Methods and apparatus are disclosed for regular expression matching, especially for, but not limited to high-speed applications such as in a packet switching system (e.g., a router). One implementation includes a matching mechanism for processing each character of a plurality of input characters to progressively generate keyword indications of matched keywords as matched keywords are identified, and for generating one or more matching indications of matched base expressions and non-keyword expressions. These indications are received by a matched regular expression detection mechanism which generates one or more matched regular expression indications based on said one or more keyword indications and said one or more matching indications. In one implementation, the matched regular expression detection mechanism maintains a keyword data structure, which is updated as matched keyword indications are received to ensure they are matched in a proper order. One implementation uses a bitmap to track the matched keywords and AND-SHIFT-OR operations to efficiently update the bitmap.

 
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> Method for correlating gene expression profiles with protein expression profiles

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