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Clarke, J.M., Ruedemann, R., Luther, D.D., 1902. Contact Lines of Upper Siluric Formations on the Brockport and Medina Quadrangles, 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. 517-523.
Clarke, J.M., 1894. New or Rare Species of Fossils from the Horizons of the Livonian Salt Shaft. New York State Museum Annual Report 47, 353-383.
Clarke, J.M., 1892. Terataspis grandis. New York State Museum Annual Report 44, 111-114.
Clarke, J.M., 1899. Geological Time. Science 10, 695.
Clarke, J.M., 1903. Construction of the Olean Hock Section, 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. 996-999.
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, J.M., 1908. Early Devonic History of New York and Eastern North America; Part I, 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., 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., 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., 1919. New Paleozoic Crustaceans, 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. 129-142.
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., Hall, J., 1895. New Species of Brachiopoda Described in Paleontology of New York, v.8, pt1 and 2. New York State Museum Annual Report 48, 16-18, 323-372.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.

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