Below is an abridged list of publications from the last few years, together with a selection of older ones. (See all publications instead)
Buck, B.H., Bjelland, H.V., Bockus, A., Chambers, M.l, Costa-Pierce, B.A., Dewhurst, T., Ferreira, J.G., Føre, H.M., Fredriksson, D.W., Goseberg, N., Holmyard, J., Isbert, W., Krause, G., Markus, T., Papandroulakis, N., Sclodnick, T., Silkes, B., Strand, Å., Troell, M., Wieczorek, D, van den Burg, S.W.K., Heasman, K.G., 2024. Resolving the term “offshore aquaculture” by decoupling “exposed” and “distance from the coast”. Front. Aquac. 3:1428056.
Bayer, S.R., Cubillo, A.M., Rose, J.M., Ferreira, J.G., Dixon, M., Alvarado, A., Barr, J., Bernatchez, G., Meseck, S., Poach, M., Pousse, E., Wikfors, G.H., Bricker, S., 2024. Refining the Farm Aquaculture Resource Management Model for Shellfish Nitrogen Removal at the Local Scale. Estuaries and Coasts.
Cubillo, A., Lopes, A.S., Ferreira, J.G., Moore, H., Service, M., Bricker, S.B., 2023. Quantification and valuation of the potential of shellfish ecosystem services in mitigating coastal eutrophication. Estuarine, Coastal, and Shelf Science, 293, 108469.
Ferreira, J.G., Bernard-Jannin, L., Cubillo, A., Lencart-Silva, J., Diedericks, G.P.J., Moore, H., Service, M., Nunes, J.P., 2023. From soil to sea: an ecological modelling framework for sustainable aquaculture. Aquaculture 557, 1-14.
Barry Antonio Costa-Pierce, Abigail B. Bockus, Bela H. Buck, Sander W.K. van den Burg, Thierry Chopin, Joao G. Ferreira, Nils Goseberg, Kevin G. Heasman, Johan Johansen, Sandra E. Shumway, Neil A. Sims, Albert G. J. Tacon, 2022. A Fishy Story Promoting a False Dichotomy to Policy-Makers: It Is Not Freshwater vs. Marine Aquaculture, Reviews in Fisheries Science & Aquaculture, 30:4, 429-446, DOI: 10.1080/23308249.2021.2014175
Panicz, R., B. Całka, A. Cubillo, J. G. Ferreira, J. Guilder, S. Kay, A. Kennerley, A. Lopes, J. Lencart e Silva, N. Taylor, P. Eljasik, J. Sadowski, P. Hofsoe-Oppermann, S. Keszka 2022. Impact of climate driven temperature increase on inland aquaculture: application to land-based production of common carp (Cyprinus carpio L.). Transboundary and Emerging Diseases DOI: 10.1111/tbed.14577
Cubillo, A., Ferreira, J.G., Lencart-Silva, J., Taylor, N.G.H., Kennerley, A., Guilder, J., Kay, S., Kamermans, P. 2021. Direct effects of climate change on productivity of European aquaculture. Aquaculture International 29(1–2) DOI:10.1007/s10499-021-00694-6

Ferreira, J.G., Taylor, N.G.H., Cubillo, A., Lencart-Silva, J., Pastres, R., Bergh, Ø., Guilder, J., 2021. An integrated model for aquaculture production, pathogen interaction, and environmental effects. Aquaculture 536, 1-16,

Santa Marta, A., J.G. Ferreira, G.C. Pitcher, J. Lencart e Silva, 2020. Sustainable shellfish aquaculture in Saldanha Bay, South Africa. African Journal of Marine Science 42:2, 151-166, DOI: 10.2989/1814232X.2020.1760935

Suzanne B. Bricker, Raymond E. Grizzle, Philip Trowbridge, Julie M. Rose, Joao G. Ferreira, Katharine Wellman, Changbo Zhu, Eve Galimany, Gary H. Wikfors, Camille Saurel, Robin Landeck Miller, James Wands, Robert Rheault, Jacob Steinberg, Annie P. Jacob, Erik D. Davenport, Suzanne Ayvazian, Marnita Chintala, Mark A. Tedesco, 2020. Bioextractive Removal of Nitrogen by Oysters in Great Bay Piscataqua River Estuary, New Hampshire, USA. Estuaries and Coasts 43:23–38
Rui Gomes Ferreira, Joao G. Ferreira, Frans-Joost Boogert, Richard A. Corner, Joao Pedro Nunes, Jon Grant, Johan Johansen, William F. Dewey, 2020. A multimetric investor index for aquaculture: Application to the European Union and Norway. Aquaculture 516
Alhambra Martínez Cubillo, João G. Ferreira, Christopher Michael Pearce, Robert Marshall, Dan Cheney, Bobbi Hudson, 2018. Ecosystem services of geoduck farming in South Puget Sound, USA: a modeling analysis. Aquaculture International,
Joao G. Ferreira, Richard A. Corner, Heather Moore, Matthew Service, Suzanne B. Bricker, Robert Rheault, 2018. Ecological carrying capacity for shellfish aquaculture—sustainability of naturally occurring filter-feeders and cultivated bivalves. Journal of Shellfish Research, 37 (3), 1–18.
S.B. Bricker, J.G. Ferreira, C.B. Zhu, J. Rose, E. Galimany, G. Wikfors, C. Saurel, R. Landeck Miller, J. Wands, P. Trowbridge, R. Grizzle, K. Wellman, R. Rheault, J. Steinberg, A. Jacob, E. Davenport, S. Ayvazian, M. Chintala, M. Tedesco 2018. The role of shellfish aquaculture in reduction of eutrophication in an urban estuary. Environ. Sci. Technol, 52 (1), 173–183.
Mendoza-Beltran, A., Chiantore, M., Pecorino, D., Corner, R.A., Ferreira, J.G., Cò, R., Fanciulli, L., Guinée, J.B., 2017. Accounting for inventory data and methodological choice uncertainty in a comparative life cycle assessment: the case of integrated multi-trophic aquaculture in an offshore Mediterranean enterprise. Int J Life Cycle Assessment DOI 10.1007/s11367-017-1363-2
Lopes, A.S., J.G. Ferreira, C. Vale, J. Johansen, 2017. The mass balance of production and consumption: Supporting policy-makers for aquatic food security. Estuarine, Coastal and Shelf Science, 188, 212-223.
Nobre, A.M., Soares, F., Ferreira, J.G., 2017. A mass balance model to assess food limitation in commercial oyster nurseries. Journal of Shellfish Research, 36(3), 737-748.
A.M. Cubillo, J.G. Ferreira, S.M.C. Robinson, C.M. Pearce, R.A. Corner, and J. Johansen 2016. Role of deposit feeders in integrated multi-trophic aquaculture - a model analysis. Aquaculture, 453, 54-66.
J.G. Ferreira, S.B. Bricker 2016. Goods and services of extensive aquaculture: shellfish culture and nutrient trading. Aquaculture International, 24 (3), 803–825. DOI 10.1007/s10499-015-9949-9
R. Filgueira, C. J. Byron, L. A. Comeau, B. Costa-Pierce, P. J. Cranford, J. G. Ferreira, J. Grant, T. Guyondet, H. M. Jansen, T. Landry, C. W. McKindsey, J. K. Petersen, G. K. Reid, S. M. C. Robinson, A. Smaal, R. Sonier, Ø. Strand, T. Strohmeier 2015. An integrated ecosystem approach for assessing the potential role of cultivated bivalve shells as part of the carbon trading system. Mar. Ecol. Prog. Ser. 518:281-287.
M.J. Botelho, C. Vale, J.G. Ferreira 2015. Profiles of paralytic shellfish toxins in bivalves of low and elevated toxicities following exposure to Gymnodinium catenatum blooms in Portuguese estuarine and coastal waters. Chemosphere,
J.M. Rose, S.B. Bricker, J.G. Ferreira, 2015. Comparative analysis of modeled nitrogen removal by shellfish farms. Mar. Pollut. Bull. 91 (1), 185-190.
J.G. Ferreira, L. Falconer, J. Kittiwanich, L. Ross, C. Saurel, K. Wellman, C.B. Zhu, P. Suvanachai, 2015. Analysis of production and environmental effects of Nile tilapia and white shrimp culture in Thailand. Aquaculture, 447, 23-36.
C. Saurel, J.G. Ferreira, D. Cheney, A. Suhrbier, B. Dewey, J. Davis, J. Cordell, 2014. Ecosystem goods and services from Manila clam culture in Puget Sound: a modelling analysis. Aquaculture Environment Interactions, 5, 255-270.
J.G. Ferreira, C. Saurel, J.D. Lencart e Silva, J.P. Nunes, F. Vazquez, 2014. Modelling of interactions between inshore and offshore aquaculture. Aquaculture, 426–427, 154-164.
Botelho, M.J., Raimundo, J., Vale, C., Ferreira, J.G., 2014. Partitioning of paralytic shellfish toxins in sub-cellular fractions of the digestive gland of the cockle Cerastoderma edule: Changes under post-bloom natural conditions. Ecotoxicology and Environmental Safety 104, 365-372.
A. Borja, M. Elliott, J.H. Andersen, J. Carstensen, A.C. Cardoso, J.G. Ferreira, A.S. Heiskanen, J.C. Marques, J. Neto, H. Teixeira, M.C. Uyarra, L. Uusitalo, N. Zampoukas, 2013. Good Environmental Status of marine ecosystems: What is it and how do we know when we have attained it? Mar. Pol. Bull., 76, 16-27.
Ferreira, J.G., C. Saurel, J.M. Ferreira, 2012. Cultivation of gilthead bream in monoculture and integrated multi-trophic aquaculture. Analysis of production and environmental effects by means of the FARM model. Aquaculture 358–359 (2012) 23–34.
M.J. Botelho, C. Vale, R. Velez Grilo, J.G. Ferreira 2012. Uptake and release of paralytic shellfish toxins by the clam Ruditapes decussatus exposed to Gymnodinium catenatum and subsequent depuration. Marine Environmental Research 77 (2012) 23-29.
Nobre A.M., Bricker S.B., Ferreira J.G., Yan X., de Wit M., Nunes J.P., 2011. Integrated environmental modelling and assessment of coastal ecosystems, application for aquaculture management. Coastal Management, Volume 39 (5).
C. Silva, J.G. Ferreira, S.B. Bricker, T. A. DelValls, M.L. Martín-Díaz and E. Yañez 2011. Site selection for shellfish aquaculture by means of GIS and farm-scale models, with an emphasis on data-poor environments. Aquaculture, 318, 444-457.
J.G. Ferreira, J.H. Andersen, A. Borja, S.B. Bricker, J. Camp, M. Cardoso da Silva, E. Garcés, A.S. Heiskanen, C. Humborg, L. Ignatiades, C. Lancelot, A. Menesguen, P. Tett, N. Hoepffner, U., Claussen, 2011. Overview of eutrophication indicators to assess environmental status within the European Marine Strategy Framework Directive. Estuarine Coastal and Shelf Science, 93, 117-131.
J. P. Nunes, J. G. Ferreira, S. B. Bricker, B. O'Loan, T. Dabrowski, B. Dallaghan, A. J. S. Hawkins, B. O'Connor, T. O'Carroll, 2011. Towards an ecosystem approach to aquaculture: assessment of sustainable shellfish cultivation at different scales of space, time and complexity. Aquaculture, 315, 369-383.
Nobre, A. M., Ferreira, J. G., Nunes, J. P., Yan, X., Bricker, S., Corner, R., Groom, S., Gu, H., Hawkins, A., Hutson, R., Lan, D., Lencart e Silva, J. D., Pascoe, P., Telfer, T., Zhang, X., Zhu, M., 2010. Assessment of coastal management options by means of multilayered ecosystem models. Estuarine, Coastal and Shelf Science, 87, 43-62.
A.M. Nobre, J.K. Musango, M.P. de Wit, J.G. Ferreira, 2009. A dynamic ecological-economic modeling approach for aquaculture management. Ecological Economics, 68, 3007-3017.
A.M. Nobre, J.G. Ferreira, 2009. Integration of ecosystem-based tools to support coastal zone management. Journal of Coastal Research, SI 56: 1676-1680.
J.G. Ferreira, A. Sequeira, A.J.S. Hawkins, A. Newton, T. Nickell, R. Pastres, J. Forte, A. Bodoy, S.B. Bricker, 2009. Analysis of coastal and offshore aquaculture: application of the FARM model to multiple systems and shellfish species. Aquaculture, 292, 129-138.
Borja, A., Bricker, S.B., Dauer, D.M., Demetriades, N.T., Ferreira, J.G., Forbes, A.T., Hutchings, P., Jia, X., Kenchington, R., Marques, J.C., Zhu, C.B. 2008. Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide. Marine Pollution Bulletin, 56, 1519–1537.
J.G. Ferreira, A.J.S. Hawkins, P. Monteiro, H. Moore, M. Service, P.L. Pascoe, L. Ramos, A. Sequeira, 2008. Integrated Assessment of Ecosystem-Scale Carrying Capacity in Shellfish Growing Areas. Aquaculture, 275, 138-151.
A. Sequeira, J.G. Ferreira, A.J. Hawkins, A. Nobre, P. Lourenço, X.L. Zhang, X. Yan, T. Nickell, 2008. Trade-offs between shellfish aquaculture and benthic biodiversity: A modelling approach for sustainable management. Aquaculture, 274, 313-328.
J. G. Ferreira, C. Vale, C.V. Soares, F.Salas, P.E. Stacey, S. B. Bricker, M.C. Silva, J.C. Marques, 2007. Monitoring of coastal and transitional waters under the EU Water Framework Directive. Environmental Monitoring and Assessment, 135 (1-3), 195-216 .
Older publications
Martins, I., Lopes, R.J., Lillebø, A.I., Neto, J.M., Pardal, M.A., Ferreira, J.G., Marques, J.C., 2007. Significant variations in the productivity of green macroalgae in a mesotidal estuary: implications to the nutrient loading of the system and the adjacent coastal area. Marine Pollution Bulletin, 54 (6), 678-690 .
Xiao, Y., Ferreira, J.G., Bricker, S.B., Nunes, J.P., Zhu, M., Zhang X., 2007. Trophic Assessment in Chinese Coastal Systems - Review of methodologies and application to the Changjiang (Yangtze) Estuary and Jiaozhou Bay. Estuaries and Coasts, 30(6), 1-18.
D. Whitall, S.B.Bricker, J.G.Ferreira, A.M.Nobre, T. Simas, M.C. Silva, 2007. Assessment of Eutrophication in Estuaries: Pressure-State-Response and Nitrogen Source Apportionment. Environmental Management,.40:678-690.
T.C. Simas, J.G. Ferreira, 2007. Nutrient enrichment and the role of salt marshes in the Tagus estuary (Portugal). Estuarine, Coastal and Shelf Science, 75, 393-407.
J. G. Ferreira, A.J.S. Hawkins, S.B. Bricker, 2007. Management of productivity, environmental effects and profitability of shellfish aquaculture – the Farm Aquaculture Resource Management (FARM) model. Aquaculture, 264, 160-174.
J.G. Ferreira, S.B. Bricker, T.C. Simas, 2007. Application and sensitivity testing of an eutrophication assessment method on coastal systems in the United States and European Union. J. Environmental Management, 82, 433-445.
A. R. Franco, J. G. Ferreira, A. M. Nobre, 2006. Development of a growth model for penaeid shrimp. Aquaculture, 259, 268-277.
J. G. Ferreira, A. M. Nobre, T. C. Simas, M. C. Silva, A. Newton, S. B. Bricker, W. J. Wolff, P.E. Stacey, A. Sequeira, 2006. A methodology for defining homogeneous water bodies in estuaries Application to the transitional systems of the EU Water Framework Directive. Estuarine, Coastal and Shelf Science, 66 (3/4), 468-482.
J.G.Ferreira, W.J.Wolff, T.C.Simas, S.B.Bricker, 2005. Does biodiversity of estuarine phytoplankton depend on hydrology? Ecological Modelling, 187(4) 513-523.
A.M.Nobre, J.G.Ferreira, A.Newton, T.Simas, J.D.Icely, R.Neves, 2005. Management of coastal eutrophication: Integration of field data, ecosystem-scale simulations and screening models. Journal of Marine Systems, 56 (3/4), 375-390.
Tett, P., Gilpin, L., Svendsen, H., Erlandsson, C.P., Larsson, U., Kratzer, S., Fouilland, E., Janzen, C., Lee, J., Grenz, C., Newton, A., Ferreira, J.G., Fernandes, T., Scory, S., 2003. Eutrophication and some European waters of restricted exchange. Continental Shelf Research, 23, 1635-1671.
Bricker, S.B., J.G. Ferreira, T. Simas, 2003. An Integrated Methodology for Assessment of Estuarine Trophic Status. Ecological Modelling, 169(1), 39-60.
Alvera-Azcarate, A., Ferreira, J.G., & Nunes, J.P., 2003. Modelling eutrophication in mesotidal and macrotidal estuaries. The role of intertidal seaweeds. Estuarine, Coastal and Shelf Science, 57(4), 715-724.
Nunes, J.P, Ferreira, J.G., Gazeau, F., Lencart-Silva, J., Zhang, X.L, Zhu M.Y. & Fang J.G., 2003. A model for sustainable management of shellfish polyculture in coastal bays. Aquaculture, 219/1-4,  257-277.
Simas, T., Nunes, J.P. & Ferreira, J.G., 2001. Effects of global climate change on coastal salt marshes. Ecological Modelling. 139 (1), 1-15.
Ferreira, J.G., 2000. Development of an estuarine quality index based on key physical and biogeochemical features. Ocean & Coastal Management, 43/1, 99-122.
Macedo, M.F., Ferreira, J.G. and Duarte, P., 1998. Dynamic behaviour of photosynthesis-irradiance curves determined from oxygen production during variable incubation periods. Mar. Ecol. Prog. Series, 165, 31-43.
Ferreira, J.G., Duarte, P. and Ball, B., 1998. Trophic Capacity of Carlingford Lough for Aquaculture - Analysis by Ecological Modelling. Aquatic Ecology Vol. 31, 4, 361-378.
Duarte, P. & Ferreira, J.G., 1997. Dynamic modelling of photosynthesis in marine and estuarine ecosystems. Environmental Modelling and Assessment, 2, 83-93.
Ferreira, J.G., 1995. EcoWin - An object-oriented ecological model for aquatic ecosystems. Ecol. Modelling, 79, 21-34.


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