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Clarke, J.M., 1900. Paropsonema cryptophya: a Peculiar Echinoderm from the Intumescenszone (Portage Beds) of Western New York, in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 172-186.
Clarke, J.M., 1899. Paleontology, University Handbook. The University of the State of New York, Albany, New York.
Clarke, J.M., 1892. On Cordania, a Proposerd New Genus of Trilobites. New York State Museum Annual Report 45, 440-443.
Clarke, J.M., 1902. The Onondaga Lake Squids. Science 16, 991.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1902. Indigene and Alien Faunas of the New York Devonic, in: Merrill, J.H., Clarke, J.M. (Eds.), Report Of The State Paleontologist 1901. The University of the State of New York, Albany, New York, pp. 664-684.
Clarke, J.M., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
Clarke, J.M., 1915. A New Glacial Park. Science 41, 382-383.
Clarke, J.M., 1894. Succession of the Fossil Faunas in the Section of the Levonia Salt Shaft. New York State Museum Annual Report 47, 325-352.
Clarke, J.M., 1892. Coronura aspectans. New York State Museum Annual Report 44, 105-109.
Clarke, J.M., 1903. Mastodons of New York, in: Merrill, J.H., Clarke, J.M. (Eds.), Report Of The State Paleontologist 1902. The University of the State of New York, Albany, New York, pp. 934-958.
Clarke, J.M., 1924. A Colossal Devonian Glass Sponge, in: Clarke, J.M. (Ed.), Eighteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 121-122.
Clarke, J.M., 1902. Notes of Paleozoic Crustaceans. New York State Museum Annual Report 54, 83-119.
Clarke, J.M., 1914. A Fossil Botanical Garden. Science 40, 884.
Clarke, J.M., 1919. The Death of Lady Allardyce. Science 50, 585.
Clarke, J.M., 1898. Notes on Some Crustaceans from the Chemung Group of New York. New York State Museum Annual Report 49, 729-738.

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