1. Ramos, E., A. Puente, J.A. Juanes, J.M. Neto, A. Pedersen, I. Bartsch and R. Melo, 2014. Biological validation of physical coastal waters classification along the NE Atlantic region based on rocky macroalgae distribution. Estuarine Coastal Shelf Sci., 147: 103-112.
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2. Neto, J.M., M.J. Feio, H. Teixeira, J. Patricio, S.R.Q. Serra, J.N. Franco and E. Constantino, 2014. Transitional and freshwater bioassessments: One site, two perspectives? Mar. Pollut. Bull., 78: 153-164.
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3. Borja, A., T.C. Prins, N. Simboura, J.H. Andersen, T. Berg, J.C. Marques and L. Uusitalo, L. 2014. Tales from a thousand and one ways to integrate marine ecosystem components when assessing the environmental status. Front. Mar. Sci., 1: 1-20.
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4. Pinto, R., V.N. de Jonge, J.M. Neto, T. Domingos, J.C. Marques and J. Patricio, 2013. Towards a DPSIR driven integration of ecological value, water uses and ecosystem services for estuarine systems. Ocean Coastal Manage., 72: 64-79.
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5. Neto, J.M., D.V. Barroso and P. Barria, 2013. Seagrass Quality Index (SQI), a Water Framework Directive compliant tool for the assessment of transitional and coastal intertidal areas. Ecol. Indic., 30: 130-137.
6. Modesto, V., J.N. Franco, R. Sousa, J. Patricio, J.C. Marques amd J.M. Neto, 2013. Spatial and temporal dynamics of Corbicula fluminea (Muller, 1774) in relation to environmental variables in the Mondego Estuary (Portugal). J. Molluscan Stud., 79: 302-309.
7. Mascaro, O., T. Alcoverro, K. Dencheva, I. Diez, J.M. Gorostiaga, D. Krause-Jensen J. Romero, 2013. Exploring the robustness of macrophyte-based classification methods to assess the ecological status of coastal and transitional ecosystems under the Water Framework Directive. Hydrobiologia, 704: 279-291.
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8. Marques, L., A. Carrico, F. Bessa, R. Gaspar, J.M. Neto and J. Patricio, 2013. Response of intertidal macrobenthic communities and primary producers to mitigation measures in a temperate estuary. Ecol. Indic., 25: 10-22.
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9. Marba, N., D. Krause-Jensen, T. Alcoverro, S. Birk, A. Pedersen, J.M. Neto and C.M. Duarte, 2013. Diversity of European seagrass indicators: patterns within and across regions. Hydrobiologia, 704: 265-278.
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10. Mantas, V.M., A.J.S.C. Pereira, J. Neto, J., Patricio and J.C. Marques, 2013. Monitoring estuarine water quality using satellite imagery. The Mondego river estuary (Portugal) as a case study. Ocean Coastal Manage., 72: 13-21.
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11. Kristensen, E., J.M. Neto, M. Lundkvist, L. Frederiksen, M.A. Pardal, T. Valdemarsen and M.R. Flindt, 2013. Influence of benthic macroinvertebrates on the erodability of estuarine cohesive sediments: Density-and biomass-specific responses. Estuarine Coastal Shelf Sci., 134: 80-87.
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12. Ceia, F.R., J. Patricio, J., Franco, R. Pinto, S. Fernandez-Boo, V. Losi and J.M. Neto, 2013. Assessment of estuarine macrobenthic assemblages and ecological quality status at a dredging site in a southern Europe estuary. Ocean Coastal Manage., 72: 80-92.
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13. Cacador, I., J.M. Neto, B. Duarte, D.V. Barroso, M. Pinto and J.C. Marques, 2013. Development of an Angiosperm Quality Assessment Index (AQuA-Index) for ecological quality evaluation of Portuguese water bodies-A multi-metric approach. Ecol. Indic., 25: 141-148.
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14. Borja, A., M. Elliott, J.H. Andersen, A.C. Cardoso, J. Carstensen, J.G. Ferreira and N. Zampoukas, 2013. Good Environmental Status of marine ecosystems: What is it and how do we know when we have attained it? Mar. Pollut. Bull., 76: 16-27.
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15. Basset, A., E. Barbone, A. Borja, M. Elliott, G. Jona-Lasinio, J.C. Marques and H. Teixeira, 2013. Natural variability and reference conditions: setting type-specific classification boundaries for lagoon macroinvertebrates in the Mediterranean and Black Seas. Hydrobiologia, 704: 325-345.
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16. van der Linden, P., J. Patricio, A. Marchini, N. Cid, J.M. Neto and J.C. Marques, 2012. A biological trait approach to assess the functional composition of subtidal benthic communities in an estuarine ecosystem. Ecol. Indic., 20: 121-133.
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17. Verissimo, H., J.M. Neto, H. Teixeira, J.N. Franco, B.D. Fath, J.C. Marques and J. Patricio, 2012. Ability of benthic indicators to assess ecological quality in estuaries following management. Ecol. Indic., 19: 130-143.
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18. Re: Brito, A.C., V. Brotas, M. Caetano, T.P. Coutinho, A.A. Bordalo, J. Icely, J.M. Neto, J. Serodio and T. Moita, 2012. Defining phytoplankton class boundaries in Portuguese transitional waters: An evaluation of the ecological quality status according to the Water Framework Directive. Ecol. Indic., 24: 254-255.
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19. Ramos, E., J.A. Juanes, C. Galvan, J.M. Neto, R. Melo, A. Pedersen and B. Gonzalez, 2012. Coastal waters classification based on physical attributes along the NE Atlantic region. An approach for rocky macroalgae potential distribution. Estuarine Coastal Shelf Sci., 112: 105-114.
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20. Perez-Dominguez, R., S. Maci, A. Courrat, M. Lepage, A. Borja, A. Uriarte and M. Elliott, 2012. Current developments on fish-based indices to assess ecological-quality status of estuaries and lagoons. Ecol. Indic., 23: 34-45.
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21. Patricio, J., H. Adao, J.M. Neto, A.S. Alves, W. Traunspurger and J.C. Marques, 2012. Do nematode and macrofauna assemblages provide similar ecological assessment information? Ecol. Indic., 14: 124-137.
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22. Neto, J.M., R. Gaspar, L. Pereira and J.C. Marques, 2012. Marine Macroalgae Assessment Tool (MarMAT) for intertidal rocky shores. Quality assessment under the scope of the European Water Framework Directive. Ecol. Indic., 19: 39-47.
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23. Goncalves, C.I., S. Pasquaud, R. Gamito, V.F. Fonseca, J.L. Costa, K. Erzini and H. Cabral, 2012. Robustness of the Estuarine Fish Assessment Index (EFAI) regarding water body definition criteria. Ecol. Indic., 20: 1-8.
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24. Gaspar, R., L. Pereira and J.M. Neto, 2012. Ecological reference conditions and quality states of marine macroalgae sensu Water Framework Directive: An example from the intertidal rocky shores of the Portuguese coastal waters. Ecol. Indic., 19: 24-38.
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25. Gamito, S., J. Patricio, J.M. Neto, J.C. Marques and H. Teixeira, 2012. The importance of habitat-type for defining the reference conditions and the ecological quality status based on benthic invertebrates: The Ria Formosa coastal lagoon (Southern Portugal) case study. Ecol. Indic., 19: 61-72.
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26. Gamito, S., J. Patricio, J.M. Neto, H. Teixeira and J.C. Marques, 2012. Feeding diversity index as complementary information in the assessment of ecological quality status. Ecol. Indic., 19: 73-78.
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27. Franco, J.N., F.R. Ceia, J. Patricio, V. Modesto, J. Thompson, J.C.Marques and J.M. Neto, 2012. Population dynamics of Corbicula fluminea (Muller, 1774) in mesohaline and oligohaline habitats: Invasion success in a Southern Europe estuary. Estuarine Coastal Shelf Sci., 112: 31-39.
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28. Cabral, H.N., V.F. Fonseca, R. Gamito, C.I. Goncalves, J.L. Costa, K. Erzini and M.J. Costa, 2012. Ecological quality assessment of transitional waters based on fish assemblages in Portuguese estuaries: the Estuarine Fish Assessment Index (EFAI). Ecol. Indic., 19: 144-153.
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29. Brito, A.C., V. Brotas, M. Caetano, T.P. Coutinho, A.A. Bordalo, J. Icely and T. Moita, 2012. Defining phytoplankton class boundaries in Portuguese transitional waters: An evaluation of the ecological quality status according to the Water Framework Directive. Ecol. Indic., 19: 5-14.
30. Borja, A., E. Barbone, A. Basset, G. Borgersen, M. Brkljacic, M. Elliott and A. Trayanova, 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: 499-513.
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31. Pinto, R., J. Patricio, J.M. Neto, F. Salas and J.C. Marques, 2010. Assessing estuarine quality under the ecosystem services scope: Ecological and socioeconomic aspects. Ecol. Complexity, 7: 389-402.
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32. Neto, J.M., H. Teixeira, J. Patricio, A. Baeta, H. Verissimo, R. Pinto and J.C. Marques, 2010. The response of estuarine macrobenthic communities to natural-and human-induced changes: dynamics and ecological quality. Estuaries Coasts, 33: 1327-1339.
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33. Couto, T., J. Patricio, J.M. Neto, F.R. Ceia, J. Franco and J.C. Marques, 2010. The influence of mesh size in environmental quality assessment of estuarine macrobenthic communities. Ecol. Indic., 10: 1162-1173.
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34. Teixeira, H., J.M. Neto, J. Patricio, H. Verissimo, R. Pinto, F. Salas and J.C. Marques, 2009. Quality assessment of benthic macroinvertebrates under the scope of WFD using BAT, the Benthic Assessment Tool. Mar. Pollut. Bull., 58: 1477-1486.
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35. Pinto, R., J. Patricio, A. Baeta, B.D. Fath, J.M. Neto and J.C. Marques, 2009. Review and evaluation of estuarine biotic indices to assess benthic condition. Ecol. Indicators, 9: 1-25.
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36. Patricio, J., J.M. Neto, H. Teixeira, F. Salas and J.C. Marques, 2009. The robustness of ecological indicators to detect long-term changes in the macrobenthos of estuarine systems. Mar. Environ. Res., 68: 25-36.
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37. Garel, E., S. Nunes, J.M. Neto, R. Fernandes, R. Neves, J.C. Marques and O. Ferreira, 2009. The autonomous Simpatico system for real-time continuous water-quality and current velocity monitoring: examples of application in three Portuguese estuaries. Geo-Mar. Lett., 29: 331-341.
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38. Alves, A.S., H. Adao, J. Patricio, J.M. Neto, M.J. Costa and J.C.Marques, 2009. Spatial distribution of subtidal meiofauna communities along a salinity gradient in two Southern European estuaries (Portugal). J. Mar. Biol. Assoc. U. K., 89: 1-12.
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39. Adao, H., A.S. Alves, J. Patricio, J.M. Neto, M.J. Costa and J.C. Marques, 2009. Spatial distribution of subtidal Nematoda communities along the salinity gradient in southern European estuaries. Acta oecologica, 35: 287-300.
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40. Teixeira, H., F. Salas, J.M. Neto, J. Patricio, R. Pinto, H. Verissimo and J.C. Marques, 2008. Ecological indices tracking distinct impacts along disturbance-recovery gradients in a temperate NE Atlantic Estuary-guidance on reference values. Estuarine Coastal Shelf Sci., 80: 130-140.
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41. Teixeira, H., F. Salas, A. Borja, J.M. Neto and J.C. Marques, 2008. A benthic perspective in assessing the ecological status of estuaries: the case of the Mondego estuary (Portugal). Ecol. Indic., 8: 404-416.
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42. Neto, J.M., M.R. Flindt, J.C. Marques and M.A. Pardal, 2008. Modelling nutrient mass balance in a temperate meso-tidal estuary: implications for management. Estuarine Coastal Shelf Sci., 76: 175-185.
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43. Martinho, F., R. Leitao, J.M. Neto, H. Cabral, F. Lagardere and M.A. Pardal, 2008. Estuarine colonization, population structure and nursery functioning for 0-group sea bass (Dicentrarchus labrax), flounder (Platichthys flesus) and sole (Solea solea) in a mesotidal temperate estuary. J. Appl. Ichthyology, 24: 229-237.
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44. De Paz, L., J.M. Neto, J.C. Marques and A.J. Laborda, 2008. Response of intertidal macrobenthic communities to long term human induced changes in the Eo estuary (Asturias, Spain): Implications for environmental management. Mar. environ. Res., 66: 288-299.
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45. Viegas, I., F. Martinho, J. Neto and M. Pardal, 2007. Population dynamics, distribution and secondary production of the brown shrimp Crangon crangon (L.) in a southern European estuary. Latitudinal variations. Scientia Marina, 71: 345-460.
46. Patricio, J., J.M. Neto, H. Teixeira and J.C. Marques, 2007. Opportunistic macroalgae metrics for transitional waters. Testing tools to assess ecological quality status in Portugal. Mar. Pollut. Bull., 54: 1887-1896.
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47. Martins, I., R.J. Lopes, A.I. Lillebo, J.M. Neto, M.A. Pardal, J.G. Ferreira and J.C. Marques, 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. Mar. Pollut. Bull., 54: 678-690.
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48. Martinho, F., R. Leitao, I. Viegas, M. Dolbeth, J.M. Neto, H.N. Cabral and M.A. Pardal, 2007. The influence of an extreme drought event in the fish community of a southern Europe temperate estuary. Estuarine Coastal Shelf Sci., 75: 537-546.
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49. Martinho, F., R. Leitao, H. Cabral, J.M. Neto, J.C. Marquesa and M.A. Pardal, 2007. The use of nursery areas by fish in a temperate estuary, Portugal. Hydrobiologia, 587: 269-279.
50. Leitao, R., F. Martinho, H.N. Cabral, J.M. Neto, I. Jorge and M.A. Pardal, 2007. The fish assemblage of the Mondego estuary: composition, structure and trends over the past two decades. Hydrobiologia, 587: 269-279.
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51. Ferreira, S.M., A. Brandao, A. Baeta, J.M. Neto, A.I. Lillebo, K.T. Jensen and M.A. Pardal, 2007. Effects of restoration management on the estuarine isopod Cyathura carinata: mediation by trematodes and habitat change. Mar. Biol., 151: 109-118.
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52. Bouslama, M.F., J.M. Neto, F. Charfi-Cheikhrouha and J.C. Marques, 2007. Biology, population dynamics, and secondary production of Talitrus saltator (Amphipoda, Talitridae) at Korba beach (east coast of Tunisia). Crustaceana, 80: 1103-1119.
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53. Salas, F., C. Marcos, J.M. Neto, J. Patricio, A. Perez-Ruzafa and J.C. Marques, 2006. User-friendly guide for using benthic ecological indicators in coastal and marine quality assessment. Ocean Coastal Manage., 49: 308-331.
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54. Marques, S.C., U.M. Azeiteiro, J.C. Marques, J.M. Neto and M.A. Pardal, 2006. Zooplankton and ichthyoplankton communities in a temperate estuary: spatial and temporal patterns. J. Plankton Res., 28: 297-312.
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55. Leitao, R., F. Martinho, J.M. Neto, H. Cabral, J.C. Marques and M.A. Pardal, 2006. Feeding ecology, population structure and distribution of Pomatoschistus microps (Kroyer, 1838) and Pomatoschistus minutus (Pallas, 1770) in a temperate estuary, Portugal. Estuarine Coastal Shelf Sci., 66: 231-239.
56. Verdelhos, T., J.M. Neto, J.C. Marques and M.A. Pardal, 2005. The effect of eutrophication abatement on the bivalve Scrobicularia plana. Estuarine Coastal Shelf Sci., 63: 261-268.
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57. Martins, I., J.M. Neto, M.G. Fontes, J.C. Marques and M.A. Pardal, 2005. Seasonal variation in short-term survival of Zostera noltii transplants in a declining meadow in Portugal. Aquat. Bot., 82: 132-142.
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58. Lillebo, A.I., J.M. Neto, I. Martins, T. Verdelhos, S. Leston, P.G. Cardoso and M.A. Pardal, 2005. Management of a shallow temperate estuary to control eutrophication: the effect of hydrodynamics on the system's nutrient loading. Estuarine Coastal Shelf Sci., 65: 697-707.
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59. Baeta, A., H.N. Cabral, J.M. Neto, J.C. Marques and M.A. Pardal, 2005. Biology, population dynamics and secondary production of the green crab Carcinus maenas (L.) in a temperate estuary. Estuarine Coastal Shelf Sci., 65: 43-52.
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60. Salas, F., J.M. Neto, A. Borja and J.C. Marques, 2004. Evaluation of the applicability of a marine biotic index to characterize the status of estuarine ecosystems: the case of Mondego estuary (Portugal). Ecol. Indic., 4: 215-225.
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61. Lillebo, A.I., J.M. Neto, M.R. Flindt, J.C. Marques and M.A. Pardal, 2004. Phosphorous dynamics in a temperate intertidal estuary. Estuarine Coastal Shelf Sci., 61: 101-109.
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62. Lillebo, A.I., M.A. Pardal, J.M. Neto and J.C. Marques, 2003. Salinity as the major factor affecting Scirpus maritimus annual dynamics: Evidence from field data and greenhouse experiment. Aquat. Bot., 77: 111-120.
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63. Bastviken S.K., P.G. Eriksson, I.Martins, J.M. Neto, L. Leonardson and K. Tonderski, 2003. Wetlands and Aquatic Processes: Potential Nitrification and Denitrification on Different Surfaces in a Constructed Treatment Wetland. J. Environ. Qual., 32: 2414-2420.
64. Duarte, A.A., J.L. Pinho, M.A. Pardal, J.M. Vieira and F.S. Santos, 2001. Effect of residence times on River Mondego estuary eutrophication vulnerability. Water Sci. Technol., 44: 329-336.