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Mackinson, S, Daskalov G, Heymans JJ, Neira S, Arancibia H, Zetina-Rejón M, Jiang H, Cheng HQ, Coll M, Arreguin-Sanchez F.  2009.  Which forcing factors fit? Using ecosystem models to investigate the relative influence of fishing and changes in primary productivity on the dynamics of marine ecosystems Ecological Modelling. 220:2972-2987.
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Coll, M.  2006.  Trophic web modelling and ecological indicators for assessing ecosystem impacts of fishing in the Mediterranean Sea. Animal Biology, Vegetal Biology and Ecology. PhD Thesis
Coll, M, Palomera I, Tudela S, Sardà F.  2006.  Trophic flows, ecosystem structure and fishing impacts in the South Catalan Sea, Northwestern Mediterranean. Journal of Marine Systems. 59:63-96. Abstract
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Coll, M, Lotze HK, Romanuk TN.  2008.  Structural degradation in Mediterranean Sea food webs: Testing ecological hypotheses using stochastic and mass-balance modelling. Ecosystems. 11:939-960.
Palomera, I, Olivar MP, Salat J, Sabates A, Coll M, Garcia A, Morales-Nin B.  2007.  Small pelagic fish in the NW Mediterranean Sea: An ecological review. Progress in Oceanography. 74:377-396.
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Shin, Y.-J., Bundy A, Shannon LJ, Blanchard J, Chuenpagdee R, Coll M, Knight B, Lynam C, Piet G, Rice J et al..  2012.  Reviews in Fish Biology and Fisheries. Global in scope and regionally rich: an IndiSeas workshop helps shape the future of marine ecosystem indicators. DOI 10.1007/s11160-012-9252-z
Vargiu, G, Coll M, Palomera I, Tudela S.  2009.  Recovery scenarios of a highly exploited species, Merluccius merluccius, in the NW Mediterranean Sea using an ecosystem approach. Fisheries Centre Research Report . 17(3):33-34.
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Libralato, S, Coll M, Tudela S, Palomera I, Pranovi F.  2008.  Novel index for quantification of ecosystem effects of fishing as removal of secondary production. Marine Ecology Progress Series. 355:107-129. Abstract
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Palomera, I., Coll M, Tudela S.  2007.  Modelling the ecological role of small pelagic fish in the Catalan Sea (NW Mediterranean). CIESM 38th Congress. .
Coll, M, Libralato S.  2009.  Modelling marine food webs in the Mediterranean Sea. Fisheries Centre Research Report. 17(3):124-125.
Coll, M, Piroddi C, Palomera I, Arneri E, Christensen V.  2009.  Main drivers of marine resources and food-web changes in the Mediterranean Sea. Ecopath 25 Years Conference Proceedings: Extended Abstracts . :148-150.
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Allain, V., Nicol S, Polovina J, Coll M, Olson R, Griffiths S, Dambacher J, Young J, Jurado-Molina J, Hoyle S et al..  2012.  International workshop on opportunities for Ecosystem Approaches to Fisheries Management in the Pacific Ocean tuna fisheries. Reviews in Fish Biology and Fisheries. In press
Coll, M, Bahamon N, Sarda F, Palomera I, Tudela S, Suuronen P.  2008.  Improved trawl selectivity: effects on the ecosystem in the South Catalan Sea (NW Mediterranean). Marine Ecology-Progress Series. 355:131-147.
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Tsagarakis, K, Coll M, Giannoulaki M, Papakonstantinou C, A. M.  2010.  Food-web traits of the North Aegean Sea continental shelf (Eastern Mediterranean, Greece) and comparison with other Mediterranean ecosystems. Estuarine Coastal and Shelf Science. 88:233-248.
Libralato, S, Coll M, Tempesta M, Santojanni A, Spoto M, Palomera I, Arneri E, Solidoro C.  2010.  Food-web traits of protected and exploited areas of the Adriatic Sea. Biological Conservation. 143:2182–2194.
Coll, M, Santojanni A, Palomera I, Arneri E.  2009.  Food-web changes in the Adriatic Sea over the last three decades. Marine Ecology Progress Series. 381:17-37. Abstract
Fouzai, N, Coll M, Palomera I, Santojanni A, Arneri E, Christensen V.  2012.  Fishing management scenarios to rebuild exploited resources and ecosystems of the Northern-Central Adriatic (Mediterranean Sea). Journal of Marine Systems. 102-105
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Shannon, LJ, Coll M, Neira S.  2009.  Exploring the dynamics of ecological indicators using food web models fitted to time series of abundance and catch data. Ecological Indicators. 9:1078-1095. Abstract
Link, JS, Pranovi F, Coll M, Libralato S, Christensen V, Legault C.  2009.  Exploring novel metrics of ecosystem overfishing using energy budget model outputs. Ecopath 25 Years Conference Proceedings: Extended Abstracts . :153.
Libralato, S, Arneri E, Bahamon N, Coll M, Cossarini G, Morello EB, Palomera I, Santojanni A, Solidoro C.  2010.  Effects of climate-driven changes on the North-Central Adriatic Food web: insights from an End-to-End approach.
Coll, M.  2008.  Ecosystem-based assessment of the effects of increasing trawl selectivity in the Mediterranean. Switching to square-meshed nets. A first step on the long journey towards sustainability. WWF Mediterranean Technical Report. :68.
Tsagarakis, K, Coll M, Giannoulaki M, Papakonstantinou C, Machias A.  2009.  Ecosystem structure and functional traits of the N. Aegean Sea (E. Mediterranean, Greece). Fisheries Centre Research Report. 17(3):84-85.
Coll, M, Libralato S, Tudela S, Palomera I, Pranovi F.  2008.  Ecosystem Overfishing in the Ocean. PLoS ONE. 3:e3881. Abstract
Coll, M, Bundy A, Shannon LJ.  2008.  Ecosystem Modelling Using the Ecopath with Ecosim Approach. Computers in Fisheries Research, Second edition . :225-291.
Forestal, F, Coll M, Christensen V, Die D.  2012.  Ecosystem effects of Bluefin Tuna (Thunnus thynnus thynnus) aquaculture in the North-Western Mediterranean Sea. Marine Ecology Progress Series. 456