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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., 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.
Clarke, J.M., Ruedemann, R., Luther, D.D., 1902. Contact Lines of Upper Siluric Formations on the Brockport and Medina Quadrangles, 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. 517-523.
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., 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., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
Clarke, J.M., 1901. Marcellus Limestones of Central and Western New York and Their Fauna, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 115-138.
Clarke, J.M., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
Clarke, J.M., 1902. The Water Biscuit of Squaw Island, Canandaigua Lake, N.Y.. New York State Museum Annual Report 54, 195-198.
Clarke, J.M., 1914. A Fossil Botanical Garden. Science 40, 884.
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.

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