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Artwork
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Book Chapter
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.
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. 2001. Case study: hitchhikers in or on marine baitworms and their packing material. In Toolkit for Managing Invasive Species. Toolkit for Managing Invasive Species. United Nations Global Invasive Species Program.
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.; Minchin, D.; Gollasch, S.; Olenin, S. 2006. Characterizing vectors of marine invasions. In Marine Bioinvasions: Ecology, Conservation and Management Perspectives. Rilov, G., Crooks, J., Eds.. Marine Bioinvasions: Ecology, Conservation and Management Perspectives. Springer: Heidelberg, Germany.
Davis, J. A. 2000. Chlorinated Hydrocarbons in the San Francisco Estuary and its Watershed. In Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.. Draft Chapter in Spies, R.B. (ed.). Contaminants and Toxicity in the Sacramento-San Joaquin Delta, Its Cathchment, and the San Francisco Estuary - A CALFED White Paper. Applied Marine Sciences, Livermore, CA.
Cohen, A. N. 2002. Dispersal Ecology. Blackwell Publishing: Oxford.
Grossinger, R. M. 2001. Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems.. Egan, D., Howell, E., Eds.. The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems. Island Press: Washington D.C.
Grossinger, R. M. 2005. Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Egan, D., Howell, E. A., Trans.. The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Island Press.
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.
Cohen, A. N.; Lambert, C. C.; Harris, L. H.; Chapman, J. W.; Schwindt, E.; Reardon, K.; Rao, L. C.; Murray, S. N.; Ljubenkov, J. C.; Lambert, G.; et al. 2003. Exotic Organisms in Southern California Bays and Harbors. Page 22 in:. In Abstracts, Third International Conf. on Marine Bioinvasions, Mar. 16-19, Scripps Institution of Oceanography, La Jolla, CA. Abstracts, Third International Conf. on Marine Bioinvasions, Mar. 16-19, Scripps Institution of Oceanography, La Jolla, CA. p p. 22.
Cohen, A. N. 1994. The hidden costs of California's water. In Life on the Edge: A Resource Guide to California's Endangered Wildlife. Life on the Edge: A Resource Guide to California's Endangered Wildlife. Biosystems Books: Santa Cruz, CA. pp 288-302.
Cohen, A. N.; Nordby, J. C.; Beissinger, S. R. 2002. The impact of an invasive Atlantic cordgrass (Spartina alterniflora) on San Francisco Bay Song Sparrow populations: direct and indirect influence. In Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Silver Spring, MD.
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.; 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.; McGourty, K.; Cosentino-Manning, N.; De La Cruz, S. E. Wainwri; Elliot, M.; Allen, S. 2007. Introduction for 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. p 35.
Cohen, A. N. 2001. Invasions in the San Francisco Estuary. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Brewster, E. 2006. Land Grant Research and the Pictorial Collection. In Exploring the Bancroft Library. Exploring the Bancroft Library. The Bancroft Library/Signature Books. Vol. In Faulhab, p 196.
Collins, J. N.; Schwarzbach, S. E.; Luoma, S. N.; Yee, D.; Davis, J. A. 2000. Mercury and tidal wetland restoration. In Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.. Chapter 6 in Brown, L. (ed.). DRAFT CALFED Whitepaper on: Ecological Processes in Tidal Wetlands of the Sacramento-San Joaquin Estuary and Their Implications for Proposed Restoration Efforts of the Ecosystem Restoration Program.
Cohen, A. N. 2003. On Mitten Crabs and Lung Flukes. In IEP Newsletter. IEP Newsletter. Vol. 16, pp 48-51.
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Davis, J. A.; Richardson, C. J. 1987. Natural and artificial wetland ecosystems - ecological opportunities and limitations. In Aquatic Plants for Water Treatment and Resource Recovery. K.R., R., Smith, W. H., Eds.. Aquatic Plants for Water Treatment and Resource Recovery. University of Florida: Gainesville, FL.
Grossinger, R. M.; Beller, E. E. 2011. Oak Landscapes in the Recent Past. In Oaks in the Urban Landscape: Selection, Care, and Preservation. Costello, L. R., Hagen, B. W., Jones, K. S., Eds.. Oaks in the Urban Landscape: Selection, Care, and Preservation. University of California Agriculture and Natural Resources: Richmond, CA.
Sutton, R.; Xie, Y.; Moran, K. D.; Teerlink, J. 2019. Occurrence and Sources of Pesticides to Urban Wastewater and the Environment. In Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. American Chemical Society: Washington, DC. pp 63-88.

Municipal wastewater has not been extensively examined as a pathway by which pesticides contaminate surface water, particularly relative to the well-recognized pathways of agricultural and urban runoff. A state-of-the-science review of the occurrence and fate of current-use pesticides in wastewater, both before and after treatment, indicates this pathway is significant and should not be overlooked. A comprehensive conceptual model is presented to establish all relevant pesticide-use patterns with the potential for both direct and indirect down-the-drain transport. Review of available studies from the United States indicates 42 pesticides in current use. While pesticides and pesticide degradates have been identified in wastewater, many more have never been examined in this matrix. Conventional wastewater treatment technologies are generally ineffective at removing pesticides from wastewater, with high removal efficiency only observed in the case of highly hydrophobic compounds, such as pyrethroids. Aquatic life reference values can be exceeded in undiluted effluents. For example, seven compounds, including three pyrethroids, carbaryl, fipronil and its sulfone degradate, and imidacloprid, were detected in treated wastewater effluent at levels exceeding U.S. Environmental Protection Agency (US EPA) aquatic life benchmarks for chronic exposure to invertebrates. Pesticides passing through wastewater treatment plants (WWTPs) merit prioritization for additional study to identify sources and appropriate pollution-prevention strategies. Two case studies, diazinon and chlorpyrifos in household pesticide products, and fipronil and imidacloprid in pet flea control products, highlight the importance of identifying neglected sources of environmental contamination via the wastewater pathway. Additional monitoring and modeling studies are needed to inform source control and prevention of undesirable alternative solutions.

Cohen, A. N. 2005. Order Tanaidacea. In The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coasts. Carlton, J. T., Ed.. The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coasts. University of California Press: Berkeley, CA.
Cohen, A. N. 2006. The Panama Canal: Cutting a canal through Central America. In Bridging Divides: Maritime Canals as Invasion Corridor. Cohen, A. N., Gollasch, S., Galil, B. S., Eds.. Bridging Divides: Maritime Canals as Invasion Corridor. Kluwer Academic Publishing: Dordrecht, The Netherlands.
Cohen, A. N. 2006. The Panama Canal: Species Introductions and the Panama Canal. In Bridging Divides: Maritime Canals as Invasion Corridors. Cohen, A. N., Gollasch, S., Galil, B. S., Eds.. Bridging Divides: Maritime Canals as Invasion Corridors. Kluwer Academic Publishing: Dordrecht, The Netherlands.
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.
NOAA,. 2007. San Francisco Bay, CA: Comprehensive ecosystem evaluation needed to discern causes of chlorophyll a increases. In 2007 National Eutrophication Assessment. 2007 National Eutrophication Assessment. Washington, D.C. pp 113-114.
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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. 2002. Success factors in the establishment of human-dispersed organisms. In Dispersal Ecology: The 42nd Symposium of the British Ecological Society, held at the University of Reading, 2-5 April 2001. Bullock, J. M., Kenward, R. E., Hails, R. S., Eds.. Dispersal Ecology: The 42nd Symposium of the British Ecological Society, held at the University of Reading, 2-5 April 2001. British Ecological Society and Blackwell Publishing: Oxford UK. pp 374-394.
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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.
Hoenicke, R.; Bleier, C. 2007. Watershed Management and Land Use. CCMP Implementation Committee.
Cohen, A. N. 2000. Weeding the garden. In Preserving Wildlife: An International Perspective. Michael, M. A., Ed.. Preserving Wildlife: An International Perspective. Prometheus Books: Amherst NY. pp 84-92.
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Conference Paper
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.
Carlton, J. T. 1996. The Invaded estuary (abstract). In In: Third Biennial State of the Estuary Conf.. In: Third Biennial State of the Estuary Conf. San Francisco, CA.
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Conference Proceedings
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Cohen, A. N.; Weinstein, A.; Carlton, J. T. 1999. Aquatic bioinvasions in the San Francisco Estuary. Berkeley Society for Conservation Biology Annual Meeting.
Cohen, A. N. 1998. Biological invasions and opportunities for their regulation on the west coast of the United States. Proc. Eighth Int'l Zebra Mussel and Aquatic Nuisance Species Conf..
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Cohen, A. N. 1997. Biological invasions: An unregulated threat to estuarine biodiversity. Ann. Mtg., Society for Conservation Biology, Victoria BC (abstract)..
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Cohen, A. N. 1997. Biological invasions in the San Francisco Estuary. Ann. Mtg., American Fisheries Society, Aug 24-28, Monterey CA (abstract)..
Cohen, A. N. 1998. Biological invasions in the San Francisco Estuary. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, 14.
McKee, L. J. .; Wittner, E.; Leatherbarrow, J. E.; Lucas, V.; Grossinger, R. M. 2001. Building a regionally consistent base map for the Bay Area: The National Hydrography Data Set. Abstracts of the 5th Biannual State of the Estuary Conference – San Francisco Estuary: Achievements, trends and the future, pp 108.
McKee, L. J. .; Hoenicke, R.; Leatherbarrow, J. E. 2001. Contaminant contributions from the Guadalupe River and Coyote Creek watersheds to the lower South San Francisco Bay. Abstracts of the 5th Biannual State of the Estuary Conference – San Francisco Estuary: Achievements, trends and the future.
Cohen, A. N. 1998. Exotic organisms; California's Emerging Environmental Challenges. California's Emerging Environmental Challenges; Proceedings of a Workshop, 5-9 to 5-13.
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Cohen, A. N. 1998. Exotic species in California's coastal waters. Sanctuary Currents '98, Symposium on the Monterey Bay National Marine Sanctuary.
Cohen, A. N. 1998. The exotic species threat to California's coastal resources. California and the World Ocean '97, 1418-1426.
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. 1997. The invasion of the estuaries. Proc. Second International Spartina Conference, Mar 20-21, 1997, 6-9.
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Cohen, A. N. 1998. The invasion of the Pacific Coast by the European green crab. Eighth International Zebra Mussel and Aquatic Nuisance Species Conference, Page 44.
Cohen, A. N. 1998. The invasion of the Pacific Coast by the European green crab Carcinus maenas. Proc. Eighth Int'l Zebra Mussel and Aquatic Nuisance Species Conf., 173-177.
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Cohen, A. N. 1999. Invasions status and policy on the U. S. west coast. First National Conference on Marine Bioinvasion, 40-45.
Cohen, A. N. 2000. Invasions status and policy on the U. S. west coast. in: Proc. First Nat'l Conf. on Marine Bioinvasions, Jan. 24-27, 1999, Cambridge MA, 40-45.
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Cohen, A. N. 1997. Marine biological invasions: lessons from the San Francisco Estuary. Ann. Mtg., Estuarine Research Federation, Providence RI (abstract)..
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.
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Cohen, A. N. 1999. Prevention vs. control of biological invasions. First National Conference on Marine Bioinvasions.
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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..
Cohen, A. N. 2002. The release of pest species by marine aquaculture: lessons from a South African parasite introduced into California waters. Invasions in Aquatic Ecosystems: Impacts on Restoration and Potential for Control, Proceedings of a Workshop, April 25, 1998, 9-13.
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Cohen, A. N.; Zabin, C. J. 2006. Shells as vectors. Proceedings of the 2006 West Coast Native Oyster Restoration Workshop.
Greenfield, B. K. 2008. Spatial and temporal patterns in food web accumulation of Hg. San Francisco Bay Mercury Coordination Meeting.
Connor, M. S.; Davis, J. A. 2008. The State of San Francisco Bay: Water Quality. National Water Quality Monitoring Conference.
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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. 2001. Success factors in human-dispersed organisms. Dispersal, Annual Symposium of the British Ecological Society, Page 8.
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Cohen, A. N. 2008. Zebra & quagga mussel invasions in the western US. International Association of Great Lakes Research (IAGLR).
Factsheet
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Whipple, A.; Grantham, T.; Desanker, G.; Hunt, L.; Merrill, A.; Hackenjos, B.; Askevold, R. A. 2019. Chinook Salmon Habitat Quantification Tool: User Guide (Version 1.0). Prepared for American Rivers. Funded by the Natural Resources Conservation Service Conservation Innovation Grant (#69-3A75-17-40), Water Foundation and Environmental Defense Fund. A report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 953. San Francisco Estuary Institute: Richmond, CA.

The Salmon Habitat Quantification Tool provides systematic, transparent, and consistent accounting of the spatial extent, temporal variability, and quality of salmon habitat on the landscape. It is part of the multi-species assessment of the Central Valley Habitat Exchange (CVHE, www.cvhe.org). The suitability criteria applied in the tool were established by Stillwater Sciences and the Technical Advisory Committee (TAC), and the Chinook salmon HQT habitat evaluation and User Guide development was led by American Rivers and the San Francisco Estuary Institute. The approach uses commonly-applied concepts for evaluating suitable habitat based on modeling, with methods adapted from the hydrospatial analysis approach developed by Alison Whipple (2018).

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Sutton, R. 2016. Microplastic Contamination in San Francisco Bay - Fact Sheet. 2015, Revised 2016. SFEI Contribution No. 770.
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Moran, K.; Askevold, R. 2022. Microplastics from Tire Particles in San Francisco Bay Factsheet. SFEI Contribution No. 1074. San Francisco Estuary Institute: Richmond, CA.

As we drive our cars, our tires shed tiny particles

When it rains, stormwater runoff carries tire particles—and the toxic chemicals they contain—from city streets and highways to storm drains and fish habitat in creeks and estuaries like San Francisco Bay. Stormwater washes trillions of tire particles into the Bay each year.

How do tires affect wildlife?

A recent study found a highly toxic chemical (“6PPD-quinone”) derived from vehicle tires in Bay Area stormwater at levels that are lethal to coho salmon. New data indicate that steelhead, a salmon species still migrating through the Bay to surrounding watersheds, are also sensitive to this chemical.

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Sun, J.; Sutton, R.; Ferguson, L.; Overdahl, K. 2020. New San Francisco Bay Contaminants Emerge. SFEI Contribution No. 931. San Francisco Estuary Institute: Richmond, CA.

In 2016, the RMP launched a novel investigation to detect new or unexpected contaminants in Bay waters, as well as treated sewage (or wastewater) discharged to the Bay. This study used non-targeted analysis, a powerful tool that provides a broad, open-ended view of thousands of synthetic and naturally-derived chemicals simultaneously. We identified hundreds of contaminants, and the results have opened our eyes to urban stormwater runoff as an important pathway for emerging contaminants to enter the Bay.

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