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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., 1902. Dictyonine Hexactinellid Sponges from the Upper Devonic of New York. New York State Museum Annual Report 54, 187-190.
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., 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., 1908. The Beginings of Dependent Life, in: Clarke, J.M. (Ed.), Fourth Report Of The Director Of The Science Division. The University of the State of New York, Albany, New York, pp. 146-169.
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., 1901. The Maryland Eocene Book. Science 14, 27.
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., 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., 1914. The Eastman-Zittell Paleontology. Science 39, 723-725.
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., 1922. The Age of the Earth from the Paleontological Viewpoint. Proceedings of the American Philosophical Society 61, 272-282.
Clarke, J.M., 1899. Notes on the Early Stages of Certain Goniatites. New York State Museum Annual Report 50, 163-169.
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.

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