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You can have access to these papers in Angel Borja’s ResearchGate profile

55.– Joydas, T. V., S. Manokaran, A. Borja, L. Rabaoui, K. P. Manikandan, T. T. M. Ashraf, K. M. Aarif, S. A. Hussain, M. H. Baig, M. Shoeb, P. K. Krishnakumar, M. A. Qurban, 2021. A baseline quantitative assessment of deep-sea benthic fauna of the Gulf of Aqaba (Northern Saudi Arabia, Red Sea). Marine Pollution Bulletin, 164: 112028.

54.- Santibañez-Aguascalientes, N. A., Á. Borja, J. L. Montero-Muñoz, M. T. Herrera-Dorantes, P.-L. Ardisson, 2020. Setting reference conditions to assess the ecological status of the sublittoral and bathyal benthic communities of the southern Gulf of Mexico. Ecological Indicators, 111: 105964.

53.- Borja, A., G. Chust, I. Muxika, 2019. Chapter Three – Forever young: The successful story of a marine biotic index. Advances in Marine Biology, 82: 93-127.

52.- Caswell, B. A., C. L. J. Frid, A. Borja, 2019. An ecological status indicator for all time: Are AMBI and M-AMBI effective indicators of change in deep time? Marine Pollution Bulletin, 140: 472-484.

51.- Rabaoui, L., Y.-J. Lin, R. H. Roa-Ureta, J. Dagoy, T. V. Joydas, A. Borja, I. Muxika, J. Franco, K. Al-Abdulkader, R. Loughland, H. Alnazry, M. A. Qurban, 2019. Recovery of benthic communities from small-scale shrimp trawling: Evidence from using ecological indices over a short temporal scale. Ecological Indicators, 99: 299-309.

50.- Aylagas, E., Á. Borja, I. Muxika, N. Rodríguez-Ezpeleta, 2018. Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecological Indicators, 95: 194-202.

49.- Pelletier, M. C., D. J. Gillett, A. Hamilton, T. Grayson, V. Hansen, E. W. Leppo, S. B. Weisberg, A. Borja, 2018. Adaptation and application of multivariate AMBI (M-AMBI) in US coastal waters. Ecological Indicators, 89: 818-827.

48.- Mistri, M., A. Borja, I. F. Aleffi, C. Lardicci, D. Tagliapietra, C. Munari, 2018. Assessing the ecological status of Italian lagoons using a biomass-based index. Marine Pollution Bulletin, 126: 600-605

47.- Joydas, T.W., M.A. Qurban, A. Borja, P.K. Krishnakumar, A. Alsuwailem, 2017. Macrobenthic community structure in the northwestern Arabian Gulf, twelve years after the 1991 Oil Spill. Frontiers in Marine Science, 4: 10.3389/fmars.2017.00248

46.- Aylagas, E., I. Mendibil, A. Borja, N. Rodriguez-Ezpeleta, 2016. Marine sediment sample pre-processing for macroinvertebrates metabarcoding: mechanical enrichment and homogenization. Frontiers in Marine Science, 3: 10.3389/fmars.2016.00203.

45.- Aylagas, E., A. Borja, X. Irigoien, N. Rodriguez-Ezpeleta, 2016. Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment. Frontiers in Marine Science, 3: DoI: 10.3389/fmars.2016.00096.

44.- Feebarani, J., T.V. Joydas, R. Damodaran, A. Borja, 2016. Benthic quality assessment in a naturally- and human-stressed tropical estuary. Ecological Indicators, 67: 380-390.

43.- Cai, W., A. Borja, K.X. Lin, Y. Zhu, J. Zhou, L. Liu, 2015. Assessing the benthic quality status of the Bohai Bay (China) with proposed modifications of M-AMBI. Acta Oceanologica Sinica, 34(10): 111-121.

42.- Borja, A., S.L. Marín, I. Muxika, L. Pino, J.G. Rodríguez, 2015. Is there a possibility of ranking benthic quality assessment indices to select the most responsive to different human pressures? Marine Pollution Bulletin, 97 : 85-94.

41.- Gillett, D.J., S.B. Weisberg, T. Grayson, A. Hamilton, V. Hansen, E.W. Leppo, M.C. Pelletier, A. Borja, D. Cadien, D. Dauer, R. Diaz, M. Dutch, J.L. Hyland, M. Kellog, P. Larsen, J. Levinton, R. Llansó, L.L. Lovel, P. Montagna, D. Pasko, C.A. Phillips, C. Rakocinski, J.A. Ranasinghe, D.M. Sanger, H. Teixeira, R.F. Van Dolah, R.G. Velarde, K.I. Welch, 2015. Effect of ecological group classification schemes on performance of the AMBI index in US coastal waters. Ecological Indicators, 50: 99-107.

40.- Daief, Z., A. Borja, L. Joulami, M. Azzi, A. Fahde, H. Bazairi, 2014. Assessing benthic ecological status of urban sandy beaches (Northeast Atlantic, Morocco) using M-AMBI. Ecological Indicators, 46: 586-595.

39.- Borja, A., S. Marín, R. Núñez, I. Muxika, 2014. Is there a significant relationship between the benthic status of an area, determined by two broadly-used indices, and best professional judgment? Ecological Indicators, 45: 308-312.

38.- Cai, W., Á. Borja, L. Liu, W. Meng, I. Muxika, J.G. Rodríguez, 2014. Assessing benthic health under multiple human pressures in Bohai Bay (China), using density and biomass in calculating AMBI and M-AMBI. Marine Ecology, 35:180-192.

37.- Aylagas, E., Á. Borja, N. Rodríguez-Ezpeleta, 2014. Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI). PLoS ONE, 9(3): e90529. doi:10.1371/journal.pone.0090529

36.- Basset, A., E. Barbone, A. Borja, M. Elliott, G. Jona-Lasinio, J.C. Marques, K. Mazik, I. Muxika, J.M. Neto, S. Reizopoulou, I. Rosati, H. Teixeira, 2013. Natural variability and reference conditions: setting type-specific classification boundaries for lagoon macroinvertebrates in the Mediterranean and Black Seas. Hydrobiologia, 704(1): 325-345.

35.- Muxika, I., P.J. Somerfield, Á. Borja, R.M. Warwick, 2012. Assessing proposed modifications to the AZTI marine biotic index (AMBI), using biomass and production. Ecological Indicators, 12(1): 96-104.

34.- Teixeira, H., S.B. Weisberg, A. Borja, J.A. Ranasinghe, D.B. Cadien, R.G. Velarde, L.L. Lovell, D. Pasko, C.A. Phillips, D.E. Montagne, K. Ritter, F. Salas, J.C. Marques, 2012. Calibration and Validation of the AZTI’s Marine Biotic Index (AMBI) for Southern California Marine Bays. Ecological Indicators, 12(1): 84-95.

33.- Forchino, A., A. Borja, F. Brambilla, J. G. Rodríguez, I. Muxika, G. Terova, M. Saroglia, 2011. Evaluating the influence of off-shore cage aquaculture on the benthic ecosystem in Alghero Bay (Sardinia, Italy) using AMBI and M-AMBI. Ecological Indicators, 11(5): 1112-1122.

32.- Borja, A., E. Barbone, A. Basset, G. Borgersen, M. Brkljacic, M. Elliott, J.M. Garmendia, J.C. Marques, K. Mazik, I. Muxika, J.M. Neto, K. Norling, J.G. Rodríguez, I. Rosati, B. Rygg, H. Teixeira, A. Trayanova, 2011. Response of single benthic metrics and multimetric methods to anthropogenic pressure gradients, in five distinct European coastal and transitional ecosystems. Marine Pollution Bulletin, 62(3): 499-513.

31.- Borja, A., B.G. Tunberg, 2011. Assessing benthic health in stressed subtropical estuaries, eastern Florida, USA using AMBI and M-AMBI. Ecological Indicators, 11: 295-303.

30.- Pérez, L., Borja, Á., Rodríguez G., Muxika, I., 2009. Long-term environmental, anthropogenic and climatic factors explaining spatial and temporal distribution of soft-bottom benthic communities within the Basque estuaries. Revista de Investigación Marina, 14: 22 pp.

29.- Nickell, T.D., C. J. Cromey, Á. Borja, K.D. Black, 2009. The benthic impacts of a large cod farm – are there indicators for sustainability? Aquaculture, 295(3-4): 226-237.

28.- Borja, A., A. Miles, A. Occhipinti-Ambrogi, T. Berg, 2009. Current status of macroinvertebrate methods used for assessing the quality of European marine waters: implementing the Water Framework Directive. Hydrobiologia, 633(1): 181-196.

27.- Borja, A., J.G. Rodríguez, K. Black, A. Bodoy, C. Emblow, T.F. Fernandes, J. Forte, I. Karakassis, I. Muxika, T.D. Nickell, N. Papageorgiou, F. Pranovi, K. Sevastou, P. Tomassetti, D. Angel, 2009. Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fin and shellfish aquaculture located in sites across Europe. Aquaculture, 293: 231-240.

26.- Borja, A., I. Muxika, J.G. Rodríguez, 2009. Paradigmatic responses of marine benthic communities to different anthropogenic pressures, using M-AMBI, within the European Water Framework Directive. Marine Ecology, 30: 214-227.

25.- Borja, A., J. Bald, J. Franco, J. Larreta, I. Muxika, M. Revilla, J.G. Rodríguez, O. Solaun, A. Uriarte, V. Valencia, 2009. Using multiple ecosystem components in assessing ecological status in Spanish (Basque Country) Atlantic marine waters. Marine Pollution Bulletin, 59(1-3): 54-64.

24.- Borja, A., A. Ranasinghe, S.B. Weisberg, 2009. Assessing ecological integrity in marine waters, using multiple indices and ecosystem components: challenges for the future. Marine Pollution Bulletin, 59(1-3): 1-4.

23.- Borja, A., I. Muxika, 2008. Biological Communities as a Forensic Tool in Marine Environments, Chapter 7, pp. 219-249, in Methods in Environmental Forensics (Stephen Mudge Ed.), CRC Press, Taylor & Francis Group, Boca Ratón, 386 pp.

22.- Borja, A., J. Mader, I. Muxika, J.G. Rodríguez, J. Bald, 2008. Using M-AMBI in assessing benthic quality within the Water Framework Directive: some remarks and recommendations. Marine Pollution Bulletin, 56: 1377-1379.

21.- de Paz, L., J. Patrício, J.C. Marques, Á. Borja, A.J. Laborda, 2008. Ecological Status assessment in the lower Eo estuary (Spain). The challenge of habitat heterogeneity integration: a benthic perspective. Marine Pollution Bulletin, 56: 1275-1283.

20.- Garmendia, M., Á., Borja, I., Muxika, 2008. Long-term environmental, climatic and anthropogenic factors affecting subtidal soft-bottom benthic communities, within the Basque coast. Revista de Investigación Marina, 2: 28 pp.

19.- Teixeira, H., F. Salas, Á. Borja, J. Neto, J.C. Marques, 2008. A benthic perspective in assessing the ecological status of estuaries: the case of the Mondego estuary (Portugal). Ecological Indicators, 8(4):  404-416.

18.- Borja, A.; Dauer, D.; Díaz, R.; Llansó, R.J.; Muxika, I.; Rodríguez, J.G.; Schaffner, L., 2008. Assessing estuarine benthic quality conditions in Chesapeake Bay: a comparison of three indices. Ecological Indicators, 8(4): 395-403.

17.- Borja, A., D.M. Dauer, 2008. Assessing the environmental quality status in estuarine and coastal systems: comparing methodologies and indices. Ecological Indicators, 8(4): 331-337.

16.- Muxika, I., L. Ibaibarriaga, J.I. Sáiz-Salinas, Á. Borja, 2007. Minimal sampling requirements for a precise assessment of soft-bottom macrobenthic communities, using AMBI. Journal of Experimental Marine Biology and Ecology, 349: 323-333.

15.- Borja, A., A.B. Josefson, A. Miles, I. Muxika, F. Olsgard, G. Phillips, J.G. Rodríguez, B. Rygg, 2007. An approach to the intercalibration of benthic ecological status assessment in the North Atlantic ecoregion, according to the European Water Framework Directive. Marine Pollution Bulletin, 55: 42-52.

14.- Muxika, I., Á. Borja, J. Bald, 2007. Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status, according to the European Water Framework Directive, Marine Pollution Bulletin, 55: 16-29.

13.- Borja, A., I. Muxika, J. Franco, 2006. Long-term soft-bottom benthos recovery, following urban and industrial sewage treatment in the Nervión estuary (southern Bay of Biscay). Marine Ecology Progress Series, 313: 43-55.

12.- Borja, A., I. Muxika, 2005. Guidelines for the use of AMBI (AZTI’s marine biotic index) in the assessment of the benthic ecological quality. Marine Pollution Bulletin, 50: 787-789.

11.- Muniz, P., N. Venturini, A.M.S. Pires-Vanin, L.R. Tommasi, A. Borja, 2005. Testing the applicability of a Marine Biotic Index (AMBI) for assessing the ecological quality of soft-bottom benthic communities in the South America Atlantic region. Marine Pollution Bulletin, 50: 624-637.

10.- Borja, A., I. Muxika, 2005. Do benthic indicator tools respond to all impact sources?, The case of AMBI (Azti Marine Biotic Index), p 15-18. Magni, P., J. Hyland, G. Manzella, H. Rumohr, P. Viaroli, A. Zenetos (Eds.). Proceedings of the Workshop “Indicators of Stress in the Marine Benthos”, Torregrande-Oristano (Italy), 8–9 October 2004. Paris, UNESCO/IOC, IMC, 2005. iv + 46 pp., OC Workshop Reports, 195.

9.- Muxika, I.; Borja, Á.; Bonne, W., 2005. The suitability of the marine biotic index (AMBI) to new impact sources along European coasts. Ecological Indicators 5(1): 19-31.

8.- Salas, F., Nieto, J.M., Borja, A., Marques, J.C., 2004. Evaluation of the applicability of a marine biotic index to characterise the status of estuarine ecosystems: the case of Mondego estuary (Portugal). Ecological Indicators, 4: 215-225.

7.- Borja, A., J. Franco, I. Muxika, 2004. The Biotic Indices and the Water Framework Directive: the required consensus in the new benthic monitoring tools. Marine Pollution Bulletin, 48(3-4): 405-408.

6.- Borja, A., J. Franco, V. Valencia, J. Bald, I. Muxika, M.J. Belzunce, O. Solaun, 2004. Implementation of the European Water Framework Directive from the Basque Country (northern Spain): a methodological approach, Marine Pollution Bulletin, 48(3-4): 209-218.

5.- Gorostiaga, J.M., Á. Borja, I. Díez, G. Francés, S. Pagola-Carte, J.I. Sáiz Salinas, 2004. Recovery of benthic communities, in polluted systems. In: Borja, A. and Collins, M. (Eds.). Oceanography and Marine Environment of the Basque Country, Elsevier Oceanography Series, 70: 549-578, Elsevier, Amsterdam.

4.- Borja, Á., Franco, J., Muxika, I., 2003. Classification tools for marine ecological quality assessment: the usefulness of macrobenthic communities in an area affected by a submarine outfall. ICES CM 2003/Session J-02, Tallinn (Estonia), 24-28 September, 2003.

3.- Muxika, I., Borja, Á., Franco, J., 2003. The use of a biotic index (AMBI) to identify spatial and temporal impact gradients on benthic communities in an estuarine area. ICES CM 2003/Session J-01, Tallinn (Estonia), 24-28 September, 2003.

2.- Borja, A.; I. Muxika, J. Franco, 2003. The application of a Marine Biotic Index to different impact sources affecting soft-bottom benthic communities along European coasts. Marine Pollution Bulletin, 46: 835-845.

1.- Borja, A., J. Franco, V. Pérez, 2000. A marine biotic index to establish the ecological quality of soft bottom benthos within European estuarine and coastal environments. Marine Pollution Bulletin, 40(12): 1100-1114.