Kazanidis, G.; Orejas, C.; Borja, A.; Kenchington, E.; Henry, L.-A.; Callery, O.; Carreiro-Silva, M.; Egilsdottir, H.; Giacomello, E.; Grehan, A.; Menot, L.; Morato, T.; Ragnarsson, S.A.; Rueda, J.L.; Stirling, D.; Stratmann, T.; van Oevelen, D.; Palialexis, A.; Johnson, D.; Roberts, J.M. (2020). Assessing the environmental status of selected North Atlantic deep-sea ecosystems. Ecol. Indic. 119: 106624. https://dx.doi.org/10.1016/j.ecolind.2020.106624
Hering, D.; Borja, A.; Jones, J.I.; Pont, D.; Boets, P.; Bouchez, A.; Bruce, K.; Drakare, S.; Hänfling, B.; Kahlert, M.; Leese, F.; Meissner, K.; Mergen, P.; Reyjol, Y.; Segurado, P.; Vogler, A.; Kelly, M. (2018). Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Wat. Res. 138: 192-205. https://hdl.handle.net/10.1016/j.watres.2018.03.003
Pelletier, M.C.; Gillett, D.J.; Hamilton, A.; Grayson, T.; Hansen, V.; Leppo, E.W.; Weisberg, S.B.; Borja, A. (2018). Adaptation and application of multivariate AMBI (M-AMBI) in US coastal waters. Ecol. Indic. 89: 818-827. https://hdl.handle.net/10.1016/j.ecolind.2017.08.067
Pinarbasi, K.; Galparsoro, I.; Borja, A.; Stelzenmüller, V.; Ehler, C.; Gimpel, A. (2017). Decision support tools in marine spatial planning: Present applications, gaps and future perspectives. Mar. Policy 83: 83-91. https://hdl.handle.net/10.1016/j.marpol.2017.05.031
Borja, A.; Elliott, M.; Uyarra, M.C.; Carstensen, J.; Mea, M. (Ed.) (2016). Bridging the gap between policy and science in assessing the health status of marine ecosystems. Frontiers Media: Lausanne. ISBN 978-2-88945-004-6. 293 pp. hdl.handle.net/10.3389/978-2-88945-004-6
Chust, G.; Villarino, E.; Chenuil, A.; Irigoien, X.; Bizsel, N.; Bode, A.; Broms, C.; Claus, S.; Fernández de Puelles, M.L.; Fonda Umani, S.; Hoarau, G.; Mazzocchi, M.G.; Mozetic, P.; Vandepitte, L.; Veríssimo, H.; Zervoudaki, S.; Borja, A. (2016). Dispersal similarly shapes both population genetics and community patterns in the marine realm. NPG Scientific Reports 6(28730): 12 pp. hdl.handle.net/10.1038/srep28730
Cochrane, S.; Andersen, J.H.; Berg, T.; Blanchet, H.; Borja, A.; Carstensen, J.; Elliott, M.; Hummel, H.; Niquil, N.; Renaud, P.E. (2016). What Is Marine Biodiversity? Towards Common Concepts and Their Implications for Assessing Biodiversity Status. Front. Mar. Sci. 3: 248. dx.doi.org/10.3389/fmars.2016.00248
Lepage, M.; Harrison, T.; Breine, J.; Cabral, H.; Coates, S.; Galván, C.; García, P.; Jager, Z.; Kelly, F.; Mosch, E.C.; Pasquaud, S.; Scholle, J.; Uriarte, A.; Borja, A. (2016). An approach to intercalibrate ecological classification tools using fish in transitional water of the North East Atlantic. Ecol. Indic. 67: 318-327. https://hdl.handle.net/10.1016/j.ecolind.2016.02.055
Patrício, J.; Little, S.; Mazik, K.; Papadopoulou, K.-N.; Smith, C.J.; Teixeira, H.; Hoffmann, H.; Uyarra, M.C.; Solaun, O.; Zenetos, A.; Kaboglu, G.; Kryvenko, O.; Churilova, T.; Moncheva, S.; Bucas, M.; Borja, A.; Hoepffner, N.; Elliott, M. (2016). European Marine Biodiversity Monitoring Networks: Strengths, weaknesses, opportunities and threats. Front. Mar. Sci. 3: 1-18. https://hdl.handle.net/10.3389/fmars.2016.00161
St. John, M.A.; Borja, A.; Chust, G.; Heath, M.; Grigorov, I.; Mariani, P.; Martin, A.P.; Santos, R.S. (2016). A dark hole in our understanding of marine ecosystems and their services: perspectives from the mesopelagic community. Front. Mar. Sci. 3: 31. https://hdl.handle.net/10.3389/fmars.2016.00031
Uusitalo, L.; Blanchet, H.; Andersen, J.H.; Beauchard, O.; Berg, T.; Bianchelli, S.; Cantafaro, A.; Carstensen, J.; Carugati, L.; Cochrane, S.; Danovaro, R.; Heiskanen, A.-S.; Karvinen, V.; Moncheva, S.; Murray, C.; Neto, J.M.; Nygård, H.; Pantazi, M.; Papadopoulou, N.; Simboura, N.; Srebaliene, G.; Uyarra, M.C.; Borja, A. (2016). Indicator-based assessment of marine biological diversity–lessons from 10 case studies across the European seas. Front. Mar. Sci. 3: 1-21. https://hdl.handle.net/10.3389/fmars.2016.00159
van der Linden, P.; Borja, A.; Rodríquez, J.G.; Muxika, I.; Galparsoro, I.; Patrício, J.; Veríssimo, H.; Marques, J.C. (2016). Spatial and temporal response of multiple trait-based indices to natural- and anthropogenic seafloor disturbance (effluents). Ecol. Indic. 69: 617-628. https://hdl.handle.net/10.1016/j.ecolind.2016.05.020
Birchenough, S.N.R.; Reiss, H.; Degraer, S.; Mieszkowska, N.; Borja, A.; Buhl-Mortensen, L.; Braeckman, U.; Craeymeersch, J.; De Mesel, I.; Kerckhof, F.; Kröncke, I.; Parra, S.; Rabaut, M.; Schröder, A.; Van Colen, C.; Van Hoey, G.; Vincx, M.; Wätjen, K. (2015). Climate change and marine benthos: a review of existing research and future directions in the North Atlantic. Wiley Interdisciplinary Reviews: Climate Change 6(2): 203-223. https://hdl.handle.net/10.1002/wcc.330
Duarte, C.M.; Borja, A.; Carstensen, J.; Elliott, M.; Krause-Jensen, D.; Marbà, N. (2015). Paradigms in the recovery of estuarine and coastal ecosystems. Est. Coast. 38(4): 1202-1212. hdl.handle.net/10.1007/s12237-013-9750-9
Borja, A. (2014). Grand challenges in marine ecosystems ecology. Front. Mar. Sci. 1: 1-6. hdl.handle.net/10.3389/fmars.2014.00001
Stelzenmüller, V.; Breen, P.; Stamford, T.; Thomsen, F.; Badalamenti, F.; Borja, A.; Buhl-Mortensen, L.; Carlstöm, J.; D'Anna, G.; Dankers, N.M.J.A.; Degraer, S.; Dujin, M.; Fiorentino, F.; Galparsoro, I.; Giakoumi, S.; Gristina, M.; Johnson, K.; Jones, P.J.S.; Katsanevakis, S.; Knittweis, L.; Kyriazi, Z.; Pipitone, C.; Piwowarczyk, J.; Rabaut, M.; Sørensen, T.K.; van Dalfsen, J.A.; Vassilopoulou, V.; Fernández, T.V.; Vincx, M.; Vöge, S.; Weber, A.; Wijkmark, N.; Jak, R.; Qiu, W.; ter Hofstede, R. (2013). Monitoring and evaluation of spatially managed areas: A generic framework for implementation of ecosystem based marine management and its application. Mar. Policy 37: 149-164. dx.doi.org/10.1016/j.marpol.2012.04.012
Zorita, I.; Solaun, O.; Borja, A.; Franco, J.; Muxika, I.; Pascual, M. (2013). Spatial distribution and temporal trends of soft-bottom marine benthic alien species collected during the period 1989–2008 in the Nervión estuary (southeastern Bay of Biscay). J. Sea Res. 83: 104-110. https://hdl.handle.net/10.1016/j.seares.2013.04.009
Borja, A.; Barbone, E.; Basset, A.; Borgersen, G.; Brkljacic, M.; Elliott, M.; Garmendia, J.M.; Marques, J.C.; Mazik, K.; Muxika, I.; Neto, J.M.; Norling, K.; Rodríguez, J.G.; Rosati, I.; Rygg, B.; Teixeira, H.; Trayanova, A. (2011). Response of single benthic metrics and multi-metric methods to anthropogenic pressure gradients, in five distinct European coastal and transitional ecosystems. Mar. Pollut. Bull. 62(3): 499-513. hdl.handle.net/10.1016/j.marpolbul.2010.12.009
Ferreira, J.G.; Andersen, J.H.; Borja, A.; Bricker, S.B.; Camp, J.; Cardoso da Silva, M.; Garcés, E.; Heiskanen, A.-S.; Humborg, C.; Ignatiades, L.; Lancelot, C.; Menesguen, A.; Tett, P.; Hoepffner, N.; Claussen, U. (2011). Overview of eutrophication indicators to assess environmental status within the European Marine Strategy Framework Directive. Est., Coast. and Shelf Sci. 93(2): 117-131. dx.doi.org/10.1016/j.ecss.2011.03.014
Pascual, M.; Borja, A.; Vanden Eede, S.; Deneudt, K.; Vincx, M.; Galparsoro, I.; Legorburu, I. (2011). Marine biological valuation mapping of the Basque continental shelf (Bay of Biscay), within the context of marine spatial planning. Est., Coast. and Shelf Sci. 95(1): 186-198. dx.doi.org/10.1016/j.ecss.2011.08.031
Borja, A.; Elliott, M.; Carstensen, J.; Heiskanen, A.-S.; van de Bund, W.J. (2010). Marine management – Towards an integrated implementation of the European Marine Strategy Framework and the Water Framework Directives. Mar. Pollut. Bull. 60(2): 2175-2186. https://hdl.handle.net/10.1016/j.marpolbul.2010.09.026
Borja, A.; Dauer, D.M.; Elliott, M.; Simenstad, C.A. (2010). Medium- and long-term recovery of estuarine and coastal ecosystems: patterns, rates and restoration effectiveness. Est. Coast. 33(6): 1249–1260. http://hdl.handle.net/10.1007/s12237-010-9347-5
Hering, D.; Borja, A.; Carstensen, J.; Carvalho, L.; Elliott, M.; Feld, C.K.; Heiskanen, A.-S.; Johnson, R.K.; Moe, J.; Pont, D.; Solheim, A.L.; van de Bund, W. (2010). The European Water Framework Directive at the age of 10: a critical review of the achievements with recommendations for the future. Sci. Total Environ. 408(19): 4007-4019. hdl.handle.net/10.1016/j.scitotenv.2010.05.031
Teixeira, H.; Borja, A.; Weisberg, S.B.; Ranasinghe, J.A.; Cadien, D.B.; Dauer, D.M.; Dauvin, J.-C.; Degraer, S.; Diaz, R.J.; Grémare, A.; Karakassis, I.; Llansó, R.J.; Lovell, L.L.; Marques, J.C.; Montagne, D.E.; Occhipinti-Ambrogi, A.; Rosenberg, R.; Sardá, R.; Schaffner, L.C.; Velarde, R.G. (2010). Assessing coastal benthic macrofauna community condition using best professional judgement – Developing consensus across North America and Europe. Mar. Pollut. Bull. 60(4): 589-600. dx.doi.org/10.1016/j.marpolbul.2009.11.005
Van Hoey, G.; Borja, A.; Birchenough, S.; Buhl-Mortensen, L.; Degraer, S.; Fleischer, D.; Kerckhof, F.; Magni, P.; Muxika, I.; Reiss, H.; Schröder, A.; Zettler, M.L. (2010). The use of benthic indicators in Europe: From the Water Framework Directive to the Marine Strategy Framework Directive. Mar. Pollut. Bull. 60(12): 2187-2196. dx.doi.org/10.1016/j.marpolbul.2010.09.015
Uriarte, A.; Borja, A. (2009). Assessing fish quality status in transitional waters, within the European Water Framework Directive. Setting boundary classes and responding to anthropogenic responses. Est., Coast. and Shelf Sci. 82(2): 214-224. dx.doi.org/10.1016/j.ecss.2009.01.008
Borja, A.; Josefson, A.B.; Miles, A.; Muxika, I.; Olsgard, F.; Phillips, G.; Rodríguez, J.G.; Rygg, B. (2007). An approach to the intercalibration of benthic ecological status assessment in the North Atlantic ecoregion, according to the European Water Framework Directive. Mar. Pollut. Bull. 55(Spec. Issue 1-6): 42-52. http://dx.doi.org/10.1016/j.marpolbul.2006.08.018
Borja, A.; Josefson, A.B.; Miles, A.; Muxika, I.; Olsgard, F.; Phillips, G.; Rodríguez, J.G.; Rygg, B. (2007). An approach to the intercalibration of benthic ecological status assessment in the North Atlantic ecoregion, according to the European Water Framework Directive, in: Devlin, M. et al. (Ed.) Implementation of the Water Framework Directive in European marine waters. Marine Pollution Bulletin, 55(Spec. Issue 1-6): pp. 42-52. http://dx.doi.org/10.1016/j.marpolbul.2006.08.018
Muxika, I.; Borja, A.; Bald, J. (2007). Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status, according to the European Water Framework Directive. Mar. Pollut. Bull. 55(Spec. Issue 1-6): 16-29. http://dx.doi.org/10.1016/j.marpolbul.2006.05.025
Muxika, I.; Borja, A.; Bald, J. (2007). Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status, according to the European Water Framework Directive, in: Devlin, M. et al. (Ed.) Implementation of the Water Framework Directive in European marine waters. Marine Pollution Bulletin, 55(Spec. Issue 1-6): pp. 16-29
Borja, A.; Muxika, I.; Bald, J. (2006). Protection of the goose barnacle Pollicipes pollicipes, Gmelin, 1790 population: the Gaztelugatxe Marine Reserve (Basque Country, northern Spain). Sci. Mar. (Barc.) 70(2): 235-242
Muxika, I.; Borja, A.; Bonne, W. (2005). The suitability of the marine biotic index (AMBI) to new impact sources along European coasts. Ecol. Indic. 5: 19-31
Borja, A.; Franco, J.; Pérez, V. (2000). A marine biotic index to establish the ecological quality of soft-bottom benthos within European estuarine and coastal environments. Mar. Pollut. Bull. 40(12): 1100-1114. http://dx.doi.org/10.1016/S0025-326X(00)00061-8
Borja, A. (1988). Biología y ecología de tres especies de moluscos gasteropodos intermareales: Rissoa parva, Barleeia unifasciata y Bittium reticulatum. 3. Produccion = Biology and ecology of three species of molluskan gasteropods: Rissoa parva, Barleeia unifasciata and Bittium reticulatum. 3. Production. Cah. Biol. Mar. 29(3): 319-330
Borja, A. (1987). Biologia y ecologia de tres especies de molluscos gasteropodos intermareales: Rissoa parva, Barleeia unifasciata y Bittium reticulatum 2. Crecimiento = Biology and ecology of three species of intertidal gastropods: Rissoa parva, Barleeia unifasciata and Bittium reticulatum 2. Growth. Cah. Biol. Mar. 28(3): 351-360
Borja, A. (1986). La alimentacion y distribucion del espacio en tres molluscos gastropodos: Rissoa parva (da Costa), Barleeia unifasciata (Montagu) y Bittium reticulatum (da Costa). Cah. Biol. Mar. 27(1): 69-75
Borja, A. (1986). Biología y ecologia de tres especies de molluscos gasterópodos intermareales: Risso parva, Barleeia unifasciata y Bittium reticulatum. 1. Estructura y dinámica de las poblaciones = Biology and ecology of three intertidal gastropods: Rissoa parva, Barleeia unifasciata and Bittium reticulatum. 1. Population structure and dynamics. Cah. Biol. Mar. 27(4): 491-507
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