The RECOMB Satellite Conferences on Systems Biology and Computational Proteomics were held December 1–3, 2006, at La Jolla, California. The Systems Biology meeting brought researchers together on various aspects of systems biology, including integration of genome-wide microarray, proteomic, and metabolomic data, inference and comparison of biological networks, and model testing through design of experiments. Specific topics included:– Pathway mapping and evolution in protein interaction networks– Inference of protein signaling networks for understanding cellular responses and developmental programs– Model prediction of drug mechanism of action and toxicity– Multi-scale methods which bridge abstract and detailed models– Systematic design of genome-scale experiments– Modeling and recognition of regulatory elements– Identification and modeling of cis-regulatory regions– Modeling the structure and function of regulatory regions– Comparative genomics of regulation