Emma J. Cooke

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Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in(More)
A model is presented describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified(More)
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single(More)
Post-genomic molecular biology has resulted in an explosion of data, providing measurements for large numbers of genes, proteins and metabolites. Time series experiments have become increasingly common, necessitating the development of novel analysis tools that capture the resulting data structure. Outlier measurements at one or more time points present a(More)
We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that(More)
A major challenge in systems biology is the ability to model complex regulatory interactions, such as gene regulatory networks, and a number of computational approaches have been developed over recent years to address this challenge. This paper reviews a number of these approaches, with a focus on probabilistic graphical models and the integration of(More)
December 21, 2016 Type Package Title Bayesian Hierarchical Clustering Version 1.26.0 Date 2011-09-07 Author Rich Savage, Emma Cooke, Robert Darkins, Yang Xu Maintainer Rich Savage <r.s.savage@warwick.ac.uk> Description The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and(More)
Oliver Windram,a,1,2 Priyadharshini Madhou,a,1,3 Stuart McHattie,b Claire Hill,a Richard Hickman,b,4 Emma Cooke,c Dafyd J. Jenkins,b Christopher A. Penfold,b Laura Baxter,b Emily Breeze,a,b Steven J. Kiddle,b,5 Johanna Rhodes,a Susanna Atwell,d Daniel J. Kliebenstein,d Youn-sung Kim,a,6 Oliver Stegle,e Karsten Borgwardt,e,f Cunjin Zhang,a,7 Alex Tabrett,a(More)
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