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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., 1905. Pierce: A Brief Sketch of its Geology, in: Clarke, J.M. (Ed.), Report Of The State Paleontologist 1903. The University of the State of New York, Albany, New York, pp. 134-172.
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., 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, 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.

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