda-Kamiya N, Toubiana D, Bai B, Górecki RJ, Fait A, Yamaguchi S, Nonogaki H. (2012) The mechanisms of hormonal regulation of endosperm cap-specific gene expression in tomato seeds. The Plant Journal 71 (4), 575-586 link

Dekkers BJ, Willems L, Bassel GW, van Bolderen-Veldkamp RP, Ligterink W, Hilhorst HW, Bentsink L. (2012) Identification of reference genes for RT-qPCR expression analysis in Arabidopsis and tomato seeds. Plant and Cell Physiology 53:28-37 link

Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ (2011) Genome-wide network model capturing seed germination revealscoordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A. 108:9709-14    Press Release link

Bassel GW, Glaab E, Marquez J, Holdsworth MJ, Bacardit J. (2011) Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. The Plant Cell 23:3101-16.  link

Gibbs DJ, Lee SC, Isa NM, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, Holdsworth MJ. (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants.  Nature 479(7373):415-8. Nature Rev Mol Cel Biol Research Highlight Press Release link

Bassel GW, Holdsworth MJ, Provart NJ. (2011) Seed bioinformatics. Methods in Molecular Biology 773:403-19 link

Nonogaki H, Bassel GW, Bewley JD (2010) Germination – still a mystery. Plant Science 179: 574-581 link

Martin RC, Asahina M, Liu P-P, Kristof JR, Coppersmith JL, Pluskota WE, Bassel GW, Goloviznina NA, Nguyen TT, Martinez-Andujar C, Kumar A., Pupel P, Nonogaki H (2010) The microRNA156 and microRNA172 gene regulation cascades at post- germinative stages in Arabidopsis. Seed Science Research 20: 79-87 link

Martin RC, Asahina M, Liu P-P, Kristof JR, Coppersmith JL, Pluskota WE, Bassel GW, Goloviznina NA, Nguyen TT, Martinez-Andujar C, Kumar A., Pupel P, Nonogaki H (2010) The regulation of post-germinative transition from the cotyledon- to vegetative-leaf stages by microRNA-targeted SQUAMOSA PROMOTER- BINDING PROTEIN LIKE13 in Arabidopsis. Seed Science Research 20: 89-96 Link

Bassel GW, Provart NJ. (2009) Gene expression analyses for elucidating mechanisms of hormonal action in plants. Methods in Molecular Biology 495:21-37. link

Sliwinksa E, Bassel GW, Bewley JD (2009) Germination of Arabidopsis thaliana seeds is not completed as a result of elongation of the radicle but of the adjacent transition zone and lower hypocotyl. Journal of Experimental Botany 60: 3587-3594 link

Usadel B, Obayashi T, Mutwil M, Giorgi F, Bassel GW, Tanimoto M, Chow A, Persson S, Provart NJ (2009) Coexpression Tools for Plant Biology: Opportunities for Hypothesis Generation and Caveats. Plant Cell and Environment 32: 1633-1651 link

Bassel GW, Fung P, Chow TF, Foong JA, Provart NJ, Cutler SR (2008) Elucidating the germination transcriptional program using small molecules. Plant Physiology 147:143-155 link

Bassel GW, Mullen RT, Bewley JD (2008) procera is a putative DELLA mutant in tomato (Solanum lycopersicon): effects on the seed and vegetative plant. Journal of Experimental Botany 59: 585-593 link

Bassel GW, Mullen RT, Bewley JD (2006) ABI3 expression ceases following, but not during, germination of tomato and Arabidopsis seeds. Journal of Experimental Botany. 57: 1291-1297 link

Gong X, Bassel GW, Wang A, Bewley JD (2005) The Emergence of Embryos from Hard Seeds is Related to the Structure of the Cell Walls of the Micropylar Endosperm, and not to Endo-ß-mannanase Activity. Annals of Botany 96: 1165-1173 link

Bassel GW, Zielinska E, Mullen RT, Bewley JD (2004) Down-regulation of DELLA genes is not essential for germination of tomato, soybean and Arabidopsis seeds. Plant Physiology 136: 2782-2789. link

Bassel GW, Mullen RT, and Bewley JD (2001) α-Galactosidase is synthesized in tomato  seeds during development and is localized in protein storage vacuoles. Canadian Journal of Botany 79: 1417-1424. link