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1908
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.
1905
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., 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.
1903
Clarke, J.M., Ruedemann, R., 1903. Guelph Fauna in the State of New York, New York State Museum Memoir. The University of the State of New York, Albany, New York.
1899
Clarke, J.M., 1899. Geological Time. Science 10, 695.
Clarke, J.M., 1899. Guide to Excursions in the Fossiliferous Rocks of New York State, University Handbook. The University of the State of New York, Albany, NY.
1892
Clarke, J.M., 1892. Genera or the Palaeozoic Brachiopoda. New York State Museum Annual Report 44, 45-48.
Clarke, J.M., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
1889
Clarke, J.M., 1889. Genera of the Paleozoic Brachiopoda. New York State Museum Annual Report 42, 389-393.
Clarke, J.M., 1889. The Genus Bronteus in the Chemung Rocks of New York. New York State Museum Annual Report 42, 403-405.