He began graduate study with James M. Robinson, who took Emmel with him to Cairo, Egypt, in 1974 as a research assistant in the international project to publish the Coptic Gnostic texts of the Nag Hammadi Codices.
[3] During those years he traveled several times to Jerusalem to meet with the Egyptologist and linguist H. J. Polotsky in order to deepen his knowledge of Coptic grammar.
In 1978 Emmel resumed his graduate study, now with Bentley Layton at Yale University, where in 1980 he discovered a part of Nag Hammadi Codex III in the Beinecke Rare Book and Manuscript Library, which had acquired the previously unidentified fragment in 1964 among a group of miscellaneous papyri.
At about that same time, he became the first scholar to see the now famous Gnostic scripture titled "The Gospel of Judas," in what is now called the Codex Tchacos, when it was offered for sale in 1983 in Geneva, Switzerland.
[14] He was a founding editor of the Journal of Coptic Studies (Leuven: Peeters, 1988–2001 with Gerald M. Browne), and he has helped to edit several scientific monograph series.