New and little known Paleozoic and Mesozoic fishes. Journal of the Academy of Natural Sciences Philadelphia, Series 2, 9, 427–448
On Symmorium, and the position of the Cladodont sharks. American Naturalist, 27, 999–1001
On the characters of some Paleozoic fishes. I. On a new Elasmobranch from the Permian; Styptobasis knightiana gen. et spec. nov., fig. 1. II. On new ichthyodorulites; Hybodus regularis sp. nov., fig. 2; Ctenacanthus amblyxiphias sp. nov., fig. 3. III. On the cranial structure of Macropetalichthys. IV. On the pectoral limb of the genus Holonema, Newb. V. On the paired fins of Megalichthys nitidus Cope. VI. On the nonactinopterygian Teleostomi. VII. On new species of Platysomidae, Platysomus palmaris and P. lacovianus. Proceedings of the United States National Museum, 14, 447–463
The Homologies of the Fins of Fishes. American Naturalist, 24, 401–423
Systematic catalogue of the species of Vertebrata found in the beds of the Permian epoch in North America, with notes and descriptions. Transactions of the American Philosophical Society, 16, 285–297
A contribution to the vertebrate paleontology of Brazil. Paleontological Bulletin, 40, 1–21
A contribution to the vertebrate paleontology of Brazil. Proceedings of the American Philosophical Society, 23(121), 1–24
Garman on Didymodus. American Naturalist, 19, 878–879
The Vertebrata of the Tertiary formations of the West. Report of the United States Geological and Geographical Survey Territories, 3: 1–1009.
Pleuracanthus and Didymodus. Science, 3(69), 645–646
The skull of a still living shark (Chlamydoselachus or Didymodus) of the Coal Measures. American Naturalist, 18, 412–413
A Carboniferous genus (Chlamydoselachus) of sharks still living. Science, 3(57), 275–276
On the structure of the skull in the elasmobranch genus Didymodus. Proceedings of the American Philosophical Society, 21(116), 572–590
On some Vertebrata from the Permian of Illinois. Proceedings of the Academy of Natural Sciences of Philadelphia, 35, 108–110
Catalogue of Vertebrata of the Permian formation of the United States. American Naturalist, 15, 162–164
A sting ray from the Green River shales of Wyoming. American Naturalist, 13, 333
Descriptions of extinct Vertebrata from the Permian and Triassic formations of the United States. Proceedings of the American Philosophical Society, 17, 182–193
Synopsis of the cold blooded Vertebrata, procured by Prof. James Orton during his exploration of Peru in 1870-77. Proceedings of the American Philosophical Society, 17, 33–49
On the Vertebrata of the Bone Bed in Eastern Illinois. Proceedings of the American Philosophical Society, 17, 52–63
Descriptions of some vertebrate remains from the Fort Union beds of Montana. Proceedings of the Academy of Natural Sciences of Philadelphia, 28, 248–261
The Vertebrata of the Cretaceous formations of the West. Report of the United States Geological Survey of the Territories, 2: 303 p., 67 pl.
Synopsis of the Vertebrata of the Miocene of Cumberland County, New Jersey. Proceedings of the American Philosophical Society, 14, 361–364
Review of the Vertebrata of the Cretaceous period found west of the Mississippi River. Sec. I. On the mutual relations of the Cretaceous and Tertiary formations of the West. Sec. II. List of species of Vertebrata from the Cretaceous formations. Bulletin of the United States Geological and Geographical Survey of the Territories, 1(2), 3–48
On the families of fishes of the Cretaceous formation in Kansas. Proceedings of the American Philosophical Society, 12(86), 327–357
Observations on the systematic relations of the fishes. American Naturalist, 5, 579–593
Fourth contribution to the history of the fauna of the Miocene and Eocene periods of the United States. Proceedings of the American Philosophical Society, 11(81), 285–294
Descriptions of some extinct fishes previously unknown. Proceedings of the Boston Society of Natural History, 12, 310–317
Second addition to the history of the fishes of the Cretaceous of United states. Proceedings of the American Philosophical Society, 11(81), 240–244
An addition to the vertebrate fauna of the Miocene period, with a synopsis of the extinct Cetacea of the United States. Proceedings of the Academy of Natural Sciences of Philadelphia, 19, 138–156
