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Clarke, J.M., 1919. The Death of Lady Allardyce. Science 50, 585.
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., 1915. A New Glacial Park. Science 41, 382-383.
Clarke, J.M., 1901. The Maryland Eocene Book. Science 14, 27.
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., 1892. Genera or the Palaeozoic Brachiopoda. New York State Museum Annual Report 44, 45-48.
Clarke, J.M., Luther, D.D., 1904. Stratigraphic and Paleontologic map of Canandaigua and Naples quadrangles, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1922. The Age of the Earth from the Paleontological Viewpoint. Proceedings of the American Philosophical Society 61, 272-282.
Clarke, N.T., 1931. The Wampum Belt Collection of the New York State Museum, in: Adams, C.C. (Ed.), Twenty-Fourth Report Of The Director Of The Division Of Science And The State Museum. The University of the State of New York, Albany, New York, pp. 85-121.
Clarke, J.M., 1894. Evolution of the Genera of the Palaeozoic Brachiopoda. New York State Museum Annual Report 47, 803-840.
Clarke, J.M., 1900. The Water Biscuit of Squaw Island, Canandaigua Lake, N. Y., in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 195-198.
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., 1914. A Fossil Botanical Garden. Science 40, 884.
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., 1925. A Natural Seismograph. Science 61, 391-392.
Clarke, J.M., 1903. Construction of the Olean Hock Section, 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. 996-999.
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.

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