(i) Protein engineering – to apply combinatorial and design approaches for constructing novel gene network components, such as our method for building customised zinc fingers to bind any desired DNA sequence (Nature Biotechnology 19, 656-60, 2001).

(ii)  Computer modelling and network analysis - to test gene network hypotheses. Recently, we published two essays comparing gene networks to self-referential arguments in ancient Greek philosophy (Nature 458:969, 2009; Bioessays 31(10):1110-5, 2009). These essays explain intuitively how a fish might make stripe patterns, and why static network arrow diagrams are dangerous.

(iii) Synthetic Gene Network construction - to obtain desired patterns or behaviours of gene expression. For example, we built an in vitro activator-repressor gene network to read synthetic morphogen gradients  (PLoS Biology 3(3), e64, 2005). More recently, we asked the question, "What happens when you add lots of new connections to an existing large gene network?". By shuffling E. coli transcription networks with promoter-ORF fusions we were able to see how tolerant the networks are to rewiring (Nature 452:840-5, 2008). 

(iv) Localised transfection - we have developed a way of targeting DNA, containing gene network constructs, to locations within a cell population. Cells can thus be transfected to micrometer resolution using magnetic beads (Nature Methods 2: 113-118,2005). 

 

 

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