Biological Sciences

People

Prof Andrew Millar

Location: Waddington 2.07

Telephone: 651 3325

Email: Andrew.Millar@ed.ac.uk

Website: http://www.amillar.org

Group members: No details available

C.V.

YearDescription
1985-1988University of Cambridge, BA Hons (I) in Genetics
1988-1994The Rockefeller University, New York- Ph.D.
1994-1995University of Virginia, NSF Centre for Biological Timing- LSRF post-doc Fellowship.
1996-2004University of Warwick, Dept. of Biological Sciences- lecturer, reader, professor.
2002-2007BBSRC Research Development Fellow
2003-2004Programme Manager of the Interdisciplinary Programme for Cellular Regulation, with Dr. Nigel Burroughs (Maths).
2004-presentUniversity of Edinburgh, School of Biological Sciences - Professor of Systems Biology.
2007-2011Director, Centre for Systems Biology at Edinburgh (CSBE)
2012-presentAssociate Director, SynthSys
2011-2013Elected to EMBO Membership and Fellowship of the Royal Society and Royal Society of Edinburgh.

Research groupings

Institute of Structural and Molecular Biology; SynthSys.

Teaching

I teach on Quantification in Life Sciences in the first year; on Plant Physiology and on Time, Light and Stress in final year Bachelor's course, as well as the Systems and Synthetic Biology Masters course.

Research interests

Our research aims to understand how the 24-hour biological clock is constructed and adjusted, why it (and other clocks) has evolved in the way that we now find it, and how it affects plant life from the cell to the ecosystem. Most of our research focuses on Arabidopsis thaliana, which is a small plant with a big following. For an even simpler version of the plant clock mechanism, we study the smallest free-living eukaryote of all, the tiny alga Ostreococcus tauri. Molecular genetics and transgenic plants help us by revealing rhythms that are usually invisible: for example, we use a reporter gene called luciferase to send us video footage when other genes are active. Mathematical modelling helps us to understand dynamic, quantitative regulation, to abstract the principles behind the molecular detail, and to cross length and time scales from the cell to the whole organism. This is particularly important in the EU FP7 TiMet project, understanding the links from the clock to plant metabolism.

Our experimental methods combine real-time video imaging of transcription and signal transduction in transgenic plants carrying reporter genes (luciferase and fluorescent proteins), with Arabidopsis mutants, molecular approaches and whole-plant physiology. Our work in Ostreococcus discovered a completely new clock mechanism that operates without rhythmic gene activity, and might be shared among all organisms, as I outline in this short video. Measuring dynamic biochemistry is a key challenge for our models, so we have been using biophysical methods with our colleagues in SynthSys, including label-free (phospho)proteomics at the KPF.

We continue to develop gene network models of the plant circadian clock mechanism and mathematical methods to analyse dynamic mechanisms, with colleagues at EPCC, Edinburgh's supercomputer centre, and external institutions. We and our collaborators built the BioDare to integrate rhythmic timeseries analysis with a data-sharing repository, the PlaSMo model repository to disseminated curated crop science, ecology and systems biology models, and we contribute to the Systems Biology Software Infrastructure, which makes high-performance computers accessible for model optimisation.

The challenge of providing global Food Security in the coming decades will require all the power of multi-scale models, to integrate understanding from plant and animal sciences, through agriculture to social science and medicine. Our work in Systems Biology can contribute to this effort with basic plant biology, with modelling methods, and with an open approach to working across the academic disciplines.

For more research details, please see the lab web page http://www.amillar.org, and the video.

Twitter: @A_J_Millar, @CSBE_SBSI, @TiMet_Project

Representative publications

For a full list of publications, please click here.

  1. Pokhilko, A., Mas, P. & Millar, A. J. 2013 Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. BMC Systems Biology. 7: 23. doi: 10.1186/1752-0509-7-23. SBML model in PlaSMo Highly accessed article.  
  2. Gould, P. D., Ugarte, N., Domijan, M., Costa, M., Foreman, J., Macgregor, D., Rose, K., Griffiths, J., Millar, A. J., Finkenstadt, B., Penfield, S., Rand, D. A., Halliday, K. J. & Hall, A. J. W. 2013 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Molecular Systems Biology. 9: 650. doi: 10.1038/msb.2013.7. SBML model in PlaSMo.
  3. Ocone, A., Millar, A.J., and Sanguinetti, G. (2013). Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics. Bioinformatics. doi: 10.1093/bioinformatics/btt069.
  4. Adams, R. , Clark, A. , Yamaguchi, A. , Hanlon, N. , Tsorman, N. , Ali, S. , Lebedeva, G. , Goltsov, A. , Sorokin, A. , Akman, O. E. , Troein, C. , Millar, A. J. , Goryanin, I. & Gilmore, S. SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology (2013) Bioinformatics. doi:10.1093/bioinformatics/btt023. Link
  5. Schaum, E. , Rost, B. , Millar, A. J. & Collins, S. (2013) Variation in plastic responses of a globally distributed picoplankton species to ocean acidification. Nature Climate Change 3, 298-302. Link
  6. van Ooijen G. and Millar A.J. (2012) Non-transcriptional oscillators in circadian timekeeping. Trends Biochem. Sci. . Online 20 August 2012. doi: 10.1016/j.tibs.2012.07.006 Link [review paper, peer-reviewed].
  7. Frank Dondelinger, Simon Rogers, Maurizio Filippone, Roberta Cretella, Tim M. Palmer, Robert W. Smith, Andrew J. Millar and Dirk Husmeier (2012) Parameter Inference In Mechanistic Models Of Cellular Regulation And Signalling Pathways Using Gradient Matching. WCSB 2012, Ninth International workshop on computational systems biology, Finland. (accepted).
  8. Gerben van Ooijen, Kirsten Knox, Katalin Kis, Francois-Yves Bouget, Andrew J. Millar (2012) Genomic transformation of the picoeukaryote Ostreococcus tauri. J. Vis. Exp. 65: e4074. doi:10.3791/4074. Link
  9. Adams, R. R. , Tsorman, N. , Stratford, K. , Akman, O. E. , Gilmore, S. , Juty, N. , Le Novere, N. , Millar, A. J. & Millar, A. J. (2012) The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models. Journal of Biological Rhythms. 27: 328-332. doi:10.1177/0748730412451077. Link
  10. Young Hun Song, Robert W. Smith, Benjamin J. To, Andrew J. Millar, Takato Imaizumi (2012) FKF1 conveys crucial timing information for CONSTANS stabilization in photoperiodic flowering. Science 336: 1045-1049. Online 25 May 2012. doi: 10.1126/science.1219644 Link Featured in: F1000Prime 4*. Multiple reviews. F1000.com/716497817  
  11. Edgar R.S.*, Green E.W.*, Zhao Y.*, van Ooijen G.*, Olmedo M.*, Qin X., Xu Y., Pan M., Valekunja E.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) Peroxiredoxins are conserved markers of circadian rhythms. Nature 485: 459-464. Online 16 May 2012. doi: 10.1038/nature11088. Link. Corrigendum 8 Aug 2012. Link.     Featured in: F1000Prime 6*. Multiple reviews. F1000.com/716597871 Ewen Callaway, A biological clock to wind them all, Nature News 16 May 2012. Debora MacKenzie, Biological clock began ticking 2.5 billion years ago, New Scientist 2865, 16 May 2012. Sarah Evert, Picking Apart Our Circadian Clock, Chemical & Engineering News, 90: 30. June 4, 2012. Andrew S.I. Loudon, Circadian Biology: A 2.5 Billion Year Old Clock, Current Biology 22: R570-R571.  
  12. Ozgur E. Akman*, Steven Watterson, Andrew Parton, Nigel Binns, Andrew J. Millar** and Peter Ghazal** (2012) Digital clocks: simple Boolean models can quantitatively describe circadian systems. J R Soc Interface 9: 2365-82. Online 12 April. *corresponding author; **senior authors. doi: 10.1098/​rsif.2012.0080 Link
  13. Benedicte Wenden, David L. K. Toner, Sarah K. Hodge, Ramon Grima, Andrew J. Millar (2012) Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proc. Natl. Acad. Sci. USA, 109: 6757-62. online 10 April. doi: 10.1073/pnas.1118814109. Link  

    Featured in: F1000Prime 3*. Multiple reviews. F1000.com/716747960  

  14. Huang W, Perez-Garcia P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P. (2012) Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science 336: 75-59. Online Mar 8. doi: 10.1126/science.1219075 Link Featured in: F1000Prime 3*. Harmer S: 2012. F1000.com/14245972  
  15. Pokhilko A, Fernandez AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ. (2012) The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 8: 574. doi: 10.1038/msb.2012 Link Featured in: Mol Syst Biol Featured Article, and Top Download. F1000Prime 3*. Harmer S: 2012. F1000.com/14247957