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Clarke, J.M., 1892. Catalogue of the Collection of Geological and Paleontological Specimens Donated by the Albany Institute to the State Museum. New York State Museum Annual Report 45, 347-369.

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.

Clarke, J.M., Schuchert, C., 1899. The Nomenclature of the New York Series of Geological Formations. Science 10, 874-878.

Clarke, J.M., 1900. Note on the Siluro-Devonic Boundary. Science 12, 406-408.

Clarke, J.M., 1901. The Maryland Eocene Book. Science 14, 27.

Clarke, J.M., 1901. Value of Amnigenin as an Indicator of Freshwater Deposits During the Devonic of New York, Ireland, and the Rhineland. New York State Museum Bulletin 49, 199-203.

Clarke, J.M., 1901. Marcellus Limestones of Central and Western New York and Their Fauna, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 115-138.

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., 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., 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., 1913. The Maryland Devonian Books. Science 38, 742-745.

Clarke, J.M., 1914. The Indian Ladder Reservation. Science 39, 418.

Clarke, J.M., 1917. The Philosophy of Geology and the Order of the State. Science 45, 125-135.

Clarke, J.M., 1922. The Age of the Earth from the Paleontological Viewpoint. Proceedings of the American Philosophical Society 61, 272-282.

Clarke, J.M., 1925. A Natural Seismograph. Science 61, 391-392.