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A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.

Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ.

Gigascience. 2019 May 1;8(5). pii: giz056. doi: 10.1093/gigascience/giz056.


Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis.

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ.

FEBS Lett. 2019 Feb;593(3):319-338. doi: 10.1002/1873-3468.13311. Epub 2018 Dec 28.


Dawn and photoperiod sensing by phytochrome A.

Seaton DD, Toledo-Ortiz G, Ganpudi A, Kubota A, Imaizumi T, Halliday KJ.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10523-10528. doi: 10.1073/pnas.1803398115. Epub 2018 Sep 25.


Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis.

Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E.

Curr Biol. 2018 Jan 22;28(2):311-318.e5. doi: 10.1016/j.cub.2017.12.021. Epub 2018 Jan 11.


Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity.

Krahmer J, Ganpudi A, Abbas A, Romanowski A, Halliday KJ.

Plant Physiol. 2018 Feb;176(2):1039-1048. doi: 10.1104/pp.17.01437. Epub 2017 Dec 18. Review. No abstract available.


Light-sensing phytochromes feel the heat.

Halliday KJ, Davis SJ.

Science. 2016 Nov 18;354(6314):832-833. No abstract available.


Photoreceptor effects on plant biomass, resource allocation, and metabolic state.

Yang D, Seaton DD, Krahmer J, Halliday KJ.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7667-72. doi: 10.1073/pnas.1601309113. Epub 2016 Jun 21.


Molecular and genetic control of plant thermomorphogenesis.

Quint M, Delker C, Franklin KA, Wigge PA, Halliday KJ, van Zanten M.

Nat Plants. 2016 Jan 6;2:15190. doi: 10.1038/nplants.2015.190. Review.


Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.

Flis A, Fernández AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ.

Open Biol. 2015 Oct;5(10). pii: 150042. doi: 10.1098/rsob.150042.


The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana.

Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ.

Nat Commun. 2015 Jul 6;6:7641. doi: 10.1038/ncomms8641.


Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors.

Bou-Torrent J, Toledo-Ortiz G, Ortiz-Alcaide M, Cifuentes-Esquivel N, Halliday KJ, Martinez-García JF, Rodriguez-Concepcion M.

Plant Physiol. 2015 Nov;169(3):1584-94. doi: 10.1104/pp.15.00552. Epub 2015 Jun 16.


Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature.

Seaton DD, Smith RW, Song YH, MacGregor DR, Stewart K, Steel G, Foreman J, Penfield S, Imaizumi T, Millar AJ, Halliday KJ.

Mol Syst Biol. 2015 Jan 19;11(1):776. doi: 10.15252/msb.20145766.


Arabidopsis cell expansion is controlled by a photothermal switch.

Johansson H, Jones HJ, Foreman J, Hemsted JR, Stewart K, Grima R, Halliday KJ.

Nat Commun. 2014 Sep 26;5:4848. doi: 10.1038/ncomms5848.


Multiscale digital Arabidopsis predicts individual organ and whole-organism growth.

Chew YH, Wenden B, Flis A, Mengin V, Taylor J, Davey CL, Tindal C, Thomas H, Ougham HJ, de Reffye P, Stitt M, Williams M, Muetzelfeldt R, Halliday KJ, Millar AJ.

Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4127-36. doi: 10.1073/pnas.1410238111. Epub 2014 Sep 2. Erratum in: Proc Natl Acad Sci U S A. 2015 May 12;112(19):E2556.


The HY5-PIF regulatory module coordinates light and temperature control of photosynthetic gene transcription.

Toledo-Ortiz G, Johansson H, Lee KP, Bou-Torrent J, Stewart K, Steel G, Rodríguez-Concepción M, Halliday KJ.

PLoS Genet. 2014 Jun 12;10(6):e1004416. doi: 10.1371/journal.pgen.1004416. eCollection 2014 Jun.


Strengths and limitations of period estimation methods for circadian data.

Zielinski T, Moore AM, Troup E, Halliday KJ, Millar AJ.

PLoS One. 2014 May 8;9(5):e96462. doi: 10.1371/journal.pone.0096462. eCollection 2014.


Interaction of light and temperature signalling.

Franklin KA, Toledo-Ortiz G, Pyott DE, Halliday KJ.

J Exp Bot. 2014 Jun;65(11):2859-71. doi: 10.1093/jxb/eru059. Epub 2014 Feb 25. Review.


Mathematical models light up plant signaling.

Chew YH, Smith RW, Jones HJ, Seaton DD, Grima R, Halliday KJ.

Plant Cell. 2014 Jan;26(1):5-20. doi: 10.1105/tpc.113.120006. Epub 2014 Jan 30. Review.


HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 is required for circadian periodicity through the promotion of nucleo-cytoplasmic mRNA export in Arabidopsis.

MacGregor DR, Gould P, Foreman J, Griffiths J, Bird S, Page R, Stewart K, Steel G, Young J, Paszkiewicz K, Millar AJ, Halliday KJ, Hall AJ, Penfield S.

Plant Cell. 2013 Nov;25(11):4391-404. doi: 10.1105/tpc.113.114959. Epub 2013 Nov 19.


Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock.

Keily J, MacGregor DR, Smith RW, Millar AJ, Halliday KJ, Penfield S.

Plant J. 2013 Oct;76(2):247-57. doi: 10.1111/tpj.12303.


Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA.

Vaistij FE, Gan Y, Penfield S, Gilday AD, Dave A, He Z, Josse EM, Choi G, Halliday KJ, Graham IA.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10866-71. doi: 10.1073/pnas.1301647110. Epub 2013 Jun 10.


Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.

Gould PD, Ugarte N, Domijan M, Costa M, Foreman J, Macgregor D, Rose K, Griffiths J, Millar AJ, Finkenstädt B, Penfield S, Rand DA, Halliday KJ, Hall AJ.

Mol Syst Biol. 2013;9:650. doi: 10.1038/msb.2013.7.


The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.

Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ.

Mol Syst Biol. 2012 Mar 6;8:574. doi: 10.1038/msb.2012.6.


An augmented Arabidopsis phenology model reveals seasonal temperature control of flowering time.

Chew YH, Wilczek AM, Williams M, Welch SM, Schmitt J, Halliday KJ.

New Phytol. 2012 May;194(3):654-65. doi: 10.1111/j.1469-8137.2012.04069.x. Epub 2012 Feb 21.


Stochastic properties of the plant circadian clock.

Guerriero ML, Pokhilko A, Fernández AP, Halliday KJ, Millar AJ, Hillston J.

J R Soc Interface. 2012 Apr 7;9(69):744-56. doi: 10.1098/rsif.2011.0378. Epub 2011 Aug 31.


A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling.

Josse EM, Gan Y, Bou-Torrent J, Stewart KL, Gilday AD, Jeffree CE, Vaistij FE, Martínez-García JF, Nagy F, Graham IA, Halliday KJ.

Plant Cell. 2011 Apr;23(4):1337-51. doi: 10.1105/tpc.110.082594. Epub 2011 Apr 8.


Light receptor action is critical for maintaining plant biomass at warm ambient temperatures.

Foreman J, Johansson H, Hornitschek P, Josse EM, Fankhauser C, Halliday KJ.

Plant J. 2011 Feb;65(3):441-52. doi: 10.1111/j.1365-313X.2010.04434.x. Epub 2010 Dec 15.


Fruit development: new directions for an old pathway.

Moran CN, Halliday KJ.

Curr Biol. 2010 Dec 21;20(24):R1081-3. doi: 10.1016/j.cub.2010.10.054.


A stress-free walk from Arabidopsis to crops.

Chew YH, Halliday KJ.

Curr Opin Biotechnol. 2011 Apr;22(2):281-6. doi: 10.1016/j.copbio.2010.11.011. Epub 2010 Dec 17. Review.


SPATULA links daytime temperature and plant growth rate.

Sidaway-Lee K, Josse EM, Brown A, Gan Y, Halliday KJ, Graham IA, Penfield S.

Curr Biol. 2010 Aug 24;20(16):1493-7. doi: 10.1016/j.cub.2010.07.028. Epub 2010 Aug 12.


Integration of light and auxin signaling.

Halliday KJ, Martínez-García JF, Josse EM.

Cold Spring Harb Perspect Biol. 2009 Dec;1(6):a001586. doi: 10.1101/cshperspect.a001586. Epub 2009 Nov 4. Review.


Prediction of photoperiodic regulators from quantitative gene circuit models.

Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ.

Cell. 2009 Dec 11;139(6):1170-9. doi: 10.1016/j.cell.2009.11.029.


A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy.

Penfield S, Josse EM, Halliday KJ.

Plant Mol Biol. 2010 May;73(1-2):89-95. doi: 10.1007/s11103-009-9571-1. Epub 2009 Nov 13.


Skotomorphogenesis: the dark side of light signalling.

Josse EM, Halliday KJ.

Curr Biol. 2008 Dec 23;18(24):R1144-6. doi: 10.1016/j.cub.2008.10.034.


Paths through the phytochrome network.

Josse EM, Foreman J, Halliday KJ.

Plant Cell Environ. 2008 May;31(5):667-78. doi: 10.1111/j.1365-3040.2008.01794.x. Epub 2008 Feb 5. Review.


Phytochrome coordinates Arabidopsis shoot and root development.

Salisbury FJ, Hall A, Grierson CS, Halliday KJ.

Plant J. 2007 May;50(3):429-38. Epub 2007 Apr 5.


DELLA-mediated cotyledon expansion breaks coat-imposed seed dormancy.

Penfield S, Gilday AD, Halliday KJ, Graham IA.

Curr Biol. 2006 Dec 5;16(23):2366-70.


Cold and light control seed germination through the bHLH transcription factor SPATULA.

Penfield S, Josse EM, Kannangara R, Gilday AD, Halliday KJ, Graham IA.

Curr Biol. 2005 Nov 22;15(22):1998-2006.


The highs and lows of plant life: temperature and light interactions in development.

Heggie L, Halliday KJ.

Int J Dev Biol. 2005;49(5-6):675-87. Review.


Plant hormones: the interplay of brassinosteroids and auxin.

Halliday KJ.

Curr Biol. 2004 Dec 14;14(23):R1008-10. Review.


The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks.

Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, Millar AJ.

Plant Cell. 2003 Nov;15(11):2719-29. Epub 2003 Oct 10.


Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses.

Kanyuka K, Praekelt U, Franklin KA, Billingham OE, Hooley R, Whitelam GC, Halliday KJ.

Plant J. 2003 Jul;35(1):57-70.


Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis.

Franklin KA, Praekelt U, Stoddart WM, Billingham OE, Halliday KJ, Whitelam GC.

Plant Physiol. 2003 Mar;131(3):1340-6.


SRL1: a new locus specific to the phyB-signaling pathway in Arabidopsis.

Huq E, Kang Y, Halliday KJ, Qin M, Quail PH.

Plant J. 2000 Aug;23(4):461-70.


Photomophogenesis: Phytochrome takes a partner!

Whitelam GC, Halliday KJ.

Curr Biol. 1999 Mar 25;9(6):R225-7. Review.


Overexpression of rice phytochrome A partially complements phytochrome B deficiency in Arabidopsis.

Halliday KJ, Bolle C, Chua NH, Whitelam GC.

Planta. 1999 Jan;207(3):401-9.


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