Cooper, J. E. 1977. Durable ichthyoplankton sampler for small boats. Progressive Fish-Culturist 39(4):170-171.
_____. 1978. Eggs and larvae of the logperch, Percina caprodes Rafinesque. American Midland Naturalist 99(2):257–269.
_____. 1978. Identification of eggs, larvae, and juveniles of the rainbow smelt, Osmerus mordax, with comparisons to larval alewife, Alosa pseudoharengus, and gizzard shad, Dorosoma cepedianum. Transactions American Fisheries Society 107(1):56–62.
_____. 1979. Description of eggs and larvae of the fantail (Etheostoma flabellare) and rainbow (E. caeruleum) darters from Lake Erie tributaries. Transactions American Fisheries Society 108(1):46–56.
_____. 1980. Egg, larval, and juvenile development of longnose dace, Rhinichthys cataractae, and river chub, Nocomis micropogon, with notes on their hybridization. Copeia 1980, No. 3:469–478.
_____. 1981. Development and replacement order of pharyngeal teeth in the golden shiner, Notemigonus crysoleucas. Ohio Journal of Science 81(1):14–18.
_____. 1985. Species accounts of mud sunfish (Acantharcus pomotis), Lake sturgeon (Acipenser fulvescens), and Blue pike (Stizostedion vitreum glaucum). Pages 174, 249, and 254 In: Species of Special Concern in Pennsylvania. H. Genoways and F. Brennan (editors). Carnegie Museum of Natural History. Spec. Publ. No. 11, Pittsburgh, Pa. 430p.
Rulifson, R. A., and J. E. Cooper. 1986. A method to determine mesh size selectivity in commercial menhaden purse seines. North American Journal of Fisheries Management 6:359–366.
Dadswell, M. J., R. J. Klauda, C. M. Moffitt, R. L. Saunders, R. A. Rulifson, and J. E. Cooper (editors) 1987. Common Strategies of Anadromous and Catadromous Fishes. American Fisheries Society Symposium 1. Bethesda, Md. 570p. ISBN 0-913235-42-3 www.fisheries.org
Rulifson, R.A., J.E. Cooper, and D.W. Stanley. 1988. Larval striped bass and the food chain: cause for concern? Pages 213–224 In: Proceedings of Symposium on Coastal Water Resources. W.L. Lyke and T.J. Hoban (editors). American Water Resources Association, Bethesda, Md. 874p.
Cooper, J. E., R. T. Eades, R. J. Klauda, and J. G. Loesch (editors). 1994. Anadromous Alosa Symposium, Tidewater Chapter, American Fisheries Society, Bethesda, MD. 169 p. ISBN 0-913235-89-X
Paper copies are available for $5 plus postage from Roger A. Rulifson, Institute for Coastal Science and Policy, Flanagan 250, East Carolina University, Greenville, NC 27858 (252-328-9400) email firstname.lastname@example.org OR a pdf file on a CD for $7 (incl. postage) from John Cooper, address and email on the home page of this website. Cash or checks, no credit cards accepted.
Cooper, J. E., S. F. Wood, and R. A. Rulifson. 1995. Extent of water lily (Nuphar lutea) beds and their use by larval fish in the Roanoke River, NC. Journal Elisha Mitchell Scientific Society 110(2):84–96.
Cooper, J.E. 1996. Parasites and cyclopoid predators of age-0 fish in the Roanoke River, NC. Estuaries 19 (1):146–161.
Cooper, J. E., R. A. Rulifson, J. J. Isley, and S. E. Winslow. 1998. Food habits and growth of juvenile striped bass Morone saxatilis in Albemarle Sound, North Carolina. Estuaries 21 (2):307–317.
Gibbs, J. and 14 coauthors. 2005. An ecological and recreational assessment of Honeywell International Inc. Hudson Farm property. SUNY—ESF, Syracuse, NY. 137 p.
Cooper, J. E., J. M. Farrell, R. M. Klindt, S. Prindle, and A. Fairbanks. 2005. Effects of seaway shipping operations on coastal habitats with ice cover in the Thousand Islands Region of the St. Lawrence River. Report to Save The River, Clayton New York. 14 p.
Cooper, J. E., J. V. Mead, J. M. Farrell, and R. G. Werner. 2008. Potential effects of spawning habitat changes on the segregation of northern pike (Esox lucius) and muskellunge (E. masquinongy) in the Upper St. Lawrence River. Hydrobiologia 601:41–53.
Haro, A., K. L. Smith, R. A. Rulifson, C. M. Moffitt, R. J. Klauda, M. J. Dadswell, R. A. Cunjak, J. E. Cooper, K. L. Beal, and T. S. Avery (editors). 2009. Challenges for Diadromous Fishes in a Dynamic Global Environment. American Fisheries Society Symposium 69, Bethesda, MD. ISBN 978-1-934874-08-0 www.fisheries.org
Cooper, J. E. 2016. Development, growth, and food of early life stages of northern pike and muskellunge in the upper St. Lawrence River. DOI 10.13140/RG.2.2.26323.68646 Based on Chapter 3 of my PhD dissertation.
Cooper, J. E. 2016. Zooplankton density and diet composition of fish larvae in three bays in the upper St. Lawrence River. DOI 10.13140/RG.2.2.31461.70888 Based on Chapter 4 of my PhD dissertation.
Benthos, invasive species, and dam studies
Cooper, J. E., and R. A. Rulifson. 1993. Benthic biocriteria assessment of the lower Roanoke River, NC. ICMR Contrib. Ser. 93–03.
Cooper, J. E., J. M. Farrell, and J. A. Toner. 2004. Predicting the effects of dam removal on the aquatic community in the Salmon River, New York. Phase 1, Baseline Data. Final report to Great Lakes Protection Fund.
Cooper, J. E. 2006. Supplemental report to the Nature Conservancy for environmental assessment of modifying the Monitor Mills Dam, NY, for fish passage.
Cooper, J. E. 2007. Corbicula fluminea (Asian clam) in the Roanoke River: a stressed population? Southeastern Naturalist 6(3):413-434.
Cooper, J. E. 2011. Unionid mussel mortality from habitat loss in the Salmon River, New York, following dam removal. Advances in Environmental Research, Vol. 14, pp.351-364. corrected table 1 numbers 2017
Cooper, J. E. 2011. Effect of dam removal on aquatic communities in the Salmon River, New York. Interim Report for 2010. Project #2005-0129-013. Submitted to National Fish and Wildlife Foundation.
Cooper, J.E., E. Wallquist, K.T. Holeck, C.E. Hoffman, E.L. Mills, and C.M. Mayer. 2012. Density and distribution of amphipods in Oneida Lake, New York, after the introduction of the exotic amphipod Echinogammarus ischnus. Northeastern Naturalist 19(2):249-266.
Cooper, J. E. 2013. Effect of dam removal on aquatic communities in the Salmon River, New York. Final report Revised. Project #2005-0129-013. (Added pebble sizes for Deer Creek transect determined in 2017)
Cooper, J. E. 2014. Dam removal and the Salmon River mussel community. Presentation at Freshwater Mollusk Conservation Society Workshop, 24 April 2014, Portland, Maine.
Cooper, J. E. 2017. Distribution and density of three uncommon or imperiled unionid mussel species in northern New York. Presentation at Freshwater Mollusk Conservation Society meeting, 27 March 2017, Cleveland, Ohio.
Illustrations can be seen in the following
Cooper, E. L. 1983. Fishes of Pennsylvania and Northeastern United States. Pennsylvania State University Press, University Park, Pa. 320p. ISBN 0-271-00337-5
Dadswell, M. J., R. J. Klauda, C. M. Moffitt, R. L. Saunders, R. A. Rulifson, and J. E. Cooper (editors) 1987. Common Strategies of Anadromous and Catadromous Fishes. American Fisheries Society Symposium 1, Bethesda, Md. 570p. ISBN 0-913235-42-3
Cooper, E. L. (editor) 1987. Carp in North America. American Fisheries Society, Bethesda, Md. 84p. ISBN 0-913235-44-X
Cooper, J. E., R. E. Eades, R. J. Klauda, and J. G. Loesch (editors). 1994. Anadromous Alosa Symposium, Tidewater Chapter, American Fisheries Society, 169p. ISBN 0-913235-89-X
Cooper, J. E. 2000. Comparative development and ecology of northern pike Esox lucius and muskellunge E. masquinongy eggs and larvae in the Upper St. Lawrence River and the implications of changes in historical spawning habitat. PhD Dissertation, SUNY-ESF.
Bunt, C., and S. J. Cooke. 2004. Ontogeny of larval greater redhorse (Moxostoma valenciennesi). American Midland Naturalist 151:93–100.
Bunt, C., T. Heiman, and N. E. Mandrak. 2013. Ontogeny of larval and juvenile black redhorse (Moxostoma duquesnei). Copeia 2013 (1):121-126.
Gostomski, T. and J. Marr. 2007. Island Life: An Isle Royale Nature Guide. Isle Royale Natural History Association, Michigan. ISBN 978-0-935289-15-2 www.irnha.org
Haro, A., K. L. Smith, R. A. Rulifson, C. M. Moffitt, R. J. Klauda, M. J. Dadswell, R. A. Cunkak, J. E. Cooper, K. L. Beal, and T. S. Avery (editors). 2009. Challenges for Diadromous Fishes in a Dynamic Global Environment. AFS Symposium 69. ISBN 978-1-934874-08-0 www.fisheries.org