Ten years of pathway analysis: current approaches and outstanding challenges.
PLoS Comput Biol. 2012 Feb; 8(2):e1002375
This well-written paper reviews methods for pathway-based analysis of 'omics' data, that is methods that provide functional context for a selected list of biological entities obtained by high throughput experiments; the strengths and weaknesses of the three generations of methods are presented, as well as perspectives on current challenges...
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