The university, as a transnational organization, has undergone important changes in the interactions of scientists at the individual, institutional, and organizational levels -- especially since the 1990’s. Furthermore, there have been profound improvements in opportunities for communication and collaboration that have likewise changed the global role that institutions of higher education play in scientific knowledge discovery, production, and diffusion. In addition, there have been recent initiatives such as the Bologna Process that aim to create comparable quality assurance standards for degree granting higher education institutions in 47 countries. These rather dramatic and recent changes in the international higher education system have affected the global flow of students and researchers, as well as academic patenting and commercialization activities. Ultimately, profound changes in academic mobility and communication have occurred in a relatively short period of time. Such transformations in the ways that scientific ideas spread suggest growing ambiguity and complexity in the modes of knowledge transmission and diffusion. While global competitive forces increasingly shape the higher education landscape, this paper focuses on changing forms of cooperation and collaboration, and the harmonization of policy initiatives that impact processes of knowledge diffusion such as patenting and publishing activities The primary goal of this presentation is to present a comparative and reflective discussion of global knowledge networks and the central role that universities play in them. Recent analyses indicate that these global knowledge networks are undergoing rapid transformation. Despite the criticisms that higher education is becoming too market driven, that it has become too commercial, that central tenets of the university such as academic freedom and tenure are being threatened (Schrecker, 2010; Thelin, 2004); there are important and relevant changes in the ways that research collaboration and cooperation are growing and indeed thriving despite this inherently competitive environment. This discussion is important for those who are concerned about shaping the efficacy of higher education institutions for the future and for those who are interested in promoting access to important aspects of educational opportunity. With this goal in mind, this paper describes the conceptual framework of invisible colleges and transboundary networks. Then also discusses the concept of self-organizing complex systems theory as it pertains to the invisible college of scientists around the globe. Next, the challenges of academic research alliances will be briefly discussed. Because students and scientists represent the backbone of science, they are central to research alliances which are a seemingly invisible and fluid aspect of trade in the global knowledge economy. As such, this paper will discuss how students and scientists are increasingly key actors in the growing trend toward international research collaboration networks. At the same time, students and academic scientists are central to the growing collaboration networks on patents granted to universities. Finally the implications of transboundary innovation networks on higher education and society will be discussed