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Merrill, F.J.H., Clarke, J.M., 1903. Report of the State Paleontologist 1902, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1903. Report of the State Paleontologist 1902, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1902. Report of the State Paleontologist 1901, 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., 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., 1899. Paleontology, University Handbook. The University of the State of New York, Albany, New York.
Merrill, F.J.H., Clarke, J.M., 1901. Paleontologic Papers 2, New York State Museum Bulletin. The University of the State of New York, Albany, New York.
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., 1900. The Oriskany Fauna of Becraft Mountain, Columbia County, New York, New York State Museum Memoir. The University of the State of New York, Albany, New York.
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., 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.
Hall, J., Clarke, J.M., 1898. A Memoir on the Paleozoic Reticulate Sponges Constituting the Family Dictyospongidae, New York State Museum Memoir. The University of the State of New York, Albany, New York.
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.
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.
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., 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., 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., 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., 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.

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