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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.
Clarke, J.M., 1903. 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.
Clarke, J.M., 1919. New Paleozoic Crustaceans, 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. 129-142.
Clarke, J.M., 1899. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
Clarke, J.M., Peck, C.H., 1905. Report of the State Botanist 1904, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1924. Rosetted Trails of the Paleozoic, 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. 128-129.
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., 1902. The Onondaga Lake Squids. Science 16, 991.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1902. Indigene and Alien Faunas of the New York Devonic, 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. 664-684.
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., 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.
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.

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