Gee, John. "Four Suggestions on the Origin of the Name Nephi." In Pressing Forward with the Book of Mormon: The FARMS Updates of the 1990s, edited by John W. Welch and Melvin J. Thorne, 1-5. Provo, UT: FARMS, 1999.

Gee, John. "Notes and Communications - A Note on the Name Nephi." Journal of Book of Mormon Studies 1, no. 1 (1992): 189-191.

Gee, John. "Notes and Communications - A Note on the Name Nephi." Journal of Book of Mormon Studies 1, no. 1 (1992): 189-191.

Gee, John. "Notes and Communications: Another Note on the Three Days of Darkness." Journal of Book of Mormon Studies 6, no. 2 (1997): 235-244.

Gee, John. "Epigraphic Considerations on Janne Sjodahl’s Experiment with Nephite Writing." Journal of Book of Mormon Studies 10, no. 1 (2001): 25, 79.

Gee, John. "The Wrong Type of Book." In Echoes and Evidences of the Book of Mormon, edited by Donald W. Parry, Daniel C. Peterson and John W. Welch, 307-329. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2002.

Gee, John. "How Not to Read Isaiah." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 37 (2020): 29-40.

Gee, John. "The Implications of Some Standard Assumptions of New Testament Scholars: Responding to a Modern Anti-Christ." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 46 (2021): 15-32.