Murray, A. & Assis, J. (2025) AI for Marine Conservation: The Prospects of using Multimodal Artificial Intelligence with Citizen Science to Monitor Coral Reefs. MSc in Bioinformatics and Computational Biology Thesis. University College Cork.

Fragkopoulou, E., Gouvêa, L. P., Balogh, V., Serrão, E. A., & Assis, J. (2025). Global Cold‐Water Coral Biodiversity Redistribution Under Projected Climate Change. Global Change Biology, 31(10).

Mestre, F., D’Amico, M., Bastazini, V. A. G., Assis, J., Jacinto, D., Marçalo, A., & Ascensão, F. (2025). Mapping global shipless areas and conflict zones between shipping and large marine vertebrates. Biological Conservation, 311.

Mackintosh, A. L., Assis, J., & Costello, M. J. (2025). Temperature-driven suitability shifts of sea lice species under climate change and the implications for salmon farming. Aquaculture Environment Interactions.

Horta, P., Schubert, N., Hoffmann, L., Assis, J., Sissini, M. N., Bergstrom, E., Bastos, E., Freire, V., Rich, W. A., Andrade, V., Dumont, S., Oliveira, I., Nunes, M., Riul, P., Figueiredo, M., Bonomi-Barufi, J., Rorig, L., Gurgel, C., Silva, J., & Santos, R. (2025). Brazilian Rhodolith Beds—Mini-Giant Mobile Reefs (pp. 87–114).

Hill, G., Gauci, C., Assis, J., & Jueterbock, A. (2025). Turning the Tide: A 2°C Increase in Heat Tolerance Can Halve Climate Change‐Induced Losses in Four Cold‐Adapted Kelp Species. Ecology and Evolution, 15(4).

Reynes, L., Legrand, T., Blanfuné, A., Assis, J., Thibaut, T., & Bottin, L. (2025). Multi-generation dispersal shapes the genetic structure of the canopy-forming seaweed Ericaria amentacea (syn. Cystoseira amentacea) in the north-western Mediterranean Sea. European Journal of Phycology, 1–16.

Anderson, A. B., Gouvêa, L., Assis, J., Serrão, E., Pinheiro, H. T., Vilar, C., Francini-Filho, R. B., Horta, P. A., Bernardino, A. F., Cordeiro, C. A. M. M., Gomes, L. E. O., Joyeux, J.-C., & Ferreira, C. E. L. (2025). Extinction risk of the endemic soft coral Phyllogorgia dilatata (Esper, 1806) in a remote island of the Brazilian coast. Marine Pollution Bulletin, 216, 118006.

Peiffer, F., Assis, J., Lima, A. R. A., Henriques, S., Pardal, M. A., Martinho, F., Gonçalves, J. M. S., Gonçalves, E. J., Correia, M., & Silva, G. J. F. (2025). Projected climate change and limited dispersal potential threaten the seahorse species Hippocampus hippocampus and Hippocampus guttulatus. Marine Biology, 172(9).

Fragkopoulou, E., Serrão, E. A., de Clerck, O., & Assis, J. (2025). Global intraspecific diversity of marine forests of brown macroalgae predicted by past climate conditions. Communications Biology, 8(1), 726.

González-Trujillo, J. D., Assis, J., Serrão, E., Costello, M. J., Fragkopoulou, E., Mendoza, M., & Araújo, M. B. (2025). Trophic convergence of marine vertebrate communities worldwide. Proceedings of the National Academy of Sciences, 122(17).

Gouvêa, L. P., Krause-Jensen, D., Duarte, C. M., & Assis, J. (2025). Projected impacts of future climate change on the aboveground biomass of seagrasses at global scale. Science of The Total Environment, 966, 178680.

Horta, P., Sissini, M. N., Fonseca, A., Turra, A., Rodrigues, A. C., Rorig, L., Bonomi‐Barufi, J., Pagliosa, P., Bastos, E., Grimaldi, G., Dias, C. E. P., Fialho, F., Oliveira, C. Y. B., Schubert, N., Silva, J., Assis, J., Gouvea, L., Alves‐Lima, C., Coelho, M. A. G., … Hall‐Spencer, J. M. (2025). Marine Forests Forever - A Necessary Multilateral Program for a Fair Future. Aquatic Conservation: Marine and Freshwater Ecosystems, 35(1).

González‐Trujillo, J. D., Naimi, B., Assis, J., & Araújo, M. B. (2024). Reshuffling of Azorean Coastal Marine Biodiversity Amid Climate Change. Journal of Biogeography.

Colaço Martins, L., Gomes-Pereira, J. N., Dionísio, G., & Assis, J. (2024). Unravelling environmental drivers and patterns of Portuguese man o’ war (Physalia physalis) blooms in two ocean regions: North Atlantic and the Southeast Pacific. Marine Pollution Bulletin, 209, 117278.

Assis, J., Serrão, E. A., Fragkopoulou, E., Legrand, T., Gouvêa, L., & Araújo, M. B. (2024). Misconception of model transferability precludes estimates of seagrass community reorganization in a changing climate. Nature Plants.

Predragovic, M., Assis, J., Sumaila, U. R., Gonçalves, J. M. S., Cvitanovic, C., & Horta e Costa, B. (2024). Up to 80% of threatened and commercial species across European marine protected areas face novel climates under high emission scenario. Npj Ocean Sustainability, 3(1), 32.

Gouvêa, L., Fragkopoulou, E., B. Araújo, M., Serrão, E. and Assis, J. (2024), Seagrass Biodiversity Under the Latest-Generation Scenarios of Projected Climate Change. J Biogeogr. https://doi.org/10.1111/jbi.15021

Predragovic, M., Assis, J., Sumaila, U.R. et al. Up to 80% of threatened and commercial species across European marine protected areas face novel climates under high emission scenario. npj Ocean Sustain 3, 32 (2024). https://doi.org/10.1038/s44183-024-00068-4

Tavares, A. I., Assis, J., Anderson, L., Raimondi, P., Coelho, N. C., Paulino, C., Ladah, L., Nakaoka, M., Pearson, G. A., & Serrao, E. A. (2024). Past and future climate effects on population structure and diversity of North Pacific surfgrasses. Journal of Biogeography, 00, 1–12.

Filbee-Dexter, K., Pessarrodona, A., Pedersen, M.F. et al. Carbon export from seaweed forests to deep ocean sinks. Nat. Geosci. (2024).

Legrand, T., Fragkopoulou, E., Vapillon, L., Gouvêa, L., Serrão, E. A., & Assis, J. (2024). Unravelling the role of oceanographic connectivity in the distribution of genetic diversity of marine forests at the global scale. Global Ecology and Biogeography, 00, e13857.

Madeira, P., Reddy, M. M., Assis, J., Bolton, J. J., Rothman, M. D., Anderson, R. J., Kandjengo, L., Kreiner, A., Coleman, M. A., Wernberg, T., de Clerck, O., Leliaert, F., Bandeira, S., Ada, A. M., Neiva, J., Pearson, G. A., & Serrão, E. A. (2024). Cryptic diversity in southern African kelp. Scientific Reports, 14(1), 11071.

Zhang, Z., Zhou, J., García Molinos, J. et al. Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area. Mar Life Sci Technol (2024).

Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier, C., Laurans, M., Mauger, S., Sourisseau, M., & Assis, J. (2024). Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes. Marine Ecology Progress Series.

Abecasis, D., Ogden, R., Winkler, A.C. et al. Multidisciplinary estimates of connectivity and population structure suggest the use of multiple units for the conservation and management of meagre, Argyrosomus regius. Sci Rep 14, 873 (2024).

Neiva J, Assis J, Fragkopoulou E, Pearson GA, Raimondi PT, Anderson L, Krause-Jensen D, Marbà N, Want A, Selivanova O, Nakaoka M, Grant WS, Konar B, Roleda MY, Sejr MK, Paulino C and Serrão EA (2024) Trans-Arctic asymmetries, melting pots and weak species cohesion in the low-dispersal amphiboreal seaweed Fucus distichus. Front. Ecol. Evol. 12:1356987.

Assis, J., Fragkopoulou, E., Gouvêa, L., Araújo, M. B., & Serrão, E. A. (2024). Kelp forest diversity under projected end-of-century climate change. Diversity and Distributions, 00, e13837.

E. Fragkopoulou, A. Sen Gupta, M.J. Costello, T. Wernberg, M.B. Araújo, E.A. Serrão, O. De Clerck, J. Assis (2023) Marine biodiversity exposed to prolonged and intense subsurface heatwaves. Nature Climate Change.

Gouvêa, L. P., Fragkopoulou, E., Cavanaugh, K., Serrão, E. A., Araújo, M. B., Costello, M. J., Westergerling, E. H. T., & Assis, J. (2023). Oceanographic connectivity explains the intra-specific diversity of mangrove forests at global scales. Proceedings of the National Academy of Sciences.

Assis, J., Alberto, F., Macaya, E. C., Castilho Coelho, N., Faugeron, S., Pearson, G. A., Ladah, L., Reed, D. C., Raimondi, P., Mansilla, A., Brickle, P., Zuccarello, G. C., & Serrão, E. A. (2023). Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scales. Scientific Reports.

Tavares, A. I., Assis, J., Larkin, P. D., Creed, J. C., Magalhães, K., Horta, P., Engelen, A., Cardoso, N., Barbosa, C., Pontes, S., Regalla, A., Almada, C., Ferreira, R., Abdoul, B. M., Ebaye, S., Bourweiss, M., dos Santos, C. V.-D., Patrício, A. R., Teodósio, A., … Serrao, E. A. (2023). Long range gene flow beyond predictions from oceanographic transport in a tropical marine foundation species. Scientific Reports.

Mackintosh, A., Goldstein Hill, G., Costello, M., Jueterbock, A., & Assis, J. (2023). Modeling Aquaculture Suitability in a Climate Change Future. Oceanography.

Abecasis, D., Fragkopoulou, E., Claro, B., & Assis, J. (2023). Biophysical modelling and graph theory identify key connectivity hubs in the Mediterranean marine reserve network. Frontiers in Marine Science.

Liu, Y., Trancoso, R., Ma, Q., Ciais, P., Gouvêa, L. P., Yue, C., Assis, J., & Blanco, J. A. (2023). Carbon density in boreal forests responds non-linearly to temperature: An example from the Greater Khingan Mountains, northeast China. Agricultural and Forest Meteorology

Marquez, L., Fragkopoulou, E., Cavanaugh, K. C., Houskeeper, H. F., & Assis, J. (2022). Artificial intelligence convolutional neural networks map giant kelp forests from satellite imagery. Scientific Reports.

Duarte, C. M., Gattuso, J., Hancke, K., Gundersen, H., & Filbee-Dexter, K. (2022). Global estimates of the extent and production of algal forests. Global Ecology and Biogeography.

Gouvea, L. P., Horta, P. A., Fragkopoulou, E., Gurgel, C. F. D., Peres, L. M. C., Bastos, E., Ramlov, F., Burle, G., Koerich, G., Martins, C. D. L., Serrão, E., & Assis, J. (2022). Phenotypic Plasticity in Sargassum Forests May Not Counteract Projected Biomass Losses Along a Broad Latitudinal Gradient. Ecosystems.

Almada, C., Santos, R., Pearson, G. A., & Serrao, E. A. (2022). Seagrass Connectivity on the West Coast of Africa Supports the Hypothesis of Grazer-Mediated Seed Dispersal. Frontiers in Marine Science.

Assis, J., Neiva, J., Bolton, J. J., Rothman, M. D., Gouveia, L., Paulino, C., Mohdnasir, H., & Serrão, E. A. (2022). Ocean currents shape the genetic structure of a kelp in southwestern Africa. Journal of Biogeography.

Liu, Y., Zhong, K., Jueterbock, A., Assis, J., & Hu, Z. (2022). The invasive alga Gracilaria vermiculophylla in the native northwest Pacific under ocean warming: Southern genetic consequence and northern range expansion. Frontiers in Marine Science.

Gouvêa, L. P., Serrão, E. A., Cavanaugh, K., Gurgel, C. F. D., Horta, P. A., & Assis, J. (2022). Global impacts of projected climate changes on the extent and aboveground biomass of mangrove forests. Diversity and Distributions.

Pessarrodona, A., Assis, J., Filbee-Dexter, K., Burrows, M. T., Gattuso, J.-P., Duarte, C. M., Krause-Jensen, D., Moore, P. J., Smale, D. A., Wernberg, T. (2022). Global seaweed productivity. Science Advances.

Assis, J., Serrão, E. A., Duarte, C. M., Fragkopoulou, E., & Krause-Jensen, D. (2022). Major expansion of marine forests in a warmer Arctic. Frontiers in Marine Science.

Fragkopoulou, E., Serrão, E. A., Clerck, O. De, Costello, M. J., Araújo, M. B., Duarte, C. M., Krause-Jensen, D., & Assis, J. (2022). Global biodiversity patterns of marine forests of brown macroalgae. Global Ecology & Biogeography.

Assis, J., Fragkopoulou, E., Serrão, E. A., Horta e Costa, B., Gandra, M., and Abecasis, D. (2021). Weak biodiversity connectivity in the European network of no-take marine protected areas. Science of the Total Environment.

Assis, J., Failler, P., Fragkopoulou, E., Abecasis, D., Touron-Gardic, G., Regalla, A., et al. (2021). Potential Biodiversity Connectivity in the Network of Marine Protected Areas in Western Africa. Frontiers in Marine Science.

Song, X.-H., Assis, J., Zhang, J., Gao, X., Choi, H.-G., Duan, D.-L., et al. (2021). Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest Pacific. Evolutionary Applications.

Shi, Z., Assis, J., and Costello, M.J. (2021). Vulnerability of Marine Species to Low Oxygen Under Climate Change in Elsevier.

Martins, M. R., Assis, J., and Abecasis, D. (2021). Biologically meaningful distribution models highlight the benefits of the Paris Agreement for demersal fishing targets in the North Atlantic Ocean. Global Ecology and Biogeography.

Anderson, A. B., Assis, J., Batista, M. B., Serrão, E., Guabiroba, H. C., Delfino, S. D. T., et al. (2021). Global warming assessment suggests the endemic Brazilian kelp beds as an endangered ecosystem. Marine Environmental Research.

Hu, Z.-M., Zhang, Q.-S., Zhang, J., Kass, J. M., Mammola, S., Fresia, P., et al. (2021). Intraspecific genetic variation matters when predicting seagrass distribution under climate change. Molecular Ecology.

Liu, F. L., Li, J. J., Liang, Z. R., Zhang, Q. S., Zhao, F. J., Jueterbock, A., Critchley, A. T., Morrell, S. L., Assis, J., Tang, Y. Z., & Hu, Z. M. (2021). A concise review of the brown seaweed Sargassum thunbergii — a knowledge base to inform large-scale cultivation efforts. Journal of Applied Phycology.

Fragkopoulou, E., Serrão, E. A., Horta, P. A., Koerich, G., and Assis, J. (2021). Bottom Trawling Threatens Future Climate Refugia of Rhodoliths Globally. Frontiers in Marine Science.

Zhang, J., Yotsukura, N., Jueterbock, A., Hu, Z. M., Assis, J., Nagasato, C., Yao, J., & Duan, D. (2020). Detecting no natural hybridization and predicting range overlap in Saccharina angustata and Saccharina japonica. Journal of Applied Phycology

Gandra, M., Assis, J., Martins, M. R., and Abecasis, D. (2020). Reduced global genetic differentiation of exploited marine fish species. Molecular Biology and Evolution.

Nasri Sissini, M., Berchez, F., Hall-Spencer, J., Ghilardi-Lopes, N., Carvalho, V. F., Schubert, N., Koerich, G., Diaz-Pulido, G., Silva, J., Serrão, E., Assis, J., Santos, R., Floeter, S. R., Rörig, L., Barufi, J. B., Bernardino, A. F., Francini-Filho, R., Turra, A., Hofmann, L. C., … Horta, P. A. (2020). Brazil oil spill response: Protect rhodolith beds. Science.

Horta, P., Pinho, P. F., Gouvêa, L., Grimaldi, G., Destri, G., Mueller, C. M., Rocha, L., Barufi, J. B., Rorig, L., Assis, J., & da Cunha, L. C. (2020). Climate Change and Brazil ’s coastal zone: socio-environmental vulnerabilities and action strategies. Sustainability in Debate.

Bueno-pardo, J., Pierce, G. J., Cabecinha, E., Grilo, C., Assis, J., Leit, F., Queiroga, H., Valavanis, V., & Pita, C. (2020). Trends and drivers of marine fish landings in Portugal since its entrance in the European Union. ICES Journal of Marine Science.

Ntuli, N. N., Nicastro, K. R., Zardi, G. I., Assis, J., McQuaid, C. D., & Teske, P. R. (2020). Rejection of the genetic implications of the “Abundant Centre Hypothesis” in marine mussels. Scientific Reports.

Krause-jensen, D., Archambault, P., Assis, J., Bartsch, I., Bischof, K., Filbee-dexter, K., Dunton, K. H., Maximova, O., Ragnarsdóttir, S. B., Sejr, M. K., Simakova, U., & Spiridonov, V. (2020). Imprint of Climate Change on Pan-Arctic Marine Vegetation. Frontiers in Marine Science.

Gouvêa, L. P., Assis, J., Gurgel, C. F. D., Serrão, E. A., Silveira, T. C. L., Santos, R., et al. (2020). Golden carbon of Sargassum forests revealed as an opportunity for climate change mitigation. Science of the Total Environment.

Pilczynska, J., Cocito, S., Boavida, J., Serrão, E. A., Assis, J., Fragkopoulou, E., & Queiroga, H. (2019). Genetic diversity increases with depth in red gorgonian populations of the Mediterranean Sea and the Atlantic Ocean. PeerJ.

Koerich, G., Assis, J., Costa, G. B., Sissini, M. N., Serrão, E. A., Rörig, L. R., et al. (2019). How experimental physiology and ecological niche modelling can inform the management of marine bioinvasions? Science of the Total Environment.

Carvalho, V. F., Assis, J., Serrão, E. A., Nunes, J. M., Batista, A. A., Batista, M. B., Barufi, J. B., Silva, J., Pereira, S. M. B., & Horta, P. A. (2019). Environmental drivers of rhodolith beds and epiphytes community along the South Western Atlantic coast. Marine Environmental Research.