Prior to arriving at Carnegie Mellon, Murphy was a Damon Runyon Cancer Research Foundation postdoctoral fellow with Dr. Charles R. Cantor at Columbia University from 1979 through 1983.

He received a Presidential Young Investigator Award[2] from the National Science Foundation shortly after joining the faculty at Carnegie Mellon in 1983.

He has co-edited two books and two special journal issues on “Cell and Molecular Imaging,” and published over 200 research papers.

He and his collaborators did extensive work on the application of flow cytometry to analyze endocytic membrane traffic beginning in the early 1980s[9][10][11] and pioneered the application of machine learning methods to high-resolution fluorescence microscope images depicting subcellular location patterns in the mid-1990s.

[14][15][16] He founded the CellOrganizer project for learning generative models of cell organization directly from microscope images.