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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., Luther, D.D., 1908. Geological Maps and Descriptions of the Portage and Nunda Quadrangles, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.
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., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
Clarke, J.M., 1899. Geological Time. Science 10, 695.
Clarke, J.M., 1902. Paleontologic Results of the Areal Survey of the Olean Quadrangle, 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. 524-528.
Clarke, J.M., 1903. 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., 1924. A Colossal Devonian Glass Sponge, 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. 121-122.
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., 1916. The Reincarnation of James Eights, Antarctic Explorer. The Scientific Monthly 2, 189-202.
Clarke, J.M., 1900. A Remarkable Occurrence of Orthoceris in the Oneonta Beds of the Chenango Valley, in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 167-171.
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., 1902. Dictyonine Hexactinellid Sponges from the Upper Devonic of New York. New York State Museum Annual Report 54, 187-190.

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