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Clarke, J.M., 1905. Catalogue of Type Specimens of Paleozoic Fossils in New York State Museum, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., Luther, D.D., 1908. Geological Maps and Descriptions of the Portage and Nunda Quadrangles, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1892. Genera or the Palaeozoic Brachiopoda. New York State Museum Annual Report 44, 45-48.
Clarke, J.M., 1914. The Eastman-Zittell Paleontology. Science 39, 723-725.
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., 1902. Notes of Paleozoic Crustaceans. New York State Museum Annual Report 54, 83-119.
Clarke, J.M., 1919. The Death of Lady Allardyce. Science 50, 585.
Clarke, J.M., 1903. Some Devonic Works, 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. 1231-1238.
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., 1900. Dictyonine hexactineIIid sponges from the Upper Devonic of New York, in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 187-194.
Clarke, J.M., Luther, D.D., 1905. Geologic Map of the Tully Quadrangle, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1889. The Genus Bronteus in the Chemung Rocks of New York. New York State Museum Annual Report 42, 403-405.
Clarke, J.M., 1892. Observations on the Terataspisgrandis, Hall, the Largest Known Trilobite. New York State Museum Annual Report 44, 111-114.
Clarke, J.M., Ruedemann, R., 1912. The Eurypterida of New York. v. 1. and v. 2, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1916. The Reincarnation of James Eights, Antarctic Explorer. The Scientific Monthly 2, 189-202.
Clarke, J.M., 1894. Evolution of the Genera of the Palaeozoic Brachiopoda. New York State Museum Annual Report 47, 803-840.

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