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1925
Clarke, J.M., 1925. A Natural Seismograph. Science 61, 391-392.
1919
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.
1915
Clarke, J.M., 1915. A New Glacial Park. Science 41, 382-383.
1913
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.
1904
Clarke, J.M., 1904. Naples Fauna in western New York, Part II, New York State Museum Memoir. The University of the State of New York, Albany, New York.
1902
Clarke, J.M., 1902. Notes of Paleozoic Crustaceans. New York State Museum Annual Report 54, 83-119.
1901
Clarke, J.M., 1901. New Agelacrinites, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 182-198.
1900
1899
Clarke, J.M., 1899. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
1898
Clarke, J.M., 1898. Notes on Some Crustaceans from the Chemung Group of New York. New York State Museum Annual Report 49, 729-738.
1895
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.
1894
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.