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Clarke, J.M., 1892. Genus Acidaspis. New York State Museum Annual Report 44, 91-101.
Clarke, J.M., 1924. A Hemiasdian Crustacean from New York Silurian Waterlimes, in: Clarke, J.M. (Ed.), Eighteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 119-120.
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., 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., 1902. Dictyonine Hexactinellid Sponges from the Upper Devonic of New York. New York State Museum Annual Report 54, 187-190.
Clarke, J.M., 1917. Contributions to the Paleontology of New York Devonian Glass Sponges, in: Clarke, J.M. (Ed.), Thirtieth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 177-198.
Clarke, J.M., 1901. The Maryland Eocene Book. Science 14, 27.
Clarke, J.M., 1914. The Eastman-Zittell Paleontology. Science 39, 723-725.
Clarke, N.T., 1931. The Wampum Belt Collection of the New York State Museum, in: Adams, C.C. (Ed.), Twenty-Fourth Report Of The Director Of The Division Of Science And The State Museum. The University of the State of New York, Albany, New York, pp. 85-121.
Clarke, J.M., 1889. The Genus Bronteus in the Chemung Rocks of New York. New York State Museum Annual Report 42, 403-405.
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, N.T., 1937. Chronological Sketch of the Archaeological Work of the State Museum, in: New York State Museum Bulletin. pp. 105-110.
Clarke, J.M., 1905. 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., 1899. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
Clarke, J.M., 1922. The Age of the Earth from the Paleontological Viewpoint. Proceedings of the American Philosophical Society 61, 272-282.

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