This article introduces a number of methods that can be useful for examining the emergence of large-scale structures in collaboration networks. The study contributes to sociological research by investigating how clusters of research collaborators evolve and sometimes percolate in a collaboration network. Typically, we find that in our networks, one cluster among the leading ones eventually wins the growth race by percolating through the network, spanning it and rapidly filling up a significant volume of it. We show how this process is governed by the dynamics of cluster growth in the network. When operating in a percolating regime, this class of networks possesses many useful functional properties, which have important sociological implications. We first develop the methodological tools to perform a study of the intrinsic clustering process. Then, to understand the actual large-scale structure formation process in the network, we apply the theoretical methods to simulate a number of realistic scenarios, including one based on actual data on the collaboration behavior of a sample of researchers. From the perspective of social science research, our methods can be adapted to suit the application domains of many other types of real social processes. © 2015, © The Author(s) 2015.