Alton C. Dooley, Jr., Eric Scott, Jeremy Green, Kathleen B. Springer, Brett S. .Dooley, Gregory James Smith, 2019. Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North American. PeerJ 7:e6614 https://doi.org/10.7717/peerj.6614
Nancy D. Moncrief and Alton C. Dooley, Jr., 2013. Using fluorescence of bones and teeth to detect remains of the Eastern Fox Squirrel (Sciurus niger) in archaeological deposits. Southeastern Archaeology 32:46-53.
Brian Lee Beatty and Alton C. Dooley, Jr., 2013. The first terrestrial mammal from the Late Miocene Eastover Formation of Virginia. Jeffersoniana 29, 6 pp.
Alton C. Dooley, Jr. and Nancy D. Moncrief, 2012. Fluorescence provides evidence of congenital erythropoietin porphyria in 7000-year-old specimens of the eastern fox squirrel (Sciurus niger) from the Devil’s Den. Journal of Vertebrate Paleontology 32:495-497.
Anna R. Trochim and A. C. Dooley, Jr., 2010. Diatom biostratigraphy and paleoecology of vertebrate-bearing Miocene localities in Virginia. Jeffersoniana 23:1-18.
Brian L. Beatty and Alton C. Dooley, Jr., 2009. Injuries in a Mysticete Skeleton from the Miocene of Virginia, With a Discussion of Buoyancy and the Primitive Feeding Mode in Chaeomysticeti. Jeffersoniana 20, 28 pp.
Alton C. Dooley, Jr., 2009. Unusual Cambrian thrombolites from the Boxley Blue Ridge Quarry, Bedford County, Virginia. Jeffersoniana 19, 13 pp.
Alton C. Dooley, Jr., 2007. Barstovian (middle Miocene) land mammals from the Carmel Church Quarry, Caroline County, Virginia. Jeffersoniana 18, 17 pp.
N. C. Fraser, P. E. Olsen, Alton C. Dooley, Jr., and T. R. Ryan, 2007. A new gliding reptile (Diapsida: ?Archosauromorpha) from the Upper Triassic (Carnian) of Virginia. Journal of Vertebrate Paleontology 27:261-265.
Alton C. Dooley, Jr. Nicholas C. Fraser, and Zhe-Xi Luo, 2004. The earliest known member of the rorqual-gray whale clade (Mammalia, Cetacea). Journal of Vertebrate Paleontology 24:453-463.
Alton C. Dooley, Jr., 2003. A review of the eastern North American Squalodontidae (Mammalia: Cetacea). Jeffersoniana 11, 26 pp.