Andrew Millar

2023

A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri

Noordally, Z. B., Hindle, M. M., Martin, S. F., Seaton, D. D., Simpson, T. I., Le Bihan, T. & Millar, A. J., 29 Sept 2023, In: Journal of Experimental Botany. 74, 18, p. 5514–5531 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Keep it simple: Using README Files to Advance Standardization in Chronobiology

Zielinski, T., Hodge, J. J. L. & Millar, A. J., Sept 2023, In: Clocks & Sleep. 5, 3, p. 499-506 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

File

2022

SARS-CoV-2 RNA levels in Scotland’s wastewater

Scorza, L., Cameron, G. J., Murray Williams, R., Findlay, D., Bolland, J., Cerghizan, B., Campbell, K., Thomson, D., Corbishley, A., Gally, D., Fitzgerald, S., Low, A., McAteer, S., Roberts, A., Fang, Z., Mayer, C. D., Frantsuzova, A., Baby, S. V., Zielinski, T. & Millar, A. J., 18 Nov 2022, In: Scientific Data. 9, 713, 9 p., 713.

Research output: Contribution to journal › Article › peer-review

Open Access

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The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

Chew, Y. H., Seaton, D. D., Mengin, V., Flis, A., Mugford, S. T., George, G. M., Moulin, M., Hume, A., Zeeman, S. C., Fitzpatrick, T. B., Smith, A. M., Stitt, M. & Millar, A. J., 30 May 2022, In: In Silico Plants. 4, 2, 15 p., diac010.

Research output: Contribution to journal › Article › peer-review

Open Access

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SynBio2Easy – a biologist-friendly tool for batch operations on SBOL designs with Excel inputs

Zielinski, T., Hay, J., Romanowski, A., Nenninger, A., McCormick, A. J. & Millar, A. J., 26 Jan 2022, In: Synthetic Biology. 7, 1, 9 p., ysac002.

Research output: Contribution to journal › Article › peer-review

Open Access

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The circadian clock gene circuit controls protein and phosphoprotein rhythms in Arabidopsis thaliana

Krahmer, J., Hindle, M., Perby, L. K., Mogensen, H. K., Nielsen, T. H., Halliday, K. J., VanOoijen, G., LeBihan, T. & Millar, A. J., 1 Jan 2022, In: Molecular & Cellular Proteomics (MCP). 21, 1, 20 p., 100172.

Research output: Contribution to journal › Article › peer-review

Open Access

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2021

Testing the inferred transcription rates of a dynamic, gene network model in absolute units

Urquiza-García, U. & Millar, A. J., 5 Aug 2021, In: In Silico Plants. diab022.

Research output: Contribution to journal › Article › peer-review

Open Access

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2020

PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO

Hay, J., Troup, E., Clark, I., Pietsch, J., Zielinski, T. & Millar, A. J., 18 May 2020, In: Wellcome Open Research .

Research output: Contribution to journal › Article › peer-review

Open Access

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2019

The grant is dead, long live the data - migration as a pragmatic exit strategy for research data preservation [version 2; peer review: 2 approved]

Zielinski, T., Hay, J. & Millar, A. J., 23 Sept 2019, In: Wellcome Open Research .

Research output: Contribution to journal › Article › peer-review

Open Access

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Expanding the bioluminescent reporter toolkit for plant science with NanoLUC

Urquiza-garcía, U. & Millar, A. J., 8 Jul 2019, In: Plant Methods. 15, 1, 68.

Research output: Contribution to journal › Article › peer-review

Open Access

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The grant is dead, long live the data - migration as a pragmatic exit strategy for research data preservation [version 1; peer review: 2 approved].

Zielinski, T., Hay, J. & Millar, A. J., 2 Jul 2019, In: Wellcome Open Research . 4, 104.

Research output: Contribution to journal › Article › peer-review

Open Access

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Better research by efficient sharing: Evaluation of free management platforms for synthetic biology designs

Urquiza-garcía, U., Zieliński, T. & Millar, A. J., 20 Jun 2019, (E-pub ahead of print) In: Synthetic Biology. 4, 1, ysz016.

Research output: Contribution to journal › Article › peer-review

Open Access

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An explanatory model of temperature influence on flowering through whole-plant accumulation of FT in Arabidopsis thaliana

Kinmonth-Schultz, H. A., MacEwen, M. J. S., Seaton, D. D., Millar, A. J., Imaizumi, T. & Kim, S-H., 15 May 2019, In: In Silico Plants. 1, 1, diz006.

Research output: Contribution to journal › Article › peer-review

Open Access

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A multi-model Framework for the Arabidopsis life cycle

Zardilis, A., Hume, A. & Millar, A., 19 Feb 2019, In: Journal of Experimental Botany. 70, 9, p. 2463–2477 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Multiple circadian clock outputs regulate diel turnover of carbon and nitrogen reserves

Flis, A., Mengin, V., Ivakov, A. A., Mugford, S. T., Hubberten, H-M., Encke, B., Krohn, N., Höhne, M., Feil, R., Hoefgen, R., Lunn, J. E., Millar, A. J., Smith, A. M., Sulpice, R. & Stitt, M., 1 Feb 2019, In: Plant, Cell and Environment. 42, 2, p. 549-573 25 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis

Krahmer, J., Goralogia, G. S., Kubota, A., Zardilis, A., Johnson, R. S., Song, Y. H., MacCoss, M. J., LeBihan, T., Halliday, K. J., Imaizumi, T. & Millar, A. J., Feb 2019, In: FEBS Letters. 593, 3, 20 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2018

Molecular basis of flowering under natural long-day conditions in Arabidopsis

Song, Y. H., Kubota, A., Kwon, M. S., Covington, M. F., Lee, N., Taagen, E. R., Laboy Cintrón, D., Hwang, D. Y., Akiyama, R., Hodge, S. K., Huang, H., Nguyen, N. H., Nusinow, D. A., Millar, A. J., Shimizu, K. K. & Imaizumi, T., 1 Oct 2018, In: Nature Plants. 4, 10, p. 824-835 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees

Edwards, K. D., Takata, N., Johansson, M., Jurca, M., Novák, O., Hényková, E., Liverani, S., Kozarewa, I., Strnad, M., Millar, A. J., Ljung, K. & Eriksson, M. E., 15 Apr 2018, In: Plant, Cell and Environment. 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Chromar, a Rule-based Language of Parameterised Objects

Honorato-Zimmer, R., Millar, A. J., Plotkin, G. D. & Zardilis, A., 10 Apr 2018, In: Electronic Notes in Theoretical Computer Science. 335, p. 49-66 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J. & Gruissem, W., 1 Mar 2018, In: Molecular Systems Biology. 14, 3, p. e7962 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2017

Guidelines for Genome-Scale Analysis of Biological Rhythms

Hughes, M. E., Abruzzi, K. C., Allada, R., Anafi, R., Arpat, A. B., Asher, G., Baldi, P., de Bekker, C., Bell-Pedersen, D., Blau, J., Brown, S., Ceriani, M. F., Chen, Z., Chiu, J. C., Cox, J., Crowell, A. M., DeBruyne, J. P., Dijk, D-J., DiTacchio, L., Doyle, F. J., & 73 othersDuffield, G. E., Dunlap, J. C., Eckel-Mahan, K., Esser, K. A., FitzGerald, G. A., Forger, D. B., Francey, L. J., Fu, Y-H., Gachon, F., Gatfield, D., de Goede, P., Golden, S. S., Green, C., Harer, J., Harmer, S., Haspel, J., Hastings, M. H., Herzel, H., Herzog, E. D., Hoffmann, C., Hong, C., Hughey, J. J., Hurley, J. M., de la Iglesia, H. O., Johnson, C., Kay, S. A., Koike, N., Kornacker, K., Kramer, A., Lamia, K., Leise, T., Lewis, S. A., Li, J., Li, X., Liu, A. C., Loros, J. J., Martino, T. A., Menet, J. S., Merrow, M., Millar, A. J., Mockler, T., Naef, F., Nagoshi, E., Nitabach, M. N., Olmedo, M., Nusinow, D. A., Ptáček, L. J., Rand, D., Reddy, A. B., Robles, M. S., Roenneberg, T., Rosbash, M., Ruben, M. D., Rund, S. S. C., Sancar, A., Sassone-Corsi, P., Sehgal, A., Sherrill-Mix, S., Skene, D. J., Storch, K-F., Takahashi, J. S., Ueda, H. R., Wang, H., Weitz, C., Westermark, P. O., Wijnen, H., Xu, Y., Wu, G., Yoo, S-H., Young, M., Zhang, E. E., Zielinski, T. & Hogenesch, J. B., 1 Oct 2017, In: Journal of biological rhythms. 32, 5, p. 380-393 14 p., 748730417728663.

Research output: Contribution to journal › Article › peer-review

Open Access

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Chromar, a language of parameterised objects

Honorato Zimmer, R., Millar, A. J., Plotkin, G. D. & Zardilis, A., 8 Aug 2017, (E-pub ahead of print) In: Theoretical Computer Science. 25 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

Marshall-colon, A., Long, S. P., Allen, D. K., Allen, G., Beard, D. A., Benes, B., Von Caemmerer, S., Christensen, A. J., Cox, D. J., Hart, J. C., Hirst, P. M., Kannan, K., Katz, D. S., Lynch, J. P., Millar, A. J., Panneerselvam, B., Price, N. D., Prusinkiewicz, P., Raila, D., Shekar, R. G., & 9 othersShrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Turk, M. J., Voit, E. O., Wang, Y., Yin, X. & Zhu, X., 15 May 2017, In: Frontiers in plant science. 8, 786.

Research output: Contribution to journal › Article › peer-review

Open Access

Valuing the project: A knowledge-action response to network governance in collaborative research

Freeman, P. & Millar, A., Jan 2017, In: Public Money & Management. 37, 1, p. 23-30

Research output: Contribution to journal › Article › peer-review

Open Access

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2016

Organ specificity in the plant circadian system is explained by different light inputs to the shoot and root clocks

Bordage, S., Sullivan, S., Laird, J., Millar, A. J. & Nimmo, H. G., 1 Oct 2016, In: New Phytologist. 212, 1, p. 136–149 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis

Flis, A., Sulpice, R., Seaton, D. D., Ivakov, A. A., Liput, M., Abel, C., Millar, A. J. & Stitt, M., 4 Aug 2016, In: Plant, Cell and Environment. 39, 9, p. 1955-1981

Research output: Contribution to journal › Article › peer-review

Open Access

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2015

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

Flis, A., Fernández, A. P., Zielinski, T., Mengin, V., Sulpice, R., Stratford, K., Hume, A., Pokhilko, A., Southern, M. M., Seaton, D. D., McWatters, H. G., Stitt, M., Halliday, K. J. & Millar, A. J., 14 Oct 2015, In: Open Biology. 5, 10, 150042.

Research output: Contribution to journal › Article › peer-review

Open Access

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A Bayesian approach for structure learning in oscillating regulatory networks

Trejo-Banos, D., Millar, A. & Sanguinetti, G., 14 Jul 2015, In: Bioinformatics. 31, 22, p. 3617-3624 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Correction: Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Chew, Y. H., Wenden, B., Flis, A., Mengin, V., Taylor, J., Davey, C. L., Tindal, C., Thomas, H., Ougham, H. J., De Reffye, P., Stitt, M., Williams, M., Muetzelfeldt, R., Halliday, K. J. & Millar, A. J., 12 May 2015, In: Proceedings of the National Academy of Sciences (PNAS). 112, 19, E2556.

Research output: Contribution to journal › Article › peer-review

Open Access

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

Seaton, D. D., Smith, R. W., Song, Y. H., MacGregor, D. R., Stewart, K., Steel, G., Foreman, J., Penfield, S., Imaizumi, T., Millar, A. J. & Halliday, K. J., 19 Jan 2015, In: Molecular Systems Biology. 11, 1, 19 p., 776.

Research output: Contribution to journal › Article › peer-review

Open Access

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Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri

Bihan, T. L., Hindle, M., Martin, S. F., Barrios-Llerena, M. E., Krahmer, J., Kis, K., Millar, A. J. & van Ooijen, G., 2015, In: Proteomics. 15, 23-24, p. 4135–4144

Research output: Contribution to journal › Article › peer-review

Open Access

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2014

Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Chew, Y. H., Wenden, B., Flis, A., Mengin, V., Taylor, J., Davey, C. L., Tindal, C., Thomas, H., Ougham, H. J., De Reffye, P., Stitt, M., Williams, M., Muetzelfeldt, R., Halliday, K. J. & Millar, A. J., 30 Sept 2014, In: Proceedings of the National Academy of Sciences (PNAS). 111, 39, p. E4127-E4136 10 p.

Research output: Contribution to journal › Article › peer-review

The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species

Hindle, M. M., Martin, S. F., Noordally, Z. B., Van Ooijen, G., Barrios-llerena, M. E., Simpson, T. I., Le Bihan, T. & Millar, A. J., 1 Aug 2014, In: BMC Genomics. 15, 1, 640.

Research output: Contribution to journal › Article › peer-review

Open Access

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Light and circadian regulation of clock components aids flexible responses to environmental signals

Dixon, L. E., Hodge, S. K., van Ooijen, G., Troein, C., Akman, O. E. & Millar, A. J., 20 May 2014, In: New Phytologist.

Research output: Contribution to journal › Article › peer-review

Open Access

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Regulatory principles and experimental approaches to the circadian control of starch turnover

Seaton, D. D., Ebenhöh, O., Millar, A. J. & Pokhilko, A., 2014, In: Journal of the Royal Society. Interface. 11, 91, 20130979.

Research output: Contribution to journal › Article › peer-review

Open Access

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Strengths and limitations of period estimation methods for circadian data

Zielinski, T., Moore, A. M., Troup, E., Halliday, K. J. & Millar, A. J., 2014, In: PLoS ONE. 9, 5, e96462.

Research output: Contribution to journal › Article › peer-review

Open Access

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2013

HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis

Macgregor, D. R., Gould, P., Foreman, J., Griffiths, J., Bird, S., Page, R., Stewart, K., Steel, G., Young, J., Paszkiewicz, K., Millar, A. J., Halliday, K. J., Hall, A. J. & Penfield, S., 19 Nov 2013, In: Plant Cell. 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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

Keily, J., MacGregor, D. R., Smith, R. W., Millar, A. J., Halliday, K. J. & Penfield, S., 31 Oct 2013, In: The Plant Journal. 76, 2, p. 247-57 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Functional analysis of the rodent CK1tau mutation in the circadian clock of a marine unicellular alga

van Ooijen, G., Martin, S. F., Barrios-Llerena, M. E., Hindle, M., Le Bihan, T., O'Neill, J. S. & Millar, A. J., 15 Oct 2013, In: BMC Cell Biology. 14, 1, 46.

Research output: Contribution to journal › Article › peer-review

Open Access

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SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology

Adams, R., Clark, A., Lebedeva, G., Millar, A. J., Gilmore, S., Yamaguchi, A., Goryanin, I., Hanlon, N., Tsorman, N., Ali, S., Goltsov, A., Sorokin, A., Akman, O. E. & Troein, C., 1 Mar 2013, In: Bioinformatics. 29, 5, p. 664-665 2 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Functional analysis of Casein Kinase 1 in a minimal circadian system

van Ooijen, G., Hindle, M., Martin, S. F., Barrios-Llerena, M., Sanchez, F., Bouget, F-Y., O'Neill, J. S., Le Bihan, T. & Millar, A. J., 2013, In: PLoS ONE. 8, 7, e70021.

Research output: Contribution to journal › Article › peer-review

Open Access

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Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics

Ocone, A., Millar, A. J. & Sanguinetti, G., 2013, In: Bioinformatics. 29, 7, p. 910-916 7 p.

Research output: Contribution to journal › Article › peer-review

Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs

Pokhilko, A., Mas, P. & Millar, A. J., 2013, In: BMC Systems Biology. 7, 1, 12 p., 23.

Research output: Contribution to journal › Article › peer-review

Open Access

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

Gould, P. D., Ugarte, N., Domijan, M., Costa, M., Foreman, J., Macgregor, D., Rose, K., Griffiths, J., Millar, A. J., Finkenstädt, B., Penfield, S., Rand, D. A., Halliday, K. J. & Hall, A. J. W., 2013, In: Molecular Systems Biology. 9, 650.

Research output: Contribution to journal › Article › peer-review

Open Access

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Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

Schaum, E., Rost, B., Millar, A. J. & Collins, S., 2013, In: Nature Climate Change. 3, p. 298–302

Research output: Contribution to journal › Article › peer-review

2012

Erratum: Digital clocks: Simple Boolean models can quantitatively describe circadian systems (Journal of the Royal Society Interface (2012) 9 (3573) DOI: 10.1098/rsif.2012.0673)

Akman, O. E., Watterson, S., Parton, A., Binns, N., Millar, A. J. & Ghazal, P., 7 Dec 2012, In: Journal of the Royal Society. Interface. 9, 77, p. 3578 1 p.

Research output: Contribution to journal › Article › peer-review

Non-transcriptional oscillators in circadian timekeeping

van Ooijen, G. & Millar, A. J., 1 Nov 2012, In: Trends in biochemical sciences. 37, 11, p. 484-492 9 p.

Research output: Contribution to journal › Article › peer-review

Digital clocks: simple Boolean models can quantitatively describe circadian systems

Akman, O. E., Watterson, S., Parton, A., Binns, N., Millar, A. J. & Ghazal, P., 7 Sept 2012, In: Journal of the Royal Society. Interface. 9, 74, p. 2365-2382 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

Adams, R. R., Tsorman, N., Stratford, K., Akman, O. E., Gilmore, S., Juty, N., Le Novère, N. & Millar, A. J., Aug 2012, In: Journal of biological rhythms. 27, 4, p. 328-332 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

Huang, W., Pérez-García, P., Pokhilko, A., Millar, A. J., Antoshechkin, I., Riechmann, J. L. & Mas, P., 6 Apr 2012, In: Science. 336, 6077, p. 75-79 5 p.

Research output: Contribution to journal › Article › peer-review

Andrew Millar

Research output

Search results