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Clarke, J.M., Luther, D.D., 1905. Geology of the Watkins and Elmira Quadrangles Accompanied by a Geologic Map, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1892. Terataspis grandis. New York State Museum Annual Report 44, 111-114.
Clarke, J.M., 1901. Amnigenia as an Indicator of Freshwater Deposits during the Devonic of New York, Ireland and the Rhineland, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 199-204.
Clarke, J.M., 1915. A New Glacial Park. Science 41, 382-383.
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., 1899. Paleontology, University Handbook. The University of the State of New York, Albany, New York.
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., 1901. The Maryland Eocene Book. Science 14, 27.
Clarke, J.M., 1908. The Beginings of Dependent Life, in: Clarke, J.M. (Ed.), Fourth Report Of The Director Of The Science Division. The University of the State of New York, Albany, New York, pp. 146-169.
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., 1892. On Cordania, a Proposerd New Genus of Trilobites. New York State Museum Annual Report 45, 440-443.
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., 1898. Notes on Some Crustaceans from the Chemung Group of New York. New York State Museum Annual Report 49, 729-738.
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.

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