The recent demonstration that biochemical pathways from diverse organisms are arranged in scale-free, rather than random, systems [Jeong et at., Nature 407 (2000) 651-654], emphasizes the importance of developing methods for the identification of biochemical nexuses - the nodes within biochemical pathways that serve as the major input/output hubs, and therefore represent potentially important targets for modulation. Here we describe a bioinformatics approach that identifies candidate nexuses for biochemical pathways without requiring functional gene annotation; we also provide proof-of-principle experiments to support this technique. This approach, called Nexxus. may lead to the identification of new signal transduction pathways and targets for drug design. (C) 2001 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.