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Clarke, J.M., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
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., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
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., 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., 1902. The Water Biscuit of Squaw Island, Canandaigua Lake, N.Y.. New York State Museum Annual Report 54, 195-198.
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., 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., 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., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1902. The Onondaga Lake Squids. Science 16, 991.
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.

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