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Clarke, J.M., Luther, D.D., 1904. Stratigraphic and Paleontologic map of Canandaigua and Naples quadrangles, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Clarke, J.M., 1905. Pierce: A Brief Sketch of its Geology, in: Clarke, J.M. (Ed.), Report Of The State Paleontologist 1903. The University of the State of New York, Albany, New York, pp. 134-172.
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., Luther, D.D., 1905. Geologic Map of the Tully Quadrangle, 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., 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., 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., 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.
Clarke, J.M., 1909. Early Devonic History of New York and Eastern North America. Part II, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., Ruedemann, R., 1912. The Eurypterida of New York. v. 1. and v. 2, New York State Museum Memoir. The University of the State of New York, Albany, New York.
Clarke, J.M., 1913. The Maryland Devonian Books. Science 38, 742-745.
Clarke, J.M., 1913. Cambrian Brachiopoda. Science 37, 488-491.
Clarke, J.M., 1913. Illustrations of the Devonic Fossils of Southern Brazil and the Faukland Islands, 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. 140-210.
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., 1914. The Eastman-Zittell Paleontology. Science 39, 723-725.
Clarke, J.M., 1914. A Fossil Botanical Garden. Science 40, 884.
Clarke, J.M., 1915. A New Glacial Park. Science 41, 382-383.

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