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Clarke, J.M., 1892. On Cordania, a Proposerd New Genus of Trilobites. New York State Museum Annual Report 45, 440-443.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1899. Paleontology, University Handbook. The University of the State of New York, Albany, New York.
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., 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., 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., 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., Luther, D.D., 1905. Geology of the Watkins and Elmira Quadrangles Accompanied by a Geologic Map, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1894. Evolution of the Genera of the Palaeozoic Brachiopoda. New York State Museum Annual Report 47, 803-840.
Clarke, J.M., 1900. A Remarkable Occurrence of Orthoceris in the Oneonta Beds of the Chenango Valley, in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 167-171.
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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