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Clarke, J.M., 1904. Naples Fauna in western New York, Part II, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1902. The Water Biscuit of Squaw Island, Canandaigua Lake, N.Y.. New York State Museum Annual Report 54, 195-198.
Clarke, J.M., 1914. The Eastman-Zittell Paleontology. Science 39, 723-725.
Clarke, J.M., 1905. Report of the State Paleontologist 1903, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
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., 1919. The Microscopic Fauna of the Bonaventure Conglomerate, in: Clarke, J.M. (Ed.), Fifthteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 147-148.
Clarke, J.M., 1901. Marcellus Limestones of Central and Western New York and Their Fauna, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 115-138.
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., 1917. Contributions to the Paleontology of New York Devonian Glass Sponges, in: Clarke, J.M. (Ed.), Thirtieth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 177-198.
Clarke, J.M., 1892. Terataspis grandis. New York State Museum Annual Report 44, 111-114.
Clarke, J.M., 1902. The Onondaga Lake Squids. Science 16, 991.
Clarke, J.M., 1913. Cambrian Brachiopoda. Science 37, 488-491.
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., Peck, C.H., 1905. Report of the State Botanist 1904, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., Ruedemann, R., 1903. Guelph Fauna in the State of New York, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1894. Report on Field -work in Chenango County. New York State Museum Annual Report 47, 723-751.

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