The myriad of high-throughput methods available for probing biological samples has drastically boosted our ability to gather comprehensive molecular-level information on an increasing number of organisms. Unfortunately, our understanding of biological systems has not grown proportionally. I will talk about two different problems in which the analysis of large pools of data can help us extract knowledge from the "sea" of available information: evolutionary processes and the organization of complex networks. First, I will show that the systematic analysis of protein families enables us to assess evolutionary relationships between species and to discriminate between theories about the origin of eukaryotes. Second, I will present a set of methods that is able to accurately extract the hierarchical organization of complex networks and how such methods are able to summarize the information stored in biochemical networks.