- Pyenson, N.D., R.B. Irmis, and J.H. Lipps. 2010. Comment on "Climate, Critters, and Cetaceans: Cenozoic Drivers of the Evolution of Modern Whales." Science, 330: 178-a.
- Domning, D. P., and N. D. Pyenson. 2008. "Snagging" Teeth and premolar homologies in Paleoparadoxiidae (Mammalia: Desmostylia). Journal of Vertebrate Paleontology 28(3):923-927.
- Pyenson, N. D., J. A. Goldbogen, and R. E. Shadwick. 2008. Understanding the evolution of lunge-feeding in Balaenopteridae by integrating biomechanics and phylogenetic comparative methods with the fossil record. Fifth Conference on Secondary Adaptation of Tetrapods to Life in Water, Kohno, N. (ed.); National Museum of Nature and Science, Tokyo, Japan. Pp. 65-66
- David, E.B., N. D. Pyenson. 2007. Diversity biases in terrestrial mammalian assemblages and quantifying the differences between museum collections and published accounts: a case study from the Miocene of Nevada. Palaeogeography, Palaeoclimatology, Palaeocology 250: 139-149. Read it
- Irmis, R. B., N. D. Pyenson, and J. H. Lipps. 2007. Formation of marine bonbeds: insights from the Middle Miocene Sharktooth Hill bonebed of California. Journal of Vertebrate Paleontology 27(3 Suppl.): 94A.
- Pyenson, N. D. 2007. Metropolitan mammoth. Berkeley Science Review 12: 52-57. Read it
- Pyenson, N. D., and K. R. Brudvik. 2007. Rare fossil baleen from the Purisima Formation of California: Implications for soft tissue preservation in shallow marine environments. Journal of Vertebrate Paleontology 27(3 Suppl.): 132A.
- Pyenson, N. D., and S. Sponberg. 2007. Reconstruction body size in extinct crown Cetacea using allometric scaling, phylogenetic comparative methods, and tests from the fossil record. In Warren, A. (ed), Conference on Australiasian Vertebrate Evolution, Palaeontology and Systematics 2007, Geological Society of Australia Abstracts 85:51-52.
- Uhen, M. D. and N. D. Pyenson. 2007. Diversity estimates, biases, and historiographic effects: resolving cetacean diversity in the Tertiary. Palaeontologia Electronica 10(2):11A:22p. Read it
- Werth, A. J., B. L. Beatty, N. D. Pyenson. 2007. Do odontocetes masticate? Investigating evidence from tooth wear, homodonty and enamel microstructure. Journal of Vertebrate Paleontology 27(3 Suppl.): 165A.
- Haasl, D.M., and N.D. Pyenson. 2006. A whale skeleton-bivalve community from the Late Miocene of California. Geological Society of America Abstracts with Programs, Vol. 38, No. 7, p. 68.
- Pyenson, N.D., and M.F. McKenna. 2006. How did early toothed whales echolocate? An investigation of morphological evidence using phylogenetic and soft tissue inference. Journal of Vertebrate Paleontology 26(3 Suppl.):113A.
- Barnes, L.G., N.D. Pyenson, and S.A. McLeod. 2005. Middle Miocene marine ecosystems and cetacean diversity as exemplified by the Sharktooth Hill Bonebed, California, USA. Evolution of Aquatic Tetrapods, Fourth Triannual Convention Abstracts. Cranbrook Institute of Science Miscellaneous Publications 1:6-7.
- Hunt, A.P., S.G. Lucas, and N.D. Pyenson. 2005. The significance of the Union Chapel Mine site: A Lower Pennsylvanian (Westphalian A) ichnological Kozentrat-Lagerstätte, Alabama, USA. Pp. 3–14 in R.J. Buta, A.K. Rindsberg, and D.C. Kapaska-Merkel (eds.), Pennsylvanian Footprints in the Black Warrior Basin of Alabama. Alabama Paleontological Society, Monograph No. 1, Birmingham, Alabama.
- Martin, A.J., and N.D. Pyenson. 2005. Behavioral significance of vertebrate trace fossils from the Union Chapel Mine Site. Pp. 59–73 in R.J. Buta, A.K. Rindsberg, and D.C. Kapaska-Merkel (eds.), Pennsylvanian Footprints in the Black Warrior Basin of Alabama. Alabama Paleontological Society, Monograph No. 1, Birmingham, Alabama.
- Pyenson, N.D. 2005. Maxilla and mandible: tooth counts, telescoping, and the evolution of dentition in Neoceti. Journal of Vertebrate Paleontology 25(3):102A.
- Pyenson, N.D., and L. Pyenson. 2005. Treating Medieval manuscripts as fossils. Science 309:698-701.
- Davis, E.B., and N.D. Pyenson. 2003. Assessing mammalian paleofaunal diversity: discrepancies between published and museum collection data for the Miocene of northwestern Nevada, USA. Geological Society of America, 2003 Annual Meeting. Abstracts with Programs, p. 498.
- Marino, L., M.D. Uhen, N.D. Pyenson, and B. Frolich. 2003. Reconstructing cetacean brain evolution using computed tomography. The Anatomical Record (Part B: New Anatomist) 272B:107-117.
- Pyenson, N.D., and D.R. Lindberg. 2003. Phylogenetic analyses of body size in Neoceti: preliminary proxies for studying cetacean ecology in the fossil record. Abstracts for the 15th Biennial Conference on the Biology of Marine Mammals, Greensboro, NC. Pp. 133-134.
- Marino, L., M.D. Uhen, N.D. Pyenson, S. Rotenberg, B. Shamsai, and B. Frolich. 2002. Brain morphometry during cetacean (dolphin, porpoise, and whale) evolution revealed by Computed Tomography. Abstracts from the Society for Neuroscience 32nd Annual Meeting, Orlando, FL.
- Pyenson, N.D., and M.D. Uhen. 2002. Understanding cetacean diversity through the Tertiary: biases, estimates, and historiographic effects. In R.E. Fordyce and M. Walker (eds.), Secondary Adaptation to Life in Water. Department of Geology, University of Otago, Dunedin, NZ. Dec. 9-13, 2002.
- Uhen, M.D., L. Marino, and N.D. Pyenson. 2002. Evolution of cetacean brains over time, through morphospace, and among lineages. In R.E. Fordyce and M. Walker (eds.), Secondary Adaptation to Life in Water. Department of Geology, University of Otago, Dunedin, NZ. Dec. 9-13.