Following the completion of his doctorate, Ganguli became a postdoctoral fellow at the University of California, San Francisco, a position he held until 2012. He had authored and co-authored a number of papers on theoretical neuroscience prior to this in the late 2000s (collaborating with Haim Sompolinsky, Peter Latham, and Ken Miller in the process) and further taught a course on advanced theoretical neuroscience with Larry Abbott, Stefano Fusi, and Ken Miller in 2008, but it was at this point that Ganguli formally transitioned into theoretical neuroscience, assuming the position at the Sloan-Swartz Center for Theoretical Neurobiology.