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Clark, S.; Bailey, H. C.; Davis, J. A. 1995. The Effects of Toxic Contaminants in Waters of the San Francisco Bay and Delta. SFEI Contribution No. 184. Prepared for Bay/Delta Oversight Council: Sacramento, CA. p 125 pp.
Cloern, J. E.; Barnard, P. L.; Beller, E. E.; Callaway, J.; Grenier, J. Letitia; Grossinger, R. M.; Whipple, A.; Mooney, H.; Zavaleta, E. 2016. Estuaries: Life on the edge. In Ecosystems of California. Ecosystems of California. University of California Press: Berkeley, CA. pp 359-388.
Cloern, J. E.; Robinson, A.; Richey, A.; Grenier, J. Letitia; Grossinger, R. M.; Boyer, K. E.; Burau, J.; Canuel, E.; DeGeorge, J. F.; Drexler, J. Z.; et al. 2016. Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

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Cloern, J. E.; Cole, B. E.; Jassby, A. D. 1997. The design of sampling transects for characterizing water quality in estuaries. Estuarine, Coastal and Shelf Science 45, 285-302 . SFEI Contribution No. 23.
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Cohen, A. N. 1999. Status of invasions and policy response on the U. S. west coast. First National Conference on Marine Bioinvasions.
Cohen, A. N. 1988. Recalculating the Tule Factor. A report for The Bay Institute of San Francisco: Sausalito, CA.
Cohen, A. N. 1999. Breifing Paper on a Monitoring Plan for Nonindigenous Organisms in the San Francisco Bay/Delta Estuary. A report for CALFED and the California Urban Water Agencies. San Francisco Estuary Institute. p Richmond CA.
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Cohen, A. N. 1996. Biological invasions of the San Francisco Bay and Delta. Summary of comments. In U. S. Fish and Wildlife Service Directorate Meeting. U. S. Fish and Wildlife Service Directorate Meeting. Ogunquit ME, June 12, 1996.
Cohen, A. N. 1995. Place Invaders. Energy and Resources News 4, 1-3.
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Cohen, A. N.; Gollasch, S.; Galil, B. S. 2006. Bridging Divides: Maritime Canals as Invasion Corridors. Monographiae Biologicae 83. Kluwer Academic Publishing: Dordrecht, The Netherlands.
Cohen, A. N.; Woo, M.; Jabari, E. 2001. Testing Ballast Water Treatment at a Municipal Wastewater Treatment Plant. California Sea Grant/National Sea Grant College Program, La Jolla CA.
Cohen, A. N. 2001. Case Study 2.5: Petition for U.S. federal action on the green seaweed Caulerpa taxifolia. Wittenberg, R., Cock, M. J. W., Eds.. United Nations Global Invasive Species Program. CAB International, Wallingford, Oxon, UK. p 31.
Cohen, A. N.; McGann, M.; Sloan, D. 1996. Documenting the intorduction of estuarine foraminifers: a San Francisco Bay Study. Ann. Mtg., Geological Society of America, Denver, CO, Oct. 1996 (abstract).
Cohen, A. N. 2002. Dispersal Ecology. Blackwell Publishing: Oxford.
Cohen, A. N.; Zabin, C. J. 2006. Shells as vectors. Proceedings of the 2006 West Coast Native Oyster Restoration Workshop.
Cohen, A. N.; Weinstein, A. 1998. The potential distribution and abundance of the zebra mussel in California. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, 65.
Cohen, A. N. 1988. Subsides in the Central Utah Project: Whose CUP is Running over?. Report for the Natural Resources Defense Council: San Francisco, CA.
Cohen, A. N. 2002. The highly invaded ecosystem of San Francisco Bay. Cawthron Institute, Nelson, New Zealand.
Cohen, A. N. 1996. Environmental Review and Mitigation of a Water Supply Project in California. A report for the Japanese Ministry of Construction, Tokyo.
Cohen, A. N.; Carlton, J. T. 2007. Introduced Marine and Estuarine Invertebrates. In The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. Carlton, J. T., Ed.. The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. University of California Press: Berkeley, Ca.
Cohen, A. N.; Schaeffer, K.; Cosentino-Manning, N. 2007. Shellfish Beds in Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service: Santa Rosa, CA. pp 50-55.
Cohen, A. N. 1989. New Justifications for Traditional Types of Water Projects, University of California: Berkeley, CA.
Cohen, A. N. 2001. Impacts from the Asian clam Potamocorbula amurensis. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N. 2002. Exotic organisms in southern California Bays and Harbors. Marine Bioinvasions Conference . SFEI Contribution No. 481.
Cohen, A. N. 2004. Invasions in the sea. SFEI Contribution No. 312. Vol. 22, pp 37-41.
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Cohen, A. N. 1989. Threatened in the nest. Pacific Discovery (Calif. Acad. Sci.) 42, 6-13.
Cohen, A. N. 1994. Storming the Bay. Terrain 24, 4,7.
Cohen, A. N. 1991. China Camp: A salt marsh guide. Pacific Discovery (Calif. Acad. Sci.) 44, 24-29.
Cohen, A. N. 1997. The San Francisco Estuary: A model system for invasions research. San Francisco Estuary Institute: Seattle, WA (abstract).
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Cohen, A. N. 2004. An Exotic Species Detection Program for the Lower Columbia River Estuary. SFEI Contribution No. 381. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2007. Tanaidacea in The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. In The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast.. Carlton, J. T., Ed.. The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. University of California Press: Berkeley, Ca.
Cohen, A. N. 2004. An Exotic Species Detection Program for Puget Sound. SFEI Contribution No. 380. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 1998. Biological invasions in the San Francisco Estuary. In Marine and Aquatic Nonindigenous Species in California: An Assessment of Current Status and Research Needs. Olin, P. G., Cassell, J. L., Eds.. Marine and Aquatic Nonindigenous Species in California: An Assessment of Current Status and Research Needs. California Sea Grant College System, University of California: La Jolla, CA. pp 7-8.
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Cohen, A. N. 1994. Impacts of invasions in the Bay and Delta. Abs. Proc. 75th Ann. Mtg., Pac. Div. Amer. Assoc. Adv. Sci..
Cohen, A. N. 1996. Stopping ballast water invaders. Native Species Network 1, 1.
Cohen, A. N. 2005. A review of Zebra Mussels' Environmental Requirements. Resources, C. A. Department, Ed.. SFEI Contribution No. 420. San Francisco Estuary Institute: Sacramento, CA.
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Cohen, A. N. 2001. Invasions in the San Francisco Estuary. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N. 1997. Biological invasions: An unregulated threat to estuarine biodiversity. Ann. Mtg., Society for Conservation Biology, Victoria BC (abstract)..
Cohen, A. N. 2000. "Case studies" on exotic species transported with oyster and marine baitworm shipments. In Toolkit on Best Practices for Prevention and Management. Toolkit on Best Practices for Prevention and Management. UN Global Invasive Species Programme.
Cohen, A. N.; Gottleib, R. 1991. Water and GrowthL Restructuring the Relationship. Public Officials for Water and Environmental Reform: Sacramento, CA.
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Cohen, A. N.; Zabin, C. J. 2009. Oyster shells as vectors for exotic species. Journal of Shellfish Research 28 (1), 163-167 . SFEI Contribution No. 709.
Cohen, A. N. 1997. Green crabs disrupting fisheries worldwide. p 7 . SFEI Contribution No. 199.
Cohen, A. N. 2005. Project Report: 2004 Rapid Assessment Survey for Exotic Species in San Francisco Bay. SFEI Contribution No. 451. San Francisco Estuary Institute: Oakland, Ca.
Cohen, A. N. 1998. Biological invasions in the San Francisco Estuary. Olin, P. G., Cassell, J. L., Eds.. California Sea Grant College System, University of California, La Jolla CA. pp 7-8.
Cohen, A. N. 2003. Introduction to the San Francisco Estuary. San Francisco Estuary Institute, Save the Bay and San Francisco Estuary Project: Oakland,CA.
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Cohen, A. N. 2003. On Mitten Crabs and Lung Flukes. In IEP Newsletter. IEP Newsletter. Vol. 16, pp 48-51.
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Cohen, A. N.; Tyler, S.; Mathieson, A.; Dyrynda, P.; Dean, H.; Calder, D.; Bullock, R.; Lambert, C.; Chapman, J.; Pederson, J.; et al. 2001. Rapid Assessment Survey of nonindigenous species in coastal Massachusetts. In: Abstracts, Second International Conf. on Marine Bioinvasions, April 9-11, 2001, New Orleans LA..
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Cohen, A. N.; Weinstein, A.; Carlton, J. T.; Emmett, M. A.; Lau, W. 2005. Global Spread of Marine Organisms in the Baitworm Trade. SFEI Contribution No. 455. San Francisco Estuary Institute: Oakland, CA.
Cohen, A. N. 2001. Success factors in human-dispersed organisms. Dispersal, Annual Symposium of the British Ecological Society, Page 8.
Cohen, A. N. 2005. Role of the Panama Canal in Introducing Exotic Organisms. In Bridging Divides - Man-made Canals and Species Invasions. Bridging Divides - Man-made Canals and Species Invasions. Kluwer Academic Publishing.
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Cohen, A. N. 2001. Success factors in human-dispersed organisms. Page 8 in:. University of Reading, UK. British Ecological Society, London. p p. 8.
Cohen, A. N. 2005. Overview of 2004/05 Rapid Assessment Shore and Channel Surveys for Exotic Species in San Francisco Bay. SFEI Contribution No. 452. San Francisco Estuary Institute: Oakland, CA.
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Cohen, A. N. 2005. Approaches to presenting the science of the San Francisco Bay/Delta estuary. SFEI Contribution No. 514. San Francisco Estuary Institute: Oakland, CA.
Cohen, A. N. 2001. Case study: transfer of pathogens and other species via oyster culture. In Toolkit for Managing Invasive Species. Toolkit for Managing Invasive Species. United Nations Global Invasive Species Program.
Cohen, A. N. 1999. Prevention vs. control of biological invasions. First National Conference on Marine Bioinvasions.
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Cohen, A. N. 2005. Bridging Divides: Maritime Canals as Invasion Corridors. Cohen, A. N., Gollasch, S., Galil, B. S., Eds.. Kluwer Academic Publishing: Dordrecht, The Netherlands.
Cohen, A. N.; Nordby, J. C. 2005. Year-end Report to the National Science Foundation. SFEI Contribution No. 456. San Francisco Estuary Institute: Oakland, CA.