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1924
Clarke, J.M., 1924. A Colossal Devonian Glass Sponge, 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. 121-122.
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., 1924. Rosetted Trails of the Paleozoic, 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. 128-129.
1922
Clarke, J.M., 1922. The Age of the Earth from the Paleontological Viewpoint. Proceedings of the American Philosophical Society 61, 272-282.
1921
Clarke, J.M., 1921. The Oldest of the Forests. The Scientific Monthly 12, 83-91.
1919
Clarke, J.M., 1919. Armstrongia: A New Genus of Devonian Glass Sponges, in: Clarke, J.M. (Ed.), Fifthteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 143-146.
Clarke, J.M., 1919. The Death of Lady Allardyce. Science 50, 585.
Clarke, J.M., 1919. The Microscopic Fauna of the Bonaventure Conglomerate, in: Clarke, J.M. (Ed.), Fifthteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 147-148.
Clarke, J.M., 1919. New Paleozoic Crustaceans, in: Clarke, J.M. (Ed.), Fifthteenth Report Of The Director Of The State Museum Science Department. The University of the State of New York, Albany, New York, pp. 129-142.
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.
1918
Clarke, J.M., 1918. Possible Derivation of the Lepadid Barnacles from the Phyllopods. Proceedings of the National Academy of Sciences 4, 384-386.
1917
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.

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