Urquiza-García U, Molina N, Halliday KJ, Millar AJ. Abundant clock proteins point to missing molecular regulation in the plant circadian clock. Mol Sys Biol 2025; bioRxiv 2024, https://doi.org/10.1101/2024.09.03.609973

Balfagón D, Pascual LS, Sengupta S, Halliday KJ, Gómez-Cadenas A, Peláez-Vico MÁ, Sinha R, Mittler R, Zandalinas SI. WRKY48 negatively regulates plant acclimation to a combination of high light and heat stress. Plant J. 2024 Mar;117(6):1642-1655. doi: 10.1111/tpj.16658.

Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal J, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, Franklin KA, Halliday KJ, Hayes S, Jiang D, Jae-Hoon J, Keiserli E, Kumar VS, Maag D, Oh E, Penfield S, Perrella G, Prat S, Reis RS, Wigge PA, Willige BC, Van Zanten M. 25 Years of thermomorphogenesis: milestones and perspectives. Review. TIPs 28;10 October 2023, Pages 1098-1100, https://doi.org/10.1016/j.tplants.2023.07.001

Santoyo-Garcia JH, Walls LE, Valdivia-Cabrera M Malci M, Jonguitud-Borrego N, Halliday KJ, Rios-Solis L. The synergetic effect from the combination of different adsorption resins in batch and semi-continuous cultivations of S. Cerevisiae cell factories to produce acetylated Taxanes precursors of the anticancer drug Taxol. Biotechnology and Bioengineering 210;8 2023. https://doi.org/10.1002/bit.28487.    

Santoyo-Garcia JH, Valdivia-Cabrera M, Ochoa-Villarreal M, Casasola-Zamora S, Ripoll M, Escrich A, Moyano E, Betancor L, Halliday KJ, Loake GJ, Rios-Solis L. Increased paclitaxel recovery from Taxus baccata vascular stem cells using novel in situ product recovery approaches. Bioresour Bioprocess. 2023 Sep 29;10(1):68. doi: 10.1186/s40643-023-00687-8.

Hussain E, Romanowski A, Halliday KJ. PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism. Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2115682119. doi: 10.1073/pnas.2115682119. 

Krahmer J, Hindle M, Perby LK, Mogensen HK, Nielsen TH, Halliday KJ, van Ooijen G, Le Bihan T, Millar AJ. The Circadian Clock Gene Circuit Controls Protein and Phosphoprotein Rhythms in Arabidopsis thaliana. Mol Cell Proteomics. 2022 Jan;21(1):100172. doi: 10.1016/j.mcpro.2021.100172. Epub 2021 Nov 3.

Romanowski A, Furniss J, Hussain E, Halliday KJ. Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development. Plant physiology 2021 Mar 9;kiab112. doi: 10.1093/plphys/kiab112.

Cebula, C, Nicholl Baines K, Lido C, Thijssen J, Halliday KJ, Hedge N, Mulvana H, Gauchotte Lindsay C. Inclusion in the time of Covid: 14 ways to seize the moment for change. NatureIndex, 9 February 2021.

Krahmer J, Abbas A, Mengin V, Ishara H, Romanowski A, Furniss J, Moraes T, Krohn N, Annunziata M-G, Feil R, Alseekh S, Obata T, Fernie AR, Stitt M, Halliday KJ. Phytochrome photoreceptors control metabolic flux and their action during seedling development determines adult plant biomass. [pre-print: https://doi.org/10.1101/762666], JExBot, 05 February 2021 https://doi.org/10.1093/jxb/erab038

Branching Out, Pippa Goldschmidt. Tales of Urban Biology (pp130-143, October 2020). Editors Larissa Pschetz, Jane McKie, and Elise Cachat, Illustrated by Pilar Garcia de Leaniz. Shoreline of Infinity Press.  Neil Williamson reads an extract from Mudlarking, published in Biopolis.

Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ. A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. 2019 May 1;8(5).

Krahmer J, Goralogia G, Kubota A, Zardilis A, Johnson R. S, Song, Y. H., … Millar A. J. (2018). Time‐resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis. FEBS Letters, 593(3), 1873–3468.13311. https://doi.org/10.1002/1873-3468.13311

Seaton D, Toledo-Ortiz G, Kubota A, Ganpudi A, Imaizumi T, & Halliday K. (2018). Dawn and photoperiod sensing by phytochrome A. BioRxiv, 253989. https://doi.org/10.1101/253989

Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers C. M. M, … Monte E. (2018). Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Current Biology, 28(2), 311–318.e5. https://doi.org/10.1016/J.CUB.2017.12.021

Krahmer J, Ganpudi A, Abbas A, Romanowski A, Halliday K. Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity. Plant Phys. 2018 176:2 p. 1039-1048

Halliday K, Davis S. Light-sensing phytochromes feel the heat. Science 2016 354:6314 p. 832-833

Quint M, Delker C, Franklin K, Wigge P, Halliday K, van Zanten M. Molecular and genetic control of plant thermomorphogenesis. Review. Nature Plants 2016 2(15190).

Yang D, Seaton DD, Krahmer J, Halliday KJ. Photoreceptor effects on plant biomass, resource allocation and metabolic state. PNAS 2016 Jun 21. pii: 201601309.

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. Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biol. 2015 5(10).

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. The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nat Commun. 2015 6:7641.

Bou-Torrent J, Toledo-Ortiz G, Ortiz-Alcaide M, Cifuentes-Esquivel N, Halliday KJ, Martinez-García JF, Rodriguez-Concepcion M. Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors. Plant Physiol. 2015 169(3):1584-94.

Seaton* DD, Smith* RW, Song YH, MacGregor DR, Stewart K, Steel G, Foreman J, Penfield S, Imaizumi T, Millar AJ,  Halliday KJ. Linked circadian outputs control plant growth and development in response to photoperiod and temperature. Mol. Syst. Biol. 2015 11(1):776.

 Johansson H, Jones HJ, Foreman J, Hemsted JR, Stewart K, Grima R, Halliday KJ. Arabidopsis cell expansion is controlled by a photothermal switch.Nat Commun. 2014 5:4848.

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.Multiscale digital Arabidopsis predicts individual organ and whole-organism growth.  Proc Natl Acad Sci U S A. 2014 111(39):E4127-36.

Chew YH, Smith RW, Jones HJ, Seaton DD, Grima R, Halliday KJ. Mathematical models light up plant signaling. Plant Cell. 2014 26(1):5-20.

Temperature and light signal integration. McWatters HG, Toledo-Ortiz G, and Halliday KJ. Book, Temperature and Plant Development. Eds: Franklin and Wigge, Feb. 2014, ISBN: 978-1-118-30820-2.

.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. High Expression of OSMOTICALLY RESPONSIVE GENES 1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis Plant Cell. 2013, Nov 19.

 Keily J, MacGregor DR, Smith RW, Millar AJ, Halliday KJ, Penfield S. Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock. Plant J. 2013, 76(2):247-57.

Costa MJ, Finkenstädt B, Roche V, Lévi F, Gould PD, Foreman J, Halliday K, Hall A, Rand DA. Inference on periodicity of circadian time series. Biostatistics. 2013, 14(4):792-806.

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. Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Mol Syst Biol. 2013;9:650.

Vaistij FE, Gan Y, Penfield S, Gilday AD, Dave A, He Z, Josse EM, Choi G, Halliday KJ, Graham IA. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA.Proc Natl Acad Sci U S A. 2013, 110(26):10866-71.

Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ. The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 2012, 8:574.

Costa MJ, Finkenstädt B, Roche V, Lévi F, Gould PD, Foreman J, Halliday K, Hall A, Rand DA. Inference on periodicity of circadian time series. Biostatistics. 2013, 14(4):792-806.

Guerriero ML, Pokhiko A, Fernández AP, Halliday KJ, Millar AJ, Hillston J. Stochastic properties of the plant circadian clock. 2011, J R Soc Interface. 2012, 9(69):744-56

Josse EM, Gan Y, Bou-Torrent J, Stewart KL, Gilday AD, Jeffree CE, Vaistij FE, Martínez-García JF, Nagy F, Graham IA, Halliday KJ. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell. 2011 (4):1337-51.

Foreman J, Johansson H, Hornitschek P, Josse EM, Fankhauser C, Halliday KJ. Light receptor action is critical for maintaining plant biomass at warm ambient temperatures. Plant J. 2011 65(3):441-52.

 Griffiths J and Halliday KJ. Plant Development: Light Exposure Directs Meristem Fate. Current Biology. 2011, 21(19):R817-9.

Moran CN and Halliday KJ, Fruit Development: New Directions for an Old Pathway Current Biology 2010, 20(24):R1081-3.

Chew YH and Halliday KJ. A stress-free walk from Arabidopsis to crops Current Opinion in Biotechnology. 2011, 22(2):281-6.

 Sidaway-Lee K, Josse EM, Brown A, Gan Y, Halliday KJ, Graham IA. and Penfield S. SPATULA Links Daytime Temperature and Plant Growth Rate Current Biology. 2010, 20(16):1493-7.

 Halliday KJ, Martínez-García JF, Josse EM .Integration of light and auxin signaling. Cold Spring Harb Perspect Biol. 2009 (6):a001586.

Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carré IA, Rand DA, Millar AJ. Prediction of photoperiodic regulators from quantitative gene circuit models. Cell. 2009, 139(6):1170-9.

 Penfield S, Josse E M, Halliday K J. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy Plant Mol Biol. 2010, 73(1-2):89-95

Josse EM, Halliday KJ. Skotomorphogenesis: the dark side of light signalling. Curr Biol. Curr Biol. 2008, 18(24):R1144-6.

 Josse EM, Foreman J, Halliday KJ. Paths through the phytochrome network. Plant Cell Environ. 2008 (5):667-78. Epub 2008. Review. PMID: 18266901 [PubMed - indexed for MEDLINE]

Salisbury FJ, Hall A, Grierson CS, Halliday KJ. Phytochrome coordinates Arabidopsis shoot and root development.  Plant J. 2007 May 50(3):429-38.

 Penfield S, Gilday AD, Halliday KJ, Graham IA. DELLA-mediated cotyledon expansion breaks coat-imposed seed dormancy. Curr Biol. 2006; 16(23):2366-70.

Penfield S, Josse EM, Kannangara R, Gilday AD, Halliday KJ, Graham IA. Cold and light control seed germination through the bHLH transcription factor SPATULA. Curr Biol. 2005, 15(22):1998-2006.

 Heggie L, Halliday KJ. The highs and lows of plant life: temperature and light interactions in development. Int J Dev Biol. 2005, 49(5-6):675-87.

 Halliday KJ. Plant hormones: the interplay of brassinosteroids and auxin. Curr Biol. 2004, 14(23):R1008-10. Review.

 Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, Millar AJ. The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. Plant Cell. 2003, (11):2719-29.

Kanyuka K, Praekelt U, Franklin KA, Billingham OE, Hooley R, Whitelam GC, Halliday KJ. Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses. Plant J. 2003, 35(1):57-70.

Halliday KJ, Whitelam GC. Changes in photoperiod or temperature alter the functional relationships between phytochromes and reveal roles for phyD and phyE. Plant Physiol. 2003, 131(4):1913-20.

 Franklin KA, Praekelt U, Stoddart WM, Billingham OE, Halliday KJ, Whitelam GC. Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis. Plant Physiol. 2003, 131(3):1340-6.

 Halliday KJ, Salter MG, Thingnaes E, Whitelam GC. Phytochrome control of flowering is temperature sensitive and correlates with expression of the floral integrator FT. Plant J. 2003, 33(5):875-85.

 Huq E, Kang Y, Halliday KJ, Qin M, Quail PH. SRL1: a new locus specific to the phyB-signaling pathway in Arabidopsis. Plant J. 2000, 23(4):461-70. 

Halliday KJ, Hudson M, Ni M, Qin M, Quail PH. poc1: an Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3, a gene encoding a phytochrome-interacting bHLH protein. Proc Natl Acad Sci U S A. 1999, 96(10):5832-7. 

Whitelam GC, Halliday KJ.Photomophogenesis: Phytochrome takes a partner!  Curr Biol. 1999, 9(6):R225-7. Review.

Halliday KJ, Bolle C, Chua NH, Whitelam GCOverexpression of rice phytochrome A partially complements phytochrome B deficiency in Arabidopsis. . Planta. 1999, 207(3):401-9.

Halliday KJ, Thomas B, Whitelam GC. Expression of heterologous phytochromes A, B or C in transgenic tobacco plants alters vegetative development and flowering time.  Plant J. 1997, 12(5):1079-90. 

Devlin PF, Halliday KJ, Harberd NP, Whitelam GC.The rosette habit of Arabidopsis thaliana is dependent upon phytochrome action: novel phytochromes control internode elongation and flowering time.  Plant J. 1996, 10(6):1127-34.

Halliday KJ, Koornneef M, Whitelam GC.Phytochrome B and at Least One Other Phytochrome Mediate the Accelerated Flowering Response of Arabidopsis thaliana L. to Low Red/Far-Red Ratio.  Plant Physiol. 1994, 104(4):1311-1315. 

BOOK

Whitelam, Garry C. / Halliday, Karen J. (eds.)
Annual Plant Reviews, Volume 30, Light and Plant Development. Edition February 2007

ISBN 978-1-4051-4538-1 - John Wiley & Sons

Detailed description
Living organisms are subject to fluctuating environmental conditions. Whereas most animals are able to move away from unfavourable conditions, plants are sessile and so must cope with whatever comes their way. Of all the environmental cues that challenge the developing plant, light can probably be considered to be the most important. In addition to its key role in plant metabolism, and hence almost all life on Earth, where it drives the process of photosynthesis, light energy also acts to regulate plant growth and development. Light quantity, quality, direction and diurnal and seasonal duration regulate processes from germination, through seedling establishment to the architecture of the mature plant and the transition to reproductive development. These developmental responses of plants to light constitute photomorphogenesis.

This volume is designed to provide the reader with state-of-the-art accounts of our current knowledge of the major classes of higher plant regulatory photoreceptors and the signal transduction networks that comprise plant developmental photobiology. Consideration is also given to the ways in which knowledge of plant photoreceptors and their signalling networks can be exploited, for instance to improve the quality and productivity of commercially-grown plants. The book is directed at researchers and professionals working in plant molecular biology, plant physiology and plant biochemistry.