This paper presents ATEM, a novel framework for studying topic evolution in scientific archives. ATEM employs dynamic topic modeling and dynamic graph embedding to explore the dynamics of content and citations within a scientific corpus. ATEM explores a new notion of citation context that uncovers emerging topics by analyzing the dynamics of citation links between evolving topics. Our experiments demonstrate that ATEM can efficiently detect emerging cross-disciplinary topics within the DBLP archive of over five million computer science articles.