Edinburgh Research Explorer

Prof Andrew Millar

Chair of Systems Biology

  1. 2019
  2. Circadian protein regulation in the green lineage II. The clock gene circuit controls a phospho-dawn in Arabidopsis thaliana

    Krahmer, J., Hindle, M., Perby, L. K., Nielsen, T. H., Van Ooijen, G., Halliday, K. J., Bihan, T. L. & Millar, A. J., 8 Sep 2019, bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

  3. 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 journalArticle

  4. 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, In : Synthetic Biology. 4, 1, ysz016.

    Research output: Contribution to journalArticle

  5. 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 journalArticle

  6. Practical steps to digital organism models, from laboratory model species to ‘Crops in silico

    Millar, A. J., Urquiza Garcia, J., Freeman, P., Hume, A., Plotkin, G. D., Sorokina, O., Zardilis, A. & Zielinski, T., 15 Apr 2019, In : Journal of Experimental Botany. 70, 9, p. 2403–2418 16 p., JEXBOT/2018/235879.

    Research output: Contribution to journalReview article

  7. 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 journalArticle

  8. 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 journalArticle

  9. 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 journalArticle

  10. 2018
  11. 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 journalArticle

  12. A multi-model Framework for the Arabidopsis life cycle

    Zardilis, A., Hume, A. & Millar, A., 29 Jun 2018, Cold Spring Harbor: bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

  13. 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 journalArticle

  14. 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 journalArticle

  15. 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 journalArticle

  16. Optimisation of plant traits using optimal control of environmental variables

    Zardilis, A., Menolascina, F. & Millar, A., 2018, (Unpublished) Proceedings of the European Control Conference 2019.

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

  17. 2017
  18. 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 others, Duffield, 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 journalArticle

  19. Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

    Seaton, D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. & Gruissem, W., 29 Aug 2017, bioRxiv, at Cold Spring Harbor Laboratory, 43 p.

    Research output: Working paper

  20. Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana

    Krahmer, J., Goralogia, G., Kubota, A., Johnson, R. S., Song, Y. H., Halliday, K., MacCoss, M. J., LeBihan, T., Imaizumi, T. & Millar, A., 28 Aug 2017, bioRxiv, at Cold Spring Harbor Laboratory, 58 p.

    Research output: Working paper

  21. Chromar, a language of parameterised objects

    Honorato Zimmer, R., Millar, A. J., Plotkin, G. D. & Zardilis, A., 8 Aug 2017, In : Theoretical Computer Science. 25 p.

    Research output: Contribution to journalArticle

  22. BioDare2, online data analysis resource

    Zielinski, T. & Millar, A., Jun 2017

    Research output: Non-textual formSoftware

  23. 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 others, Shrivastava, 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 journalArticle

  24. 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

  25. 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 journalArticle

  26. 2016
  27. 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., Oct 2016, In : New Phytologist. 212, 1, p. 136–149 14 p.

    Research output: Contribution to journalArticle

  28. Chromar, a rule-based language of parameterised objects

    Honorato Zimmer, R., Millar, A., Plotkin, G. & Zardilis, A., 7 Sep 2016, The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016). 14 p.

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

  29. 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 journalArticle

  30. qpMerge: Merging different peptide isoforms using a motif centric strategy

    Hindle, M. M., Le Bihan, T., Krahmer, J., Martin, S. F., Noordally, Z. B., Simpson, T. I. & Millar, A. J., 5 Apr 2016, (Submitted) bioRxiv, at Cold Spring Harbor Laboratory, 9 p.

    Research output: Working paper

  31. The intracellular dynamics of circadian clocks reach for the light of ecology and evolution

    Millar, A., Apr 2016, In : Annual Review of Plant Biology. 67, p. 595-618

    Research output: Contribution to journalLiterature review

  32. Practical evaluation of SEEK and OpenBIS for biological data management in SynthSys; second report

    Troup, E., Tomlinson, K., D'Mellow, K., Richards, O., Millar, A. & Zielinski, T., 11 Mar 2016, University of Edinburgh. 13 p.

    Research output: Book/ReportOther report

  33. 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 review

  34. 2015
  35. Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana

    Millar, A., Carrington, J. T., Tee, W. V. & Hodge, S., 17 Dec 2015, bioRxiv, at Cold Spring Harbor Laboratory.

    Research output: Working paper

  36. Plants in silico: Why, why now and what? --- An integrative platform for plant systems biology research

    Zhu, X-G., Lynch, J. P., LeBauer, D. S., Millar, A. J., Stitt, M. & Long, S. P., 2 Nov 2015, In : Plant, Cell and Environment. 39 , 5, p. 1049–1057

    Research output: Contribution to journalLiterature review

  37. 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

  38. Practical evaluation of SEEK and OpenBIS for biological data management in SynthSys; first report.

    Troup, E., Clark, I., Swain, P., Millar, A. & Zielinski, T., 30 Oct 2015, University of Edinburgh. 22 p.

    Research output: Book/ReportOther report

  39. 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 journalArticle

  40. 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 journalArticle

  41. 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 journalArticle

  42. Bridging the Gap between Omics and Earth System Science to better understand how Environmental Change impacts Marine Microbes

    Mock, T., Daines, S. J., Geider, R., Collins, S., Metodiev, M., Millar, A. J., Moulton, V. & Lenton, T. M., 2015, In : Global Change Biology. 22, 1, p. 61–75

    Research output: Contribution to journalLiterature review

  43. Experimental design for inference over the A. thaliana circadian clock network

    Trejo-Banos, D., Millar, A. J. & Sanguinetti, G., 2015, Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. Springer International Publishing, p. 28-39 12 p. (Lecture Notes in Computer Science; vol. 9308).

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

  44. 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., 2015, In : Molecular Systems Biology. 11, 1, 776.

    Research output: Contribution to journalArticle

  45. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana

    Krahmer, J., Hindle, M. M., Martin, S. F., Le Bihan, T. & Millar, A. J., 2015, Methods in Enzymology: Membrane Proteins—Engineering, Purification and Crystallization. Elsevier, Vol. 551. p. 405-31 27 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

  46. 2014
  47. Clocks in Algae

    Noordally, Z. B. & Millar, A., 7 Nov 2014, In : Biochemistry. 54, 2, p. 171–183

    Research output: Contribution to journalLiterature review

  48. 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

    Research output: Contribution to journalArticle

  49. 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 journalArticle

  50. Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure

    Moore, A., Zielinski, T. & Millar, A., 8 Apr 2014, Plant Circadian Networks: Methods and Protocols. Staiger, D. (ed.). Springer New York, Vol. 1158. p. 13-44 32 p. (Methods in Molecular Biology; vol. 1158).

    Research output: Chapter in Book/Report/Conference proceedingChapter

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