- Middleton, A.M., Úbeda Tomás, S., Griffiths, J., Holman, T., Hedden, P., Thomas, S.G., Phillips, A.L., Holdsworth, M.J., Bennett, M.J., King, J.R., Owen, M.R. (2012) Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signalling. PNAS (USA), published ahead of print April 20, 2012, doi:10.1073/pnas.1113666109.

Mathematical modelling approaches used to understand GA biosynthesis, perception and signalling. CPIB paper.

- Bailey-Serres, J., Fukao, T., Gibbs, D.J., Holdsworth, M.J., Lee, S.C., Licausi, F., Perata, P., Voesenek, L.A.C.J., van Dongen, J.T. (2012) Making sense of low oxygen sensing. Trends in Plant Science, 17, 1360-1385. (Review article)

Here we review current knowledge in the area of plant low oxygen sensing, focussing on our recent discoveries of the role of the N-end rule pathway in regulating low-oxygen sensing through Group VII ERF transcription factors.

- Gibbs, D.J., Lee, S.C., Isa, N.M., Gramuglia, S., Fukao, T., Bassel, G.W., Sousa Correia, C., Corbineau, F., Theodoulou, F.L., Bailey-Serres, J., Holdsworth, M.J. (2011) Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature, 479, 415–418.

We identify a molecular mechanism through which low oxygen (hypoxia) is sensed in plants, a determinant of crop survival of root waterlogging and foliage submergence. This mechanism relates stability of hypoxia-associated transcription factors to the N-end rule pathway of targeted proteolysis, thus identifying the first plant N-end rule pathway substrates. Stability is related to the sequence of the protein N-terminus. Rice orthologue proteins, including the key regulator of submergence tolerance, exhibit different stabilities due to N-terminal variations. This mechanism is homeostatic: Prior to hypoxia the substrates are degraded, during hypoxia they accumulate, and following return to normoxia they decline.

- Bassel, G.W., Glaab, E., Marquez, J., Holdsworth, M.J., Bacardit, J. (2011) Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Datasets. The Plant Cell, 23: 3101-3116.

A genome-wide network model generated using rule-based machine learning. Functional associations between genes are established by the collective ability to come together and form "rules" that accurately predict developmnetal outcome in seeds.

- Dupeux, F., Santiago, J., Betz, K., Twycross, J., Park, S-Y., Rodriguez, L., Gonzalez-Guzman, M., Jensen, M., Krasnogor, N., Holdsworth, M.J., Blackledge, M., Cutler, S., Rodriguez P. and Marquez, J. (2011) A Thermodynamic Switch Modulates Abscisic Acid Receptor Sensitivity. EMBO Journal 30: 4171 - 4184.

In this paper we significantly advance understanding of the role that ABA receptor dimerization plays in the modulation of the ABA response. We develop and validate a computational model of the interaction of receptors, hormone and phosphatases. Analysis of the dynamics of this model shows that competition for ABA binding between monomeric and dimeric receptors leads to preferential activation of monomeric receptors. Monomeric receptors provide strong and rapid response to ABA, while dimeric receptors provide weaker and slower response. By varying relative concentrations receptors, the overall ABA response can be modulated.

- Bassel, G.W., Holdsworth, M.J., Provart, N. (2011) Seed Bioinformatics. Methods in Molecular Biology 773 (8) 403-419, DOI: 10.1007/978-1-61779-231-1_23.

In this article we discuss the current tools available for seed bioinformatics.

- Pearce, S.P., King, J.R., Holdsworth, M.J. (2011) Axisymmetric indentation of curved elastic membranes by a convex rigid indenter. International Journal of Non-Linear Mechanics, 46 (9) 1128-1138

Using germination (specifically the biomechanics of endosperm rupture) as an example, this paper looks at how an elastic membrane deforms when a rigid indenter is pushed into it. The membrane is allowed to have an arbitrary shape and elastic properties, while the indenter may also take any convex shape.

- Bassel, G.W., Lan, H., Glaab, E., Gibbs, D.J., Gerjets, T., Krasnogor, N., Bonner, A.J., Holdsworth, M.J., Provart, N.J. (2011) Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. PNAS (USA), 108 (23) 9709-9714.

Front cover of PNAS features the SeedNet network.
In this manuscript we generated and analysed a genome-wide network model using publicly available data that describes global transcriptional interactions in Arabidopsis seeds that we term “SeedNet”, and show that SeedNet represents a step-change in our understanding of the regulation of germination.

- Lucas, M., Swarup, R., Paponov, I.A., Swarup, K., Casimiro, I., Lake, D., Péret, B., Zappala, S., Mairhofer, S., Whitworth, M., Wang, J.H., Ljung, K., Marchant, A., Sandberg, G., Holdsworth, M.J., Palme, K., Pridmore, T., Mooney, S., Bennett, M.J. (2011) SHORT-ROOT regulates primary, lateral and adventitious root development in Arabidopsis. Plant Physiology, 155: 384-398

- Holman, T.J, Wilson, M.H., Kenobi, K., Dryden, I.L., Hodgman, T.C., Wood, A.T.A., Holdsworth M. J. (2010) Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. Plant Methods, 6:9

- Gerjets, T., Scholefield, D., Foulkes, M.J., Lenton J.R., Holdsworth, M.J. (2010) An analysis of dormancy, ABA responsiveness, after-ripening and pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.) caryopses. Journal of Experimental Botany, 61(2): 597-607

Front cover of The Journal of Experimental Botany features wheat ears showing Pre-Harvest Sprouting (PHS).

- Foulkes M.J., Hawkesford M.J., Barraclough P.B., Holdsworth M.J., Kerr S., Kightly S., Shewry P.R. (2009) Identifying traits to improve the nitrogen economy of wheat: recent advances and future prospects. Field Crops Research, 114(3): 329-342. Review Article.

- Holman, T., Jones, P.J., Russell, L., Medurst, A., Úbeda Tomás, S., Talloji, P., Marquez, J., Schmuths, H., Tung, S-A., Taylor, I., Footitt, S., Bachmair, A., Theodoulou, F., Holdsworth, M.J. (2009) The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. PNAS (USA), 106(11): 4549-4554.

- De Marcos Lousa, C., Dietrich, D., Johnson, B., Baldwin, S.A., Holdsworth, M.J., Theodoulou, F.L., Baker, A. (2009) The NBDs that wouldn't die: A cautionary tale of the use of isolated nucleotide binding domains of ABC transporters. Commun Integr Biol, 2(2): 97-9. Opinion Article.

- Dietrich, D., Schmuths, H., DeMarcos L. C., Baldwin, J., Baldwin, S., Baker, A., Theodoulou, F., Holdsworth, M. (2009) Mutations in the Arabidopsis ABC transporter COMATOSE allow differentiation between multiple functions in planta: insights from an allelic series. Mol Biol Cell, 20: 530 –543.

- Holdsworth, M.J., Soppe, W.S., Bentsink, L. (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New phytologist, 179(1), 33-54. Invited Tansley Review.

- Holdsworth, M.J., Finch-Savage, W.E., Grappin, P., Job, D. (2008) Post-genomics dissection of seed dormancy and germination. Trends in Plant Science, 13(1): 7-13. Opinion Article.

- Carrera, E., Holman, T., Medhurst, A., Dietrich, D., Footitt, S., Theodoulou, F.L., Holdsworth, M.J. (2008) Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. The Plant Journal 53(2): 214-224.

Front cover of The Plant Journal features the output of the TAGGIT ontological classification of seed transcriptomes in different germinative states.