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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., 1908. Early Devonic History of New York and Eastern North America; Part I, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1889. Genera of the Paleozoic Brachiopoda. New York State Museum Annual Report 42, 389-393.
Clarke, J.M., 1902. Dictyonine Hexactinellid Sponges from the Upper Devonic of New York. New York State Museum Annual Report 54, 187-190.
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.
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., 1918. Possible Derivation of the Lepadid Barnacles from the Phyllopods. Proceedings of the National Academy of Sciences 4, 384-386.
Clarke, J.M., 1899. Geological Time. Science 10, 695.
Clarke, J.M., Luther, D.D., 1905. Geology of the Watkins and Elmira Quadrangles Accompanied by a Geologic Map, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1924. A Hemiasdian Crustacean from New York Silurian Waterlimes, 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. 119-120.
Clarke, J.M., 1900. Paropsonema cryptophya: a Peculiar Echinoderm from the Intumescenszone (Portage Beds) of Western New York, in: Clarke, J.M. (Ed.), Paleontologic Papers. The University of the State of New York, Albany, New York, pp. 172-186.
Clarke, J.M., 1901. Amnigenia as an Indicator of Freshwater Deposits during the Devonic of New York, Ireland and the Rhineland, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 199-204.
Clarke, J.M., 1892. Terataspis grandis. New York State Museum Annual Report 44, 111-114.
Clarke, J.M., 1915. A New Glacial Park. Science 41, 382-383.

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