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Traditional studies in the sociology of science have highlighted the self-organized character of the academic community. This article focuses on recent interrelated changes that alter that distinctive governance structure and its related patterns of competition and cooperation. The changes that we identify here are contractualization and large-scale cooperative research. We use different data sources to exemplify these new patterns and discuss the illustrative role of research clusters in German academia. Research clusters as funded by the German Research Foundation (DFG) are both a highly prestigious scarce good in the competition for reputation and resources and a means of fostering cooperation. Our analysis of this German example reveals that this new institutional configuration of universities as organizations, academic researchers, and the state has a profound effect on organizational practices. We discuss the implications of our empirical findings with regard to collegiality in academia. Ultimately, we anticipate a further weakening of collegial bonds, not only because universities and the state have become more active in shaping the nature of academic competition and cooperation but also because of the increasing strategic and individualistic orientation of academic researchers. In the final section, we summarize our findings and address the need for further research and an international comparative perspective.