Research output per year
Research output per year
- 1 - 50 out of 208 results
Search results
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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
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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
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2022
SARS-CoV-2 monitoring in Scottish wastewater: Variant Detection, FAIR data Outputs and Lessons Learned
Gilbert, N., Fletcher, I., Lyall, C., Scorza, L. C. T., Zielinski, T., Baby, S. V. & Millar, A. J., 23 Nov 2022, CREW. 47 p.Research output: Book/Report › Commissioned report
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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
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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
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Not going to waste - preserving Scotland's COVID-19 wastewater data
Scorza, L., Zielinski, T., Baby, S. V., Cameron, G. & Millar, A. J., 27 May 2022.Research output: Contribution to conference › Poster
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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
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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
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2021
Period estimation and rhythm detection in timeseries data using BioDare2, the free, online, community resource
Zieliński, T., Hay, J. & Millar, A. J., 22 Oct 2021, (E-pub ahead of print) Plant Circadian Networks: Methods and Protocols. Springer, Vol. 2398. p. 15-32 18 p. (Methods in molecular biology (Clifton, N.J.)).Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed) › peer-review
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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
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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
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2019
pyNMMSO, a python implementation of the Niching Migratory Multi-Swarm Optimiser
Hume, A., Wood, C. & Millar, A. J., 24 Dec 2019Research output: Non-textual form › Software
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Nurturing cross-disciplinary research: Institutional logics, hybrid spaces and meta-organization at a research university
Freeman, P. L., Marr, I., Millar, A. J. & Kitagawa, F., 9 Dec 2019, SocArXiv.Research output: Working paper
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Nurturing project organizations: A mode 2 mission for the university?
Freeman, P. L., Marr, I., Millar, A. J. & Kitagawa, F., 9 Dec 2019, SocArXiv.Research output: Working paper
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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
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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 Sept 2019, bioRxiv, at Cold Spring Harbor Laboratory.Research output: Working paper
Open Access -
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
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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
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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
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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
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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 journal › Review article › peer-review
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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
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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
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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
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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
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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
Open Access -
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
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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
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Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime
Noordally, Z. B., Hindle, M., Martin, S., Seaton, D. D., Simpson, T., Le Bihan, T. & Millar, A., 4 Apr 2018, bioRxiv, at Cold Spring Harbor Laboratory, 35 p.Research output: Working paper
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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
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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 proceeding › Conference contribution
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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 others, 1 Oct 2017, In: Journal of biological rhythms. 32, 5, p. 380-393 14 p., 748730417728663.Research output: Contribution to journal › Article › peer-review
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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
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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
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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
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BioDare2, online data analysis resource
Zielinski, T. & Millar, A., Jun 2017Research output: Non-textual form › Software
Open Access -
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, 15 May 2017, In: Frontiers in plant science. 8, 786.Research output: Contribution to journal › Article › peer-review
Open Access -
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
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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. 23-30Research output: Contribution to journal › Article › peer-review
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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
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Chromar, a rule-based language of parameterised objects
Honorato Zimmer, R., Millar, A., Plotkin, G. & Zardilis, A., 7 Sept 2016, The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016). 14 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
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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. 1955-1981Research output: Contribution to journal › Article › peer-review
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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, bioRxiv, at Cold Spring Harbor Laboratory, 9 p.Research output: Working paper
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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. 595-618Research output: Contribution to journal › Literature review › peer-review
Open Access -
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/Report › Other report
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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. 202Research output: Contribution to journal › Literature review › peer-review
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2015
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
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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, (E-pub ahead of print) In: Plant, Cell and Environment. 39 , 5, p. 1049–1057Research output: Contribution to journal › Literature review › peer-review
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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
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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/Report › Other report
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