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Lamanite Identity and the Book of Mormon." In Shaken Faith Syndrome: Strengthening One’s Testimony In the Face of Criticism and Doubt, 195-207. 2nd ed. Redding, CA: FairMormon, 2013.
"Book of Mormon Concerns." In Bamboozled by the CES Letter, 21-40. n.p., 2015.
" "Book of Mormon Concerns & Questions." In A CES Letter Reply: Faithful Answers For Those Who Doubt. Sandy, UT: n.p., 2018.
"KnoWhy #280 - Why Hasn’t Lehi’s DNA Been Found? (Introduction, 2013 edition of the Book of Mormon). Springville, UT: Book of Mormon Central, 2017.
The Book of Mormon at the Bar of DNA “Evidence”." Journal of Book of Mormon Studies 12, no. 1 (2003): 4-5.
"Addressing Questions surrounding the Book of Mormon and DNA Research." The FARMS Review 18, no. 1 (2006): 101-108.
"A Few Thoughts from a Believing DNA Scientist." Journal of Book of Mormon Studies 12, no. 1 (2003): 36-37.
"Appendix, On Aping Aristotle: Modern-day Simplicios." The FARMS Review 15, no. 2 (2003): lxiii-lxvii.
"Cotton and the Book of Mormon." Improvement Era 65, no. 10 (1962): 722-724, 751-753.
"Insights, Vol. 24, No. 1 (2004) In Insights, Edited by FARMS Staff. Vol. 1. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.
Insights, Vol. 23, No. 2 (2003) In Insights, Edited by FARMS Staff. Vol. 2. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2003.
U.A.S. Newsletter, no. 61 (September 9, 1961), Edited by Dee F. Green. Vol. 61. Provo, UT: University Archaeological Society, Brigham Young University, 1961.
Insights, Vol. 26, No. 2 (2006) In Insights, Edited by Maxwell Institute Staff. Vol. 2. Provo, UT: Neal A. Maxwell Institute for Religious Scholarship, 2006.
Insights, Vol. 28, No. 1 (2008) In Insights, Edited by Maxwell Institute Staff. Vol. 1. Provo, UT: Neal A. Maxwell Institute for Religious Scholarship, 2008.
Detecting Lehi's Genetic Signature: Possible, Probable, or Not?" The FARMS Review 15, no. 2 (2003): 35-90.
"Who Are the Children of Lehi?" Journal of Book of Mormon Studies 12, no. 1 (2003): 38-51, 116.
"Who Are the Children of Lehi? In Who Are the Children of Lehi? DNA and the Book of Mormon. Salt Lake City: Greg Kofford Books, 2007.
The Children of Lehi: DNA and the Book of Mormon In 2003 FAIR Conference. Orem, UT: FairMormon, 2003.
Missing the Boat to Ancient America . . . Just Plain Missing the Boat." The FARMS Review 17, no. 1 (2005): 83-106.
"Using Science to Answer Questions from Latter-day Saint History: The Case of Josephine Lyon’s Paternity." BYU Studies Quarterly 58, no. 4 (2019): 143-150.
"Is Decrypting the Genetic Legacy of America's Indigenous Populations Key to the Historicity of the Book of Mormon?" Interpreter: A Journal of Mormon Scripture 12 (2014): 237-279.
"Is Decrypting the Genetic Legacy of America’s Indigenous Populations Key to the Historicity of the Book of Mormon?" Interpreter: A Journal of Latter-day Saint Faith and Scholarship 38 (2020): 355-390.
"Joseph Smith DNA Revealed: New Clues from the Prophet’s Genes In 2008 FAIR Conference. Sandy, UT: FairMormon, 2008.
Editor's Introduction—Not So Easily Dismissed: Some Facts for Which Counterexplanations of the Book of Mormon Will Need to Account." The FARMS Review 17, no. 2 (2005): xi-xlix.
"Editor's Introduction: Of “Galileo Events,” Hype, and Suppression: Or, Abusing Science and Its History." The FARMS Review 15, no. 2 (2003): ix-lxi.
"Prolegomena to the DNA Articles." The FARMS Review 15, no. 2 (2003): 25-34.
"The FARMS Review 15/2 (2003), Edited by Daniel C. Peterson. Vol. 15. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2003.
Swimming in the Gene Pool: Israelite Kinship Relations, Genes, and Genealogy." The FARMS Review 15, no. 2 (2003): 129-164.
""New Light: The Problematic Role of DNA Testing in Unraveling Human History." Journal of Book of Mormon Studies 9, no. 2 (2000): 66-74, 83-84.
Before DNA." Journal of Book of Mormon Studies 12, no. 1 (2003): 6-23, 113-115.
""New Light." Journal of Book of Mormon Studies 9, no. 1 (2000): 70-73, 80.
DNA and the Book of Mormon In 2006 FAIR Conference. Sandy, UT: FairMormon, 2006.
DNA and the Book of Mormon." The FARMS Review 18, no. 1 (2006): 109-138.
"Elusive Israel and the Numerical Dynamics of Population Mixing." The FARMS Review 15, no. 2 (2003): 165-182.
"Reinventing the Book of Mormon." The FARMS Review 16, no. 2 (2004): 91-106.
"DNA and the Book of Mormon: A Phylogenetic Perspective." Journal of Book of Mormon Studies 12, no. 1 (2003): 24-35, 115-116.
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