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Clarke, J.M., 1892. Coronura aspectans. New York State Museum Annual Report 44, 105-109.
Clarke, J.M., 1894. Report on Field -work in Chenango County. New York State Museum Annual Report 47, 723-751.
Clarke, J.M., 1919. Armstrongia: A New Genus of Devonian Glass Sponges, 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. 143-146.
Clarke, J.M., 1899. Guide to Excursions in the Fossiliferous Rocks of New York State, University Handbook. The University of the State of New York, Albany, NY.
Clarke, J.M., Ruedemann, R., 1903. Guelph Fauna in the State of New York, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1925. A Natural Seismograph. Science 61, 391-392.
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., Peck, C.H., 1906. Report of the State Botanist 1905, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1913. Cambrian Brachiopoda. Science 37, 488-491.
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., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
Clarke, J.M., 1900. Paleontologic Papers, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1905. Report of the State Paleontologist 1903, New York State Museum Bulletin. The University of the State of New York, Albany, New York.

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