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Items: 40

1.

Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis.

Johnston IG, Bassel GW.

J R Soc Interface. 2018 Apr;15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

2.

Bridging Scales in Plant Biology Using Network Science.

Duran-Nebreda S, Bassel GW.

Trends Plant Sci. 2017 Dec;22(12):1001-1003. doi: 10.1016/j.tplants.2017.09.017. Epub 2017 Oct 10.

PMID:
29029828
3.

Network-based approaches to quantify multicellular development.

Jackson MDB, Duran-Nebreda S, Bassel GW.

J R Soc Interface. 2017 Oct;14(135). pii: 20170484. doi: 10.1098/rsif.2017.0484. Epub 2017 Oct 11. Review.

4.

Topological analysis of multicellular complexity in the plant hypocotyl.

Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW.

Elife. 2017 Jul 6;6. pii: e26023. doi: 10.7554/eLife.26023.

5.

Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds.

Topham AT, Taylor RE, Yan D, Nambara E, Johnston IG, Bassel GW.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6629-6634. doi: 10.1073/pnas.1704745114. Epub 2017 Jun 5.

6.

Quantitative analysis of the 3D cell shape changes driving soybean germination.

Souza NM, Topham AT, Bassel GW.

J Exp Bot. 2017 Mar 1;68(7):1531-1537. doi: 10.1093/jxb/erx048.

7.

The Transcription Factor ATHB5 Affects GA-Mediated Plasticity in Hypocotyl Cell Growth during Seed Germination.

Stamm P, Topham AT, Mukhtar NK, Jackson MD, Tomé DF, Beynon JL, Bassel GW.

Plant Physiol. 2017 Jan;173(1):907-917. doi: 10.1104/pp.16.01099. Epub 2016 Nov 21.

8.

In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas.

Stamm P, Strauss S, Montenegro-Johnson TD, Smith R, Bassel GW.

Methods Mol Biol. 2017;1497:99-123.

PMID:
27864762
9.

Variability in seeds: biological, ecological, and agricultural implications.

Mitchell J, Johnston IG, Bassel GW.

J Exp Bot. 2017 Feb 1;68(4):809-817. doi: 10.1093/jxb/erw397. Review.

PMID:
27784726
10.

The decision to germinate is regulated by divergent molecular networks in spores and seeds.

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.

New Phytol. 2016 Aug;211(3):952-66. doi: 10.1111/nph.14018. Epub 2016 Jun 3.

11.

Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays.

Hossain MR, Bassel GW, Pritchard J, Sharma GP, Ford-Lloyd BV.

Front Plant Sci. 2016 May 3;7:567. doi: 10.3389/fpls.2016.00567. eCollection 2016.

12.

Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6.

Nieuwland J, Stamm P, Wen B, Randall RS, Murray JA, Bassel GW.

Sci Rep. 2016 Mar 29;6:23586. doi: 10.1038/srep23586.

13.

To Grow or not to Grow?

Bassel GW.

Trends Plant Sci. 2016 Jun;21(6):498-505. doi: 10.1016/j.tplants.2016.02.001. Epub 2016 Feb 28. Review.

PMID:
26934952
14.

Quantifying morphogenesis in plants in 4D.

Bassel GW, Smith RS.

Curr Opin Plant Biol. 2016 Feb;29:87-94. doi: 10.1016/j.pbi.2015.11.005. Epub 2016 Jan 1. Review.

15.

Seed vigour and crop establishment: extending performance beyond adaptation.

Finch-Savage WE, Bassel GW.

J Exp Bot. 2016 Feb;67(3):567-91. doi: 10.1093/jxb/erv490. Epub 2015 Nov 19. Review.

PMID:
26585226
16.

Oxygen sensing coordinates photomorphogenesis to facilitate seedling survival.

Abbas M, Berckhan S, Rooney DJ, Gibbs DJ, Vicente Conde J, Sousa Correia C, Bassel GW, Marín-de la Rosa N, León J, Alabadí D, Blázquez MA, Holdsworth MJ.

Curr Biol. 2015 Jun 1;25(11):1483-8. doi: 10.1016/j.cub.2015.03.060. Epub 2015 May 14.

17.

MorphoGraphX: A platform for quantifying morphogenesis in 4D.

Barbier de Reuille P, Routier-Kierzkowska AL, Kierzkowski D, Bassel GW, Schüpbach T, Tauriello G, Bajpai N, Strauss S, Weber A, Kiss A, Burian A, Hofhuis H, Sapala A, Lipowczan M, Heimlicher MB, Robinson S, Bayer EM, Basler K, Koumoutsakos P, Roeder AH, Aegerter-Wilmsen T, Nakayama N, Tsiantis M, Hay A, Kwiatkowska D, Xenarios I, Kuhlemeier C, Smith RS.

Elife. 2015 May 6;4:05864. doi: 10.7554/eLife.05864.

18.

Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas.

Montenegro-Johnson TD, Stamm P, Strauss S, Topham AT, Tsagris M, Wood AT, Smith RS, Bassel GW.

Plant Cell. 2015 Apr;27(4):1018-33. doi: 10.1105/tpc.15.00175. Epub 2015 Apr 21.

19.

Accuracy in Quantitative 3D Image Analysis.

Bassel GW.

Plant Cell. 2015 Apr;27(4):950-3. doi: 10.1105/tpc.114.135061. Epub 2015 Mar 24.

20.

Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo.

Bassel GW, Stamm P, Mosca G, Barbier de Reuille P, Gibbs DJ, Winter R, Janka A, Holdsworth MJ, Smith RS.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8685-90. doi: 10.1073/pnas.1404616111. Epub 2014 May 27.

21.

AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis.

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.

New Phytol. 2014 Sep;203(4):1194-207. doi: 10.1111/nph.12879. Epub 2014 Jun 6.

22.

Genetic control of plant development by overriding a geometric division rule.

Yoshida S, Barbier de Reuille P, Lane B, Bassel GW, Prusinkiewicz P, Smith RS, Weijers D.

Dev Cell. 2014 Apr 14;29(1):75-87. doi: 10.1016/j.devcel.2014.02.002. Epub 2014 Mar 27.

23.

Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors.

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.

Mol Cell. 2014 Feb 6;53(3):369-79. doi: 10.1016/j.molcel.2013.12.020. Epub 2014 Jan 23.

24.

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination.

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.

Plant Physiol. 2013 Sep;163(1):205-15. doi: 10.1104/pp.113.223511. Epub 2013 Jul 15.

25.

Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks.

Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I.

Plant Cell. 2012 Oct;24(10):3859-75. doi: 10.1105/tpc.112.100776. Epub 2012 Oct 30. Review.

26.

Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatal aperture and transcriptional response to abscisic acid.

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.

Plant Cell. 2012 Jun;24(6):2483-96. doi: 10.1105/tpc.112.098574. Epub 2012 Jun 26.

27.

Mechanisms of hormonal regulation of endosperm cap-specific gene expression in tomato seeds.

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.

Plant J. 2012 Aug;71(4):575-86. doi: 10.1111/j.1365-313X.2012.05010.x. Epub 2012 Jun 11.

28.

Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants.

Gibbs DJ, Lee SC, Isa NM, Gramuglia S, Fukao T, Bassel GW, Correia CS, Corbineau F, Theodoulou FL, Bailey-Serres J, Holdsworth MJ.

Nature. 2011 Oct 23;479(7373):415-8. doi: 10.1038/nature10534.

29.

Seed bioinformatics.

Bassel GW, Holdsworth MJ, Provart NJ.

Methods Mol Biol. 2011;773:403-19. doi: 10.1007/978-1-61779-231-1_23.

PMID:
21898268
30.

Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets.

Bassel GW, Glaab E, Marquez J, Holdsworth MJ, Bacardit J.

Plant Cell. 2011 Sep;23(9):3101-16. doi: 10.1105/tpc.111.088153. Epub 2011 Sep 6.

31.

Identification of reference genes for RT-qPCR expression analysis in Arabidopsis and tomato seeds.

Dekkers BJ, Willems L, Bassel GW, van Bolderen-Veldkamp RP, Ligterink W, Hilhorst HW, Bentsink L.

Plant Cell Physiol. 2012 Jan;53(1):28-37. doi: 10.1093/pcp/pcr113. Epub 2011 Aug 18.

PMID:
21852359
32.

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions.

Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9709-14. doi: 10.1073/pnas.1100958108. Epub 2011 May 18.

33.

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.

Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ.

Plant Cell Environ. 2009 Dec;32(12):1633-51. doi: 10.1111/j.1365-3040.2009.02040.x. Epub 2009 Aug 27. Review.

34.

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.

Sliwinska E, Bassel GW, Bewley JD.

J Exp Bot. 2009;60(12):3587-94. doi: 10.1093/jxb/erp203. Epub 2009 Jul 20.

PMID:
19620183
35.

Gene expression analyses for elucidating mechanisms of hormonal action in plants.

Bassel GW, Provart NJ.

Methods Mol Biol. 2009;495:21-37. doi: 10.1007/978-1-59745-477-3_3.

PMID:
19085149
36.

Elucidating the germination transcriptional program using small molecules.

Bassel GW, Fung P, Chow TF, Foong JA, Provart NJ, Cutler SR.

Plant Physiol. 2008 May;147(1):143-55. doi: 10.1104/pp.107.110841. Epub 2008 Mar 21.

37.

Procera is a putative DELLA mutant in tomato (Solanum lycopersicum): effects on the seed and vegetative plant.

Bassel GW, Mullen RT, Bewley JD.

J Exp Bot. 2008;59(3):585-93. doi: 10.1093/jxb/erm354. Epub 2008 Feb 3.

PMID:
18250077
38.

ABI3 expression ceases following, but not during, germination of tomato and Arabidopsis seeds.

Bassel GW, Mullen RT, Bewley JD.

J Exp Bot. 2006;57(6):1291-7. Epub 2006 Mar 10.

PMID:
16531465
39.
40.

Down-regulation of DELLA genes is not essential for germination of tomato, soybean, and Arabidopsis seeds.

Bassel GW, Zielinska E, Mullen RT, Bewley JD.

Plant Physiol. 2004 Sep;136(1):2782-9. Epub 2004 Sep 3.

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