Clarke, J.A.,  D.T., Ksepka, M. Stucchi, M. Urbina, N. Giannini, S. Bertelli, Y.Narváez. and C. Boyd. 2007. Eocene penguins challenge the proposed relationship between penguin biogeography, diversity, and Cenozoic climate change. Proceedings of the National Academy of Sciences, USA 104:11545-11550.

Turner, A, D. Pol and J.A. Clarke G. Erickson and M.A. Norell. 2007. A Basal Dromaeosaurid and Size Evolution Preceding Avian Flight. Science.  317:1378-1381.

Clarke, J.A., and Middleton K.M. Bird Evolution. 2006.Current Biology 16:350-354.

Clarke, J.A., Zhou, Z. and F. Zhang. 2006. Insight into the evolution of avian flight from a new clade of Early Cretaceous ornithurines from China and the morphology of Yixianornis grabaui.  Journal. of Anatomy 208:287-308.

Clarke, J.A., M.A. Norell and D. Dashzeveg. 2005. New avian remains from the Eocene of Mongolia and the phylogenetic position of the Eogruidae (Aves, Gruoidea). Am. Mus. Novitates. 3494: 1-17.

Clarke, J. A., C., Tambussi J., Noriega G., Erickson and R. Ketcham. 2005. First definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433: 305-308. PDF

Zhou, Z., J.A. Clarke, F. Zhang and O. Wings. 2004. Gastroliths in a specimen of the Early Cretaceous bird Yanornis - An indication for earliest radical diet switching and gizzard plasticity in the lineage leading to living birds. In press. Naturwissenschaften. PDF

Clarke, J. A. 2004. The Morphology, Phylogenetic Taxonomy and Systematics of Ichthyornis and Apatornis (Avialae: Ornithurae). Bulletin Am. Mus. Nat. Hist. 286:1-179.

Clarke, J. A. and M.A. Norell. 2004. New avialan remains from the Late Cretaceous of Mangolia and a reveiw of the known avifauna of the Nemegt Formation. Am. Mus. Novitates. 3447:1-12. PDF

Clarke J. A., E.Olivero, and P. Puerta. 2003. Description of the earliest fossil penguin from South America and first Paleogene vertebrate locality reported from Tierra del Fuego. Am. Mus. Novitates. 3423: 1-18. PDF

Mayr, G. and Clarke, J., 2003. The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters. Cladistics 19: 527-553. PDF

Clarke, J.A. and M.A. Norell. 2002. The morphology and phylogenetic position of Apsaravis ukhaana from the Late Cretaceous of Mongolia. Am. Mus. Novitates. 3387:1-46.

Zhou, Z., Clarke, J. and F. Zhang. 2002. Archaeoraptor’s better half. Nature. 420: 285.

Clarke, J. A. and L. M. Chiappe. 2001. A new carinate bird from the Late Cretaceous of Patagonia (Argentina). Am. Mus. Novitates. 1-22.

Clarke, J. A. and M. A. Norell. 2001. Paleoecology (communications arising): fossil and avian evolution. Nature. 414: 508.

Cracraft, J. and J.A. Clarke. 2001. The basal clades of modern birds. In, New perspectives on the origin and early evolution of birds: proceedings of the international symposium in honor of John H. Ostrom (New Haven: Feb. 12–14, 1999). Peabody Mus. Nat. Hist., Yale Univ., 143-156.

Norell, M.A. and J.A. Clarke. 2001. Fossil that fills a critical gap in avian evolution. Nature. 409: 181-184.

Chiappe, L., Dingus, L., Jackson, F., Grellet-Tinner, G., Coria, R., Clarke, J., Garido, A., and D. Loope. 2000. Sauropod eggs and embryos from the Late Cretacous of Patagonia: First International Symposium on Dinosaur Eggs and Babies [Isona: Sept. 21-24, 1999]: Extended Abstracts, 23-29.

Dingus, L., Clarke, J., Scott, G.R., Swisher, C., Chiappe, L.M., and R. Coria. 2000. Stratigraphy and magnetostratigraphic/ faunal constraints for the age of sauropod embryo-bearing rocks in the Neuquén Group (Late Cretaceous, Neuquén Province, Argentina). Am. Mus. Novitates. 3290: 1-11.