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Clarke, J.M., 1916. The Reincarnation of James Eights, Antarctic Explorer. The Scientific Monthly 2, 189-202.
Clarke, J.M., 1899. Paleontology, University Handbook. The University of the State of New York, Albany, New York.
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., 1889. The Genus Bronteus in the Chemung Rocks of New York. New York State Museum Annual Report 42, 403-405.
Clarke, N.T., 1939. Office of Archeology, in: Adams, C.C. (Ed.), A Summary Of The Accomplishments And Functions Of The New York State Museum During The Past Century, 1836-1936. The University of the State of New York, Albany, New York, pp. 99-107.
Clarke, J.M., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
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., 1900. The Oriskany Fauna of Becraft Mountain, Columbia County, New York, New York State Museum Memoir. The University of the State of New York, Albany, New York.
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., 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. Some Devonic Works, 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. 1231-1238.
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., 1894. Succession of the Fossil Faunas in the Section of the Levonia Salt Shaft. New York State Museum Annual Report 47, 325-352.
Clarke, J.M., 1924. A Hemiasdian Crustacean from New York Silurian Waterlimes, 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. 119-120.

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