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Old News archive:

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Matt and Sarah et al. show 133 PKs in O. tauri (BMC Genomics 2014)

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Laura et al. showed flexible timing across species (New Phytol. 2014) + data in BioDare, 10 models in PlaSMo.

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Tomasz and Anne compared 6 period analysis methods (PLosone 2014),
all now online on BioDare, with step by step protocols (Meth. Mol. Biol. 2014)

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Daniel and Alexandra's clock-regulated starch degradation (JRS Interface 2013), with models in PlaSMo.

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ROBuST project identifies HOS1 as a clock gene (Plant Cell)

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ROBuST models rhythmic CBF cold pathways (Plant Journal).

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CK1 is a clock-affecting kinase in the green lineage, PLoSone and BMC Cell Bio 2013

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ROBuST temperature-compensated clock model predicts LHY regulation, Mol Syst Biol 2013.

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Alexandra's P2012 clock model explains TOC1 function and ABA input, BMC Sys Bio 2013.

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Andrea's machine learning suggests repressilator in Ostreococcus, Bioinformatics 2013

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Elisa's work shows Ostreococcus plasticity varies with location not relatedness, Nature Climate Change 2013

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Congratulations to Gerben van Ooijen, starting his lab as Royal Society Fellow.

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Gerben's review of non-transcriptional timing published in TiBS 2012

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Video protocol for Ostreococcus transformation published in JoVE 2012

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Coupled clocks make spatio-temporal waves, in PNAS 2012. Numerical data are public in BioDare

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Non-transcriptional clock marker shared across all domains of Life, in Nature 2012

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Flowering model's predicted function of FKF1 is validated, in Science 2012

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Clock model's predicted function of TOC1 is validated, in Science 2012

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Extended model finds repressilator in the plant clock, in Mol. Syst. Biol. 2012

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TiMet Logo has a new logo, from 2012

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Jan 2012: CSBE becomes SynthSys, led by Prof. Vincent Danos (Director)

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Andrew Millar elected to EMBO membership (2011) and Fellowship of the Royal Society (2012)

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Shotgun proteomics identifies 27% of Ostreococcus proteins, LeBihan et al J Proteomics 2011

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The proteasome is dispensable for non-transcriptional timing, but essential for the normal clock system, van Ooijen et al Current Biology 2011

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A non-transcriptional clock in Ostreococcus O'Neill et al. Nature 2011 (and in red blood cells!)

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9 papers in the first three months of 2011 - please see bibliography

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Data from our 2010 papers and data curated from the literature is available here.

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Plant clock model predicts function of PRR5 gene, Pokhilko et al Mol Syst Biol 2010.

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Data and analysis show how the plant clock adjusts to day length, Edwards et al Mol Syst Biol 2010.

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Link to EUClock project FP6 project ended in 2011

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Store private SBML models after optimisation with SBSI's new plugin to the PlaSMo model database.

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A fungal (Neurospora) clock model in the Bio-PEPA stochastic process algebra, Link.

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Regulatory flexibility can confer robustness to biological clocks, Akman et al. BMC Syst Biol 2010.

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CSBE's Systems Biology Software Infrastructure (SBSI) offers SBML model optimisation, tested on clock models.

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TiMet - EU FP7-funded project studies how the plant circadian clock times metabolism.

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Link to GARNet home page Andrew passed on the GARNet P.I. role in Jan 2010

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Models and timeseries data are available for the Arabidopsis photoperiod sensor from Salazar et al. Cell 2009, from the PlaSMo database of multiscale XML models.

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Congratulations on your Ph.D., Dr. Oxana Sorokina- second to graduate from the Edinburgh lab.

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Modelling the photoperiod switch in plants predicts new role for FKF1. Salazar et al. Cell 2009

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Simulated evolution shows how multiple-loop circuits contribute to timing. Troein et al. Current Biology 2009

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A light-emitting light switch in yeast, from EUClock! Sorokina et al. Journal of Biological Engineering 2009, 3:15.

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A novel machine learning algorithm applied to plant circadian data: Grzegorczyk et al. "Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler". Bioinformatics 2008.

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Synthetic Biology Standards network was launched, June 2008

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New software for sensitivity analysis of oscillator models, from Warwick (supersedes older IRC analysis).

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A general mechanism to facilitate buffering of regulatory networks: Akman et al. "Isoform switching facilitates period control in the Neurospora crassa circadian clock". Molecular Systems Biology 2008.

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PhD studentships were available (UK/UK-resident EU citizen), part of a unique 12-student cohort in Plant Systems Biology for 2008. Contact Andrew Millar or Karen Halliday for details of the ROBuST project.

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Large-scale EPSRC/BBSRC project funding: Regulation Of Biological Signalling by Temperature (ROBuST), led by K. Halliday (2008)

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BRASS 3.0 data analysis software is available, with a new analysis method as well as FFT-NLLS. (2007)

bulletNew collaboration with F.-Y. Bouget, M. Lefranc and J.Q. Smith, with ANR-BBSRC funding. (2007)
bulletVisualisation: 2-D and 3-D plots for 3-loop model are now available for download.
bulletArabidopsis 3-loop model is available for download in Circadian Modelling format, and on the Uncurated models page of BioModels, where the 2-loop model has been curated as BIOMD0000000055 (our thanks to Nicholas et al.).
bullet Centre for Systems Biology at Edinburgh (CSBE) - a BBSRC/EPSRC award of 11M aimed at modelling dynamic biological systems.
bullet PhD projects for 2007: experimental, theoretical and joint projects. Now filled, sorry.
bullet2006: Animated network diagram and movies of the Arabidopsis clock model (Locke et al. Mol Syst Biol 2005): free download.
bullet2006: Rhythmic qRT-PCR data sets from Arabidopsis for download.

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