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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.
Clarke, J.M., 1924. Rosetted Trails of the Paleozoic, 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. 128-129.
Clarke, N.T., 1937. Chronological Sketch of the Archaeological Work of the State Museum, in: New York State Museum Bulletin. pp. 105-110.
Clarke, J.M., 1892. On Cordania, a Proposerd New Genus of Trilobites. New York State Museum Annual Report 45, 440-443.
Clarke, J.M., 1919. Armstrongia: A New Genus of Devonian Glass Sponges, 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. 143-146.
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., 1902. Notes of Paleozoic Crustaceans. New York State Museum Annual Report 54, 83-119.
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., 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., 1918. Possible Derivation of the Lepadid Barnacles from the Phyllopods. Proceedings of the National Academy of Sciences 4, 384-386.
Clarke, J.M., 1892. Coronura aspectans. New York State Museum Annual Report 44, 105-109.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.

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