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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., 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., 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., 1889. Genera of the Paleozoic Brachiopoda. New York State Museum Annual Report 42, 389-393.
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.
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., 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., 1919. The Death of Lady Allardyce. Science 50, 585.
Clarke, J.M., 1908. The Beginings of Dependent Life, in: Clarke, J.M. (Ed.), Fourth Report Of The Director Of The Science Division. The University of the State of New York, Albany, New York, pp. 146-169.
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.

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