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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., 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., 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.
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., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1892. Coronura aspectans. New York State Museum Annual Report 44, 105-109.
Clarke, N.T., 1937. The Indian Groups of the New York State Museum and a Description of the Technique, in: Adams, C.C. (Ed.), Thirtieth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 101-120.
Clarke, J.M., 1916. The Reincarnation of James Eights, Antarctic Explorer. The Scientific Monthly 2, 189-202.
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., 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., 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. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
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., 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., 1905. 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.

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