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Clarke, J.M., 1901. New Agelacrinites, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 182-198.
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., 1913. Illustrations of the Devonic Fossils of Southern Brazil and the Faukland Islands, in: Clarke, J.M. (Ed.), Ninth Report Of The Director Of The Science Division. The University of the State of New York, Albany, New York, pp. 140-210.
Clarke, J.M., 1899. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
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., 1909. Early Devonic History of New York and Eastern North America. Part II, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, N.T., 1937. The Indian Groups of the New York State Museum and a Description of the Technique, in: Adams, C.C. (Ed.), Thirtieth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 101-120.
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, N.T., 1924. Method of Restoring the Cohoes Mastodon, 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. 131-133.
Clarke, N.T., 1929. The Thatcher Wampum Belts, in: Adams, C.C. (Ed.), Twenty-Second Report Of The Director Of The Division Of Science And The State Museum. The University of the State of New York, Albany, New York, pp. 53-58.
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., 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.

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