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Clarke, J.M., 1901. New Agelacrinites, in: Merrill, J.H., Clarke, J.M. (Eds.), Paleontologic Papers 2. The University of the State of New York, Albany, New York, pp. 182-198.

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., 1902. The Squids from Onondaga Lake, N.Y.. Science 16, 947-948.

Clarke, J.M., 1902. The Onondaga Lake Squids. Science 16, 991.

Clarke, J.M., 1902. A Remarkable Occurrence of Orthoceras in the Oneota Beds of the Chenango Valley, N.Y.. New York State Museum Annual Report 54, 167-171.

Clarke, J.M., 1902. Paropsonema cryptophya: A Peculiar Echinoderm from the Intumescens-zone (Portage Beds) of Western New York. New York State Museum Annual Report 54, 172-178.

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., 1902. Notes of Paleozoic Crustaceans. New York State Museum Annual Report 54, 83-119.

Clarke, J.M., 1902. The Water Biscuit of Squaw Island, Canandaigua Lake, N.Y.. New York State Museum Annual Report 54, 195-198.

Clarke, J.M., 1902. Preliminary Statement of the Paleontologic Results of the Areal Survey of the Olean Quadrangle. New York State Museum Bulletin 52, 524-528.

Clarke, J.M., 1902. A New Genus of Paleozoic Brachiopods, Eunoa, with Considerations on Discinocaris, Spathlocaris and Cardlocaris. New York State Museum Bulletin 52, 606-615.

Clarke, J.M., 1902. Paleontologic Results of the Areal Survey of the Olean Quadrangle, in: Merrill, J.H., Clarke, J.M. (Eds.), Report Of The State Paleontologist 1901. The University of the State of New York, Albany, New York, pp. 524-528.

Clarke, J.M., 1902. Indigene and Alien Faunas of the New York Devonic, in: Merrill, J.H., Clarke, J.M. (Eds.), Report Of The State Paleontologist 1901. The University of the State of New York, Albany, New York, pp. 664-684.

Clarke, J.M., Ruedemann, R., Luther, D.D., 1902. Contact Lines of Upper Siluric Formations on the Brockport and Medina Quadrangles, in: Merrill, J.H., Clarke, J.M. (Eds.), Report Of The State Paleontologist 1901. The University of the State of New York, Albany, New York, pp. 517-523.

Clarke, J.M., 1903. Mastodons of New York, 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. 934-958.

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., 1903. Some Devonic Works, 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. 1231-1238.

Clarke, J.M., 1903. Catalogue of Type Specimens of Paleozoic Fossils in New York State Museum, New York State Museum Bulletin. The University of the State of New York, Albany, New York.

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., 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.

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