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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. "Another Note on the Three Days of Darkness." In Pressing Forward with the Book of Mormon: The FARMS Updates of the 1990s, edited by John W. Welch and Melvin J. Thorne, 219-227. Provo, UT: FARMS, 1999.
Gee, John. "Two Notes on Egyptian Script." In Pressing Forward with the Book of Mormon: The FARMS Updates of the 1990s, edited by John W. Welch and Melvin J. Thorne, 244-247. Provo, UT: FARMS, 1999.
Gee, John, and Matthew Roper. ""I Did Liken All Scriptures Unto Us": Early Nephite Understandings of Isaiah Implications for "Others" in the Land." In The Fulness of the Gospel: Foundational Teachings from the Book of Mormon, edited by Camille Fronk Olson, Brian M. Hauglid, Patty Smith and Thomas A. Wayment, 51-65. Provo, UT: Religious Studies Center, 2003.
Gee, John, and Daniel C. Peterson. "Graft and Corruption: On Olives and Olive Culture in the Pre-Modern Mediterranean." In The Allegory of the Olive Tree: The Olive, the Bible, and Jacob 5, edited by Stephen D. Ricks and John W. Welch, 186-247. Provo, UT/Salt Lake City: Foundation for Ancient Research and Mormon Studies/Deseret Book, 1994.
Gee, John. ""Choose the Things That Please Me": On the Selection of the Isaiah Sections in the Book of Mormon." In Isaiah in the Book of Mormon, edited by Donald W. Parry and John W. Welch, 67-91. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.
Gee, John. "A Different Way of Seeing the Hand of the Lord." Religious Educator: Perspectives on the Restored Gospel 16, no. 2 (2015): 11-127.
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. "Limhi in the Library." Journal of Book of Mormon Studies 1, no. 1 (1992): 54-66.
Gee, John. "Notes and Communications: Two Notes on Egyptian Script." Journal of Book of Mormon Studies 5, no. 1 (1996): 162-176.
Gee, John. "Notes and Communications: New and Old Light on Shawabtis from Mesoamerica." Journal of Book of Mormon Studies 6, no. 1 (1997): 64-69.
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. "Formulas and Faith." Journal of the Book of Mormon and Other Restoration Scripture 21, no. 1 (2012): 60-65.
Gee, John. "Abraham and Idrimi." Journal of the Book of Mormon and Other Restoration Scripture 22, no. 1 (2013): 34-39.
Gee, John. "Has Olishem Been Discovered?" Journal of the Book of Mormon and Other Restoration Scripture 22, no. 2 (2013): 104-107.
Gee, John. "Robert L. Millet, By Grace Are We Saved." Review of Books on the Book of Mormon 2, no. 1 (1990): 100-106.
Gee, John. "Wilford A. Fischer and Norma J. Fischer, A Book of Mormon Guide: A Simple Way to Teach a Friend." Review of Books on the Book of Mormon 2, no. 1 (1990): 77-85.
Gee, John. "A Tragedy of Errors." Review of Books on the Book of Mormon 4, no. 1 (1992): 93-119.
Gee, John. "Daniel H. Ludlow, ed., The Encyclopedia of Mormonism." Review of Books on the Book of Mormon 5, no. 1 (1993): 172-182.
Gee, John. "La Trahison des Clercs: On the Language and Translation of the Book of Mormon." Review of Books on the Book of Mormon 6, no. 1 (1994): 51-120.
Gee, John. "The Grace of Christ." FARMS Review 22, no. 1 (2010): 247-259.
Gee, John. "A Book of Mormon Christology at Last." FARMS Review of Books 10, no. 2 (1998): 7-8.
Gee, John. "Some Notes on the Anthon Transcript." FARMS Review of Books 12, no. 1 (2000): 5-8.
Gee, John. "“Bird Island” Revisited, or the Book of Mormon through Pyramidal Kabbalistic Glasses." Review of Books on the Book of Mormon 7, no. 1 (1995): 219-228.
Gee, John. "Abracadabra, Isaac and Jacob." Review of Books on the Book of Mormon 7, no. 1 (1995): 19-84.
Gee, John. "Telling the Story of the Joseph Smith Papyri." FARMS Review of Books 8, no. 2 (1996): 46-59.
Gee, John. "Who Was Not the Pharaoh of the Exodus." FARMS Review of Books 9, no. 1 (1997): 43-50.
Gee, John. "A Seething Pot in the North: International Affairs Leading Up to Lehi's Day." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 543-560. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.
Gee, John. "Egyptian Society during the Twenty-sixth Dynasty." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 277-298. Provo, UT: Foundation for Ancient Research And Mormon Studies, 2004.
Gee, John. The Role of the Book of Abraham in the Restoration. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1997.
Gee, John. A History of the Joseph Smith Papyri and Book of Abraham. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1999.
Gee, John. The Ancient Owners of the Joseph Smith Papyri. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1999.
Gee, John. The Crocodile God of Pharaoh in Mesopotamia In Insights. Vol. 108. Foundation for Ancient Research and Mormon Studies, 1996.
Gee, John. "The Hagiography of Doubting Thomas." FARMS Review of Books 10, no. 2 (1998): 158-183.
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. "Facsimile 3 and Book of the Dead 125." In Astronomy, Papyrus, and Covenant, edited by John Gee and Brian M. Hauglid, 95-105. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.
Gee, John, William J. Hamblin, and Daniel C. Peterson. ""And I Saw the Stars": The Book of Abraham and Ancient Geocentric Astronomy." In Astronomy, Papyrus, and Covenant, edited by John Gee and Brian M. Hauglid, 1-16. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.
Astronomy, Papyrus, and Covenant In Studies in the Book of Abraham, Edited by John Gee and Brian M. Hauglid. Provo, UT: Foundation for Ancient Research and Mormon Studies, Brigham Young University, 2005.
Gee, John. Notes on the Sons of Horus. Provo, UT: FARMS, 1991.
Gee, John. "The Joseph Smith Papers Project Stumbles." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 33 (2019): 175-186.
Gee, John. "“An Obstacle to Deeper Understanding”." FARMS Review of Books 12, no. 2 (2000): 185-224.
Gee, John. "One Side of a Nonexistent Conversation." The FARMS Review 15, no. 1 (2003): 81-85.
Gee, John. "The Old Testament as Reliable History." The FARMS Review 18, no. 1 (2006): 425-430.
Gee, John. "A Method for Studying the Facsimiles." The FARMS Review 19, no. 1 (2007): 347-353.
Gee, John. "New Light on the Joseph Smith Papyri." The FARMS Review 19, no. 2 (2007): 245-259.
Gee, John. "Some Puzzles from the Joseph Smith Papyri." The FARMS Review 20, no. 1 (2008): 113-137.
Gee, John. "On Corrupting the Youth." The FARMS Review 22, no. 2 (2010): 195-228.
Gee, John. "Taking Stock." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 34 (2020): 113-118.
Gee, John. "Conclusions in Search of Evidence." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 34 (2020): 161-178.
Gee, John. Book of Mormon Word Usage: "Seal You His" In Insights. Vol. 22. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2002.
Gee, John. "Four Idolatrous Gods in the Book of Abraham." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 38 (2020): 133-152.
Gee, John. "How Not to Read Isaiah." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 37 (2020): 29-40.
Gee, John. "Prolegomena to a Study of the Egyptian Alphabet Documents in the Joseph Smith Papers." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 42 (2021): 77-98.
Gee, John. "Fantasy and Reality in the Translation of the Book of Abraham." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 42 (2021): 127-170.
Gee, John. "Eyewitness, Hearsay, and Physical Evidence of the Joseph Smith Papyri." In The Disciple as Witness: Essays on Latter-day Saint History and Doctrine in Honor of Richard Lloyd Anderson, edited by Stephen D. Ricks, Donald W. Parry and Andrew H. Hedges, 175-217. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2000.