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Clarke, J.M., 1919. The Death of Lady Allardyce. Science 50, 585.
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., 1898. Notes on Some Crustaceans from the Chemung Group of New York. New York State Museum Annual Report 49, 729-738.
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., 1894. Evolution of the Genera of the Palaeozoic Brachiopoda. New York State Museum Annual Report 47, 803-840.
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., 1905. Report of the State Paleontologist 1903, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
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., 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, 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., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
Clarke, J.M., 1919. Organic Dependence and Disease: Their Origin and Significance, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
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., 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., 1902. Dictyonine Hexactinellid Sponges from the Upper Devonic of New York. New York State Museum Annual Report 54, 187-190.
Clarke, J.M., 1913. A Notable Trilobite from Perce Rock, in: Clarke, J.M. (Ed.), Ninth Report Of The Director Of The Science Division. The University of the State of New York, Albany, New York, pp. 138-139.
Clarke, J.M., 1901. The Maryland Eocene Book. Science 14, 27.

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