Edinburgh Research Explorer

Prof Andrew Millar

Chair of Systems Biology

  1. 2020
  2. 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 journalArticle

  3. 2019
  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 2018
  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 2017
  20. 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

  21. 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

  22. 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

  23. 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

  24. BioDare2, online data analysis resource

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

    Research output: Non-textual formSoftware

  25. 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

  26. 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

  27. 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

  28. 2016
  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 2015
  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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)

  48. 2014
  49. Clocks in Algae

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

    Research output: Contribution to journalLiterature review

  50. 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

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