Thompson, John S.. "Isaiah 50-51, the Israelite Autumn Festivals, and the Covenant Speech of Jacob in 2 Nephi 6-10." In Isaiah in the Book of Mormon, edited by Donald W. Parry and John W. Welch, 123-150. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.

Thompson, John S., and Eric Smith. "Isaiah and the Latter-day Saints: A Bibliographic Survey." In Isaiah in the Book of Mormon, edited by Donald W. Parry and John W. Welch, 445-509. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.

Thompson, John S.. "The Jaredite Exodus: A Literary Perspective of a Historical Narrative." Journal of Book of Mormon Studies 3, no. 1 (1994): 104-112.

Thompson, John S.. "Hoyt W. Brewster Jr., Isaiah Plain and Simple: The Message of Isaiah in the Book of Mormon." FARMS Review of Books 9, no. 2 (1997): 11-15.

Thompson, John S.. "Lehi and Egypt." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 259-276. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.

Thompson, John S.. "The Lady at the Horizon: Egyptian Tree Goddess Iconography and Sacred Trees in Israelite Scripture and Temple Theology." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 38 (2020): 153-178.

Thompson, John S.. "“We May Not Understand Our Words”: The Book of Abraham and the Concept of Translation in The Pearl of Greatest Price." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 41 (2020): 1-48.