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

64.- Borja, A., A. Lanzén, I. Muxika, 2024. DNA-based marine benthic assessment methods can perform as morphological ones, but an intercalibration is needed. Ecological Indicators, 167: 112638.

63.- Jayachandran, P. R., T. V. Joydas, A. Borja, S. Manokaran, J. Franco, J. M. Garmendia, J. Gopi, K. P. Manikandan, M. Asharaf, R. H. Maneja, A. M. Qasem, H. Alghamdi, D. Lozano-Cortés, P. K. Krishnakumar, M. A. Qurban, 2024. Unveiling the ecological status of the Arabian Gulf’s marine ecosystem: Insights from benthic community analysis. Marine Pollution Bulletin, 205: 116571.

62.- Marín, S. L., L. Pino, R. Núñez, D. Farías, J. L. Iriarte, A. Borja, I. Muxika, 2023. Ecological status of benthic communities associated to mussel farms in South of Chile: Can it be predicted using AMBI? Regional Studies in Marine Science, 66: 103132.

61.- Santibañez-Aguascalientes, N. A., Á. Borja, P.-L. Ardisson, 2023. Assessing the large-scale and long-term changes in the southern Gulf of Mexico benthic ecological status under natural and human-induced disturbances. Estuarine, Coastal and Shelf Science, 283: 108282.

60.- Chunga-Llauce, J. A., M. T. Benavides, Á. Borja, X. Vélez-Zuazo, B. Vildoso, A. Alonso, A. S. Pacheco, V. Tasso, 2023. Assessing the ecological quality status of macrobenthic communities in a marine terminal of liquefied natural gas in Peru. Marine Environmental Research, 185: 105879.

59.- Joydas, T. V., M. A. Qurban, A. Borja, S. Manokaran, K. P. Manikandan, L. J. Rabaoui, J. M. Garmendia, T. T. M. Asharaf, K. Ayranci, A. M. Shemsi, S. Mohammed, A. U. Basali, P. Panickan, Z. Nazeer, P. S. Lyla, S. A. Khan, P. K. Krishnakumar, 2023. Ecological status of macrobenthic communities in the Saudi waters of the western Arabian Gulf. Regional Studies in Marine Science, 57: 102751.

58.- Munari, C., A. Borja, C. Corinaldesi, E. Rastelli, M. Lo Martire, V. Pitacco, M. Mistri, 2022. First Application of the AMBI Index to the Macrobenthic Soft-Bottom Community of Terra Nova Bay (Ross Sea, Southern Ocean). Water, 14: 2994.

57.- Umehara, A., Á. Borja, A. Ishida, S. Nakai, W. Nishijima, 2022. Responses of the benthic environment to reduction in anthropogenic nutrient loading in the Seto Inland Sea (Japan), based on M-AMBI assessment. Marine Environmental Research, 173: 105509.

56.- Santibañez-Aguascalientes, N.A., Á. Borja, P.-L. Ardisson, 2021. Sustainability situations for the southern Gulf of Mexico seafloor, based on environmental, benthic, and socioeconomic indicators. Science of The Total Environment, 787: 147726.

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.