Edinburgh Research Explorer

Andrew Millar

Chair of Systems Biology

  1. 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 journalArticlepeer-review

  2. 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 journalArticlepeer-review

  3. Isoform switching facilitates period control in the Neurospora crassa circadian clock

    Akman, O. E., Locke, J. C. W., Tang, S., Carré, I., Millar, A. J. & Rand, D. A., Feb 2008, In: Molecular Systems Biology. 4, 11 p., 164.

    Research output: Contribution to journalArticlepeer-review

  4. Robustness from flexibility in the fungal circadian clock

    Akman, O. E., Rand, D. A., Brown, P. E. & Millar, A. J., 2010, In: BMC Systems Biology. 4, 88

    Research output: Contribution to journalArticlepeer-review

  5. 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 journalArticlepeer-review

  6. Isoform switching facilitates period control in the Neurospora crassa circadian clock - Corrigendum

    Akman, O. E., Locke, J. C. W., Tang, S., Carre, I., Millar, A. J. & Rand, D. A., Apr 2008, In: Molecular Systems Biology. 4, p. - 1 p., 186.

    Research output: Contribution to journalArticlepeer-review

  7. 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 Sep 2012, In: Journal of the Royal Society Interface. 9, 74, p. 2365-2382 18 p.

    Research output: Contribution to journalArticlepeer-review

  8. Development of a Novel Biosensor for the Detection of Arsenic in Drinking Water

    Aleksic, J., Bizzari, F., Cai, Y., Davidson, B., Mora, K. D., Ivakhno, S., Seshasayee, S. L., Nicholson, J., Wilson, J., Elfick, A., French, C., Kozma-Bognar, L., Ma, H. & Millar, A., 2007, In: IET Synthetic Biology. 1, 40940, p. 87-90 4 p.

    Research output: Contribution to journalArticlepeer-review

  9. Attenuation of phytochrome A and B signaling pathways by the Arabidopsis circadian clock

    Anderson, S. L., Somers, D. E., Millar, A. J., Hanson, K., Chory, J. & Kay, S. A., 1997, In: The Plant Cell. 9, 10, p. 1727-43 17 p.

    Research output: Contribution to journalArticlepeer-review

  10. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

    Ashelford, K., Eriksson, M. E., Allen, C. M., D'Amore, R., Johansson, M., Gould, P., Kay, S., Millar, A. J., Hall, N. & Hall, A., 2011, In: Genome Biology. 12, 3, p. R28

    Research output: Contribution to journalArticlepeer-review

  11. The wild-type circadian period of Neurospora is encoded in the residual network of the null frq mutants

    Bain, E. L., Millar, A. J. & Turner, M. S., 2004, In: Journal of Theoretical Biology. 229, 3, p. 413-20 8 p.

    Research output: Contribution to journalArticlepeer-review

  12. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Bastow, R., Beynon, J., Estelle, M., Friesner, J., Grotewold, E., Lavagi, I., Lindsey, K., Meyers, B., Provart, N., Benfey, P., Birney, E., Braun, P., Brendel, V., Buell, R., Caccamo, M., Carrington, J., Cherry, M., Ecker, J., Eppig, J., Forster, M. & 31 others, Gutierrez, R., Hilson, P., Huala, E., Katari, M., Kersey, P., Kudla, J., Ma, H., Matsui, M., Matthews, K., May, S., Mayer, K., Millar, A., Millar, H., Mjolsness, E., Mockler, T., Nikolau, B., Nordborg, M., Rawlings, C., Schofield, P., Schoof, H., Schroeder, J. I., Sen, T. Z., Stanzione, D., Town, C., Toyoda, T., Vision, T., Walsh, S., Wang, X., Ware, D., Weckwerth, W. & Int Arabidopsis Informatics Cons, Aug 2010, In: The Plant Cell. 22, 8, p. 2530-2536 7 p.

    Research output: Contribution to journalEditorialpeer-review

  13. 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 journalArticlepeer-review

  14. Phytochrome-induced intercellular signalling activates CAB:luciferase gene expression

    Bischoff, F., Millar, A. J., Kay, S. A. & Furuya, M., Oct 1997, In: The Plant Journal. 12, 4, p. 839-849 11 p.

    Research output: Contribution to journalArticlepeer-review

  15. The circadian clock controls the expression pattern of the circadian input photoreceptor, phytochrome B

    Bognár, L. K., Hall, A., Adám, E., Thain, S. C., Nagy, F. & Millar, A. J., 1999, In: Proceedings of the National Academy of Sciences. 96, 25, p. 14652-7 6 p.

    Research output: Contribution to journalArticlepeer-review

  16. 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 journalArticlepeer-review

  17. Mathematical model of arabidopsis vegetative growth: The framework model

    Chew, Y. H. & Millar, A., 2014

    Research output: Other contribution

  18. 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 Sep 2014, In: Proceedings of the National Academy of Sciences. 111, 39, p. E4127-E4136 10 p.

    Research output: Contribution to journalArticlepeer-review

  19. 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. 112, 19, E2556.

    Research output: Contribution to journalArticlepeer-review

  20. Linking circadian time to growth rate quantitatively via carbon metabolism

    Chew, Y. H., Seaton, D., Mengin, V., Flis, A., Mugford, S. T., Smith, A. M., Stitt, M. & Millar, A., 6 Feb 2017, bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

  21. Multi-scale modelling to synergise plant systems biology and crop science

    Chew, Y. H., Seaton, D. & Millar, A., 26 Feb 2016, In: Field crops research. 202

    Research output: Contribution to journalLiterature reviewpeer-review

  22. Using higher-order dynamic Bayesian networks to model periodic data from the circadian clock of Arabidopsis Thaliana.

    Daly, R., Edwards, K. D., O'Neill, J. S., Aitken, S., Millar, A. & Girolami, M., 2009, Pattern Recognition in Bioinformatics: 4th IAPR International Conference, PRIB 2009, Sheffield, UK, September 7-9, 2009. Proceedings. Springer-Verlag GmbH, p. 67-78 12 p. (Lecture Notes in Computer Science; vol. 5780).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  23. PlaSMo: Making existing plant and crop mathematical models available to plant systems biologists

    Davey, C., Ougham, H., Millar, A., Thomas, H., Tindal, C. & Muetzelfeldt, R., Jun 2009, In: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology. 153A, 2, p. S225-S226 2 p.

    Research output: Contribution to journalArticle

  24. Protocol: Streamlined sub-protocols for floral-dip transformation and selection of transformants in Arabidopsis thaliana

    Davis, A. M., Hall, A., Millar, A. J., Darrah, C. & Davis, S. J., 27 Feb 2009, In: Plant Methods. 5, 7 p., 3.

    Research output: Contribution to journalArticlepeer-review

  25. Watching the hands of the Arabidopsis biological clock

    Davis, S. J. & Millar, A. J., 2001, In: Genome Biology. 2, 3, 4 p., reviews1008-reviews1008.4 .

    Research output: Contribution to journalArticlepeer-review

  26. TIME FOR COFFEE encodes a nuclear regulator in the Arabidopsis thaliana circadian clock

    Ding, Z., Millar, A. J., Davis, A. M. & Davis, S. J., 2007, In: The Plant Cell. 19, 5, p. 1522-36 15 p.

    Research output: Contribution to journalArticlepeer-review

  27. 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 journalArticlepeer-review

  28. Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis

    Dixon, L. E., Knox, K., Kozma-Bognar, L., Southern, M. M., Pokhilko, A. & Millar, A. J., 2011, In: Current Biology. 21, 2, p. 120-5 6 p.

    Research output: Contribution to journalArticlepeer-review

  29. Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage

    Dodd, A. N., Salathia, N., Hall, A., Kévei, E., Tóth, R., Nagy, F., Hibberd, J. M., Millar, A. J. & Webb, A. A. R., 2005, In: Science. 309, 5734, p. 630-3 4 p.

    Research output: Contribution to journalArticlepeer-review

  30. Enhancers of luminidependens define a role for brassinosteroids in floral promotion

    Domagalska, M., Schomburg, F. M., Millar, A. J., Amasino, R. M., Vierstra, R. M., Nagy, F. & Davis, S. J., 2004, In: Acta physiologiae plantarum. 26, 3, p. 30-30 1 p.

    Research output: Contribution to journalMeeting abstractpeer-review

  31. Temperature-sensitive version of P2010 Arabidopsis clock model by Mirela Domijan, from Gould et al. 2013.

    Domijan, M., Halliday, K., Hall, A. J. W., Millar, A. & Rand, D. A., 2013

    Research output: Other contribution

  32. Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis

    Dowson-Day, M. J. & Millar, A. J., 1999, In: The Plant Journal. 17, 1, p. 63-71 9 p.

    Research output: Contribution to journalArticlepeer-review

  33. The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana

    Doyle, M. R., Davis, S. J., Bastow, R. M., McWatters, H. G., Kozma-Bognár, L., Nagy, F., Millar, A. J. & Amasino, R. M., 2002, In: Nature. 419, 6902, p. 74-7 4 p.

    Research output: Contribution to journalArticlepeer-review

  34. Peroxiredoxins are conserved markers of circadian rhythms

    Edgar, R. S., Green, E. W., Zhao, Y., van Ooijen, G., Olmedo, M., Qin, X., Xu, Y., Pan, M., Valekunja, U. K., Feeney, K. A., Maywood, E. S., Hastings, M. H., Baliga, N. S., Merrow, M., Millar, A. J., Johnson, C. H., Kyriacou, C. P., O'Neill, J. S. & Reddy, A. B., 2012, In: Nature. 485, 7399, p. 459-464 6 p.

    Research output: Contribution to journalArticlepeer-review

  35. Corrigendum: Peroxiredoxins are conserved markers of circadian rhythms

    Edgar, R. S., Green, E. W., Zhao, Y., van Ooijen, G., Olmedo, M., Qin, X., Xu, Y., Pan, M., Valekunja, U. K., Feeney, K. A., Maywood, E. S., Hastings, M. H., Baliga, N. S., Merrow, M., Millar, A. J., Johnson, C. H., Kyriacou, C. P., O'Neill, J. S. & Reddy, A. B., 2012, In: Nature. 485, 7399, p. 459–464

    Research output: Contribution to journalArticle

  36. Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock

    Edwards, K. D., Lynn, J. R., Gyula, P., Nagy, F. & Millar, A. J., 2005, In: Genetics. 170, 1, p. 387-400 14 p.

    Research output: Contribution to journalArticlepeer-review

  37. 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 journalArticlepeer-review

  38. Analysis of circadian leaf movement rhythms in Arabidopsis thaliana

    Edwards, K. D. & Millar, A. J., 2007, In: Methods in Molecular Biology. 362, p. 103-13 11 p.

    Research output: Contribution to journalArticlepeer-review

  39. Quantitative analysis of regulatory flexibility under changing environmental conditions

    Edwards, K. D., Akman, O. E., Knox, K., Lumsden, P. J., Thomson, A. W., Brown, P. E., Pokhilko, A., Kozma-Bognar, L., Nagy, F., Rand, D. A. & Millar, A. J., 2 Nov 2010, In: Molecular Systems Biology. 6, 11 p., 424.

    Research output: Contribution to journalArticlepeer-review

  40. Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

    Edwards, K. D., Guerineau, F., Devlin, P. & Millar, A., Nov 2015, bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

  41. FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock

    Edwards, K. D., Anderson, P. E., Hall, A., Salathia, N. S., Locke, J. C. W., Lynn, J. R., Straume, M., Smith, J. Q. & Millar, A. J., 2006, In: The Plant Cell. 18, 3, p. 639-650 12 p.

    Research output: Contribution to journalArticlepeer-review

  42. A comparison of tobacco and poplar diurnal gene expression with the model plant Arabidopsis thaliana

    Edwards, K. D., Millar, A. J., Allen, F. & Eriksson, M. E., Jun 2009, In: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology. 153A, 2, p. S199-S199 1 p.

    Research output: Contribution to journalMeeting abstractpeer-review

  43. The circadian clock. A plant's best friend in a spinning world

    Eriksson, M. E. & Millar, A. J., 2003, In: Plant physiology. 132, 2, p. 732-8 7 p.

    Research output: Contribution to journalArticlepeer-review

  44. Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock

    Eriksson, M. E., Hanano, S., Southern, M. M., Hall, A. & Millar, A. J., 2003, In: Planta. 218, 1, p. 159-62 4 p.

    Research output: Contribution to journalArticlepeer-review

  45. Reconstruction of transcriptional dynamics from gene reporter data using differential equations

    Finkenstädt, B., Heron, E. A., Komorowski, M., Edwards, K., Tang, S., Harper, C. V., Davis, J. R. E., White, M. R. H., Millar, A. J. & Rand, D. A., 2008, In: Bioinformatics. 24, 24, p. 2901-7 7 p.

    Research output: Contribution to journalArticlepeer-review

  46. 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 journalArticlepeer-review

  47. 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 journalArticlepeer-review

  48. 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 journalArticlepeer-review

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