Browse by PML Authors

de Mora, L, Yool, A, Palmieri, J, Sellar, A, Kuhlbrodt, T, Popova, E, Jones, C and Allen, JI 2018 BGC-val: a model- and grid-independent Python toolkit to evaluate marine biogeochemical models. Geoscientific Model Development, 11 (10). 4215-4240. https://doi.org/10.5194/gmd-11-4215-2018

Ciavatta, S, Brewin, RJW, Skákala, J, Polimene, L, Artioli, Y, Allen, JI and de Mora, L 2018 Assimilation of ocean-colour plankton functional types to improve marine ecosystem simulations. Journal of Geophysical Research-Oceans. https://doi.org/10.1002/2017JC013490

Nielsen, JR, Thunberg, E, Holland, DS, Schmidt, JO, Fulton, EA, Bastardie, F, Punt, AE, Allen, I, Bartelings, H, Bertignac, M, Bethke, E, Bossier, S, Buckworth, R, Carpenter, G, Christensen, A, Christensen, V, Da-Rocha, JM, Deng, R, Dichmont, C, Doering, R, Esteban, A, Fernandes, JA, Frost, H, Garcia, D, Gasche, L, Gascuel, D, Gourguet, S, Groeneveld, RA, Guillén, J, Guyader, O, Hamon, KG, Hoff, A, Horbowy, J, Hutton, T, Lehuta, S, Little, LR, Lleonart, J, Macher, C, Mackinson, S, Mahevas, S, Marchal, P, Mato-Amboage, R, Mapstone, B, Maynou, F, Merzéréaud, M, Palacz, A, Pascoe, S, Paulrud, A, Plaganyi, E, Prellezo, R, van Putten, EI, Quaas, M, Ravn-Jonsen, L, Sanchez, S, Simons, S, Thébaud, O, Tomczak, MT, Ulrich, C, van Dijk, D, Vermard, Y, Voss, R and Waldo, S 2018 Integrated ecological-economic fisheries models-Evaluation, review and challenges for implementation. Fish and Fisheries, 19 (1). 1-29. https://doi.org/10.1111/faf.12232

Bruun, JT, Allen, JI and Smyth, TJ 2017 Heartbeat of the Southern Oscillation explains ENSO climatic resonances. Journal of Geophysical Research: Oceans, 122 (8). 6746-6772. https://doi.org/10.1002/2017JC012892

Polimene, L, Sailley, SF, Clark, DR, Mitra, A and Allen, JI 2017 Biological or Microbial Carbon Pump? The role of phytoplankton stoichiometry in ocean carbon sequestration. Journal of Plankton Research. https://doi.org/10.1093/plankt/fbw091

Holt, J, Hyder, P, Ashworth, M, Harle, J, Hewitt, HT, Liu, H, New, AL, Pickles, S, Porter, A, Popova, E, Allen, JI, Siddorn, J and Wood, R 2017 Prospects for improving the representation of coastal and shelf seas in global ocean models. Geoscientific Model Development, 10 (1). 499-523. https://doi.org/10.5194/gmd-10-499-2017

Barange, M, Butenschon, M, Yool, A, Beaumont, NJ, Fernandes, JA, Martin, AP and Allen, JI 2017 The Cost of Reducing the North Atlantic Ocean Biological Carbon Pump. Frontiers in Marine Science, 3. https://doi.org/10.3389/fmars.2016.00290

Queiros, AM, Huebert, KB, Keyl, F, Fernandes, JA, Stolte, W, Maar, M, Kay, S, Jones, MC, Hamon, KG, Hendriksen, G, Vermard, Y, Marchal, P, Teal, LR, Somerfield, PJ, Austen, MC, Barange, M, Sell, AF, Allen, JI and Peck, MA 2016 Solutions for ecosystem-level protection of ocean systems under climate change. Global Change Biology, 22. 3927-3936. https://doi.org/10.1111/gcb.13423

Beaulieu, C, Cole, H, Henson, S, Yool, A, Anderson, T, de Mora, L, Buitenhuis, ET, Butenschon, M, Totterdell, IJ and Allen, JI 2016 Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska. Biogeosciences, 13 (15). 4533-4553. https://doi.org/10.5194/bg-13-4533-2016

Cazenave, P, Torres, R and Allen, JI 2016 Unstructured grid modelling of offshore wind farm impacts on seasonally stratified shelf seas. Progress in Oceanography. https://doi.org/10.1016/j.pocean.2016.04.004

Ciavatta, S, Kay, S, Saux Picart, S, Butenschon, M and Allen, JI 2016 Decadal reanalysis of biogeochemical indicators and fluxes in the North West European shelf-sea ecosystem. Journal of Geophysical Research-Oceans, 121 (4). 1824-1845. https://doi.org/10.1002/2015JC011496

Butenschon, M, Clark, JR, Aldridge, JN, Allen, JI, Artioli, Y, Blackford, JC, Bruggeman, J, Cazenave, P, Ciavatta, S, Kay, S, Lessin, G, van Leeuwen, S, Van der Molen, J, de Mora, L, Polimene, L, Sailley, SF, Stephens, N and Torres, R 2016 ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels. Geoscientific Model Development, 9 (4). 1293-1339. https://doi.org/10.5194/gmd-9-1293-2016

de Mora, L, Butenschon, M and Allen, JI 2016 The assessment of a global marine ecosystem model on the basis of emergent properties and ecosystem function: a case study with ERSEM. Geosci. Model Dev., 9. 59-76. https://doi.org/10.5194/gmd-9-59-2016

Holt, J, Schrum, C, Cannaby, H, Daewel, U, Allen, I, Artioli, Y, Bopp, L, Butenschon, M, Fach, BA, Harle, J, Pushpadas, D, Salihoglu, B and Wakelin, S 2016 Potential impacts of climate change on the primary production of regional seas: A comparative analysis of five European seas. Progress in Oceanography, 140. 91-115. https://doi.org/10.1016/j.pocean.2015.11.004

Hyder, K, Rossberg, AG, Allen, JI, Austen, MC, Barciela, RM, Bannister, HJ, Blackwell, PG, Blanchard, JL, Burrows, MT, Defriez, E, Dorrington, TS, Edwards, KP, Garcia-Carreras, B, Heath, MR, Hembury, DJ, Heymans, JJ, Holt, JT, Houle, JE, Jennings, S, Mackinson, S, Malcolm, SJ, McPike, R, Mee, LD, Mills, DK, Montgomery, C, Pearson, D, Pinnegar, JK, Pollicino, M, Popova, EE, Rae, L, Rogers, SI, Speirs, D, Spence, MA, Thorpe, R, Turner, RK, Van der Molen, J, Yool, A and Paterson, DM 2015 Making modelling count - increasing the contribution of shelf-seas community and ecosystem models to policy development and management. Marine Policy, 61. 291-302. https://doi.org/10.1016/j.marpol.2015.07.015

Saux Picart, S, Allen, JI, Butenschon, M, Artioli, Y, de Mora, L, Wakelin, S and Holt, JT 2015 What can ecosystem models tell us about the risk of eutrophication in the North Sea?. Climatic Change. https://doi.org/10.1007/s10584-014-1071-x

Smyth, TJ, Atkinson, A, Widdicombe, S, Frost, MT, Allen, JI, Fishwick, J, Queiros, AM, Sims, DW and Barange, M 2015 The Western Channel Observatory. Progress in Oceanography, 137. 335-341. https://doi.org/10.1016/j.pocean.2015.05.020

Butenschon, M, Clark, JR, Aldridge, JN, Allen, JI, Artioli, Y, Blackford, JC, Bruggeman, J, Cazenave, P, Ciavatta, S, Kay, S, Lessin, G, van Leeuwen, S, Van der Molen, J, de Mora, L, Polimene, L, Sailley, SF, Stephens, N and Torres, R 2015 ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels. Geoscientific Model Development Discussions, 8 (8). 7063-7187. https://doi.org/10.5194/gmdd-8-7063-2015

Beaulieu, C, Cole, H, Henson, S, Yool, A, Anderson, TR, de Mora, L, Buitenhuis, ET, Butenschon, M, Totterdell, IJ and Allen, JI 2015 Marine regime shifts in ocean biogeochemical models: a case study in the Gulf of Alaska. Biogeosciences Discussions, 12 (16). 14003-14048. https://doi.org/10.5194/bgd-12-14003-2015

Wakelin, SL, Artioli, Y, Butenschon, M, Allen, JI and Holt, JT 2015 Modelling the combined impacts of climate change and direct anthropogenic drivers on the ecosystem of the northwest European continental shelf. Journal of Marine Systems, 152. 51-63. https://doi.org/10.1016/j.jmarsys.2015.07.006

Polimene, L, Mitra, A, Sailley, SF, Ciavatta, S, Widdicombe, CE, Atkinson, A and Allen, JI 2015 Decrease in diatom palatability contributes to bloom formation in the Western English Channel. Progress in Oceanography, 137. 484-497. https://doi.org/10.1016/j.pocean.2015.04.026

Queiros, AM, Bruggeman, J, Stephens, N, Artioli, Y, Butenschon, M, Blackford, JC, Widdicombe, S, Allen, JI and Somerfield, PJ 2015 Placing biodiversity in ecosystem models without getting lost in translation. Journal of Sea Research. https://doi.org/10.1016/j.seares.2014.10.004

Sailley, SF, Polimene, L, Mitra, A, Atkinson, A and Allen, JI 2015 Impact of zooplankton food selectivity on plankton dynamics and nutrient cycling. Journal of Plankton Research, 37 (3). 519-529. https://doi.org/10.1093/plankt/fbv020

Kwiatkowski, L, Yool, A, Allen, JI, Anderson, TR, Barciela, R, Buitenhuis, ET, Butenschon, M, Enright, C, Halloran, PR, Le Quere, C, de Mora, L, Racault, M-FLP, Sinha, B, Totterdell, IJ and Cox, PM 2014 iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework. Biogeosciences, 11 (24). 7291-7304. https://doi.org/10.5194/bg-11-7291-2014

Glibert, PM, Allen, JI, Artioli, Y, Beusen, A, Bouwman, L, Harle, J, Holmes, R and Holt, JT 2014 Vulnerability of coastal ecosystems to changes in harmful algal bloom distribution in response to climate change: projections based on model analysis. Global Change Biology, 20 (12). 3845-3858. https://doi.org/10.1111/gcb.12662

Holt, JT, Allen, JI, Anderson, TR, Brewin, RJW, Butenschon, M, Harle, J, Huse, G, Lehodey, P, Lindemann, C, Memery, L, Salihoglu, B, Senina, I and Yool, A 2014 Challenges in integrative approaches to modelling the marine ecosystems of the North Atlantic: Physics to fish and coasts to ocean. Progress in Oceanography, 129. 285-313. https://doi.org/10.1016/j.pocean.2014.04.024

Ciavatta, S, Torres, R, Martinez-Vicente, V, Smyth, TJ, Dall’Olmo, G, Polimene, L and Allen, JI 2014 Assimilation of remotely-sensed optical properties to improve marine biogeochemistry modelling. Progress in Oceanography, 127. 74-95. https://doi.org/10.1016/j.pocean.2014.06.002

Chust, G, Allen, JI, Bopp, L, Schrum, C, Holt, JT, Tsiaras, K, Zavatarelli, M, Chifflet, M, Cannaby, Hr, Dadou, I, Daewel, U, Wakelin, SL, Machu, E, Pushpadas, D, Butenschon, M, Artioli, Y, Petihakis, G, Smith, C, Garçon, VC, Goubanova, K, Le Vu, B, Fach, BA, Salihoglu, B, Clementi, E and Irigoien, X 2014 Biomass changes and trophic amplification of plankton in a warmer ocean. Global Change Biology, 20 (7). 2124-2139. https://doi.org/10.1111/gcb.12562

Smyth, TJ, Allen, JI, Atkinson, A, Bruun, JT, Harmer, RA, Pingree, RD, Widdicombe, CE and Somerfield, PJ 2014 Ocean Net Heat Flux Influences Seasonal to Interannual Patterns of Plankton Abundance. PLoS ONE, 9 (6). e98709. https://doi.org/10.1371/journal.pone.0098709

Barange, M, Merino, G, Blanchard, JL, Scholtens, J, Harle, J, Allison, EH, Allen, JI, Holt, JT and Jennings, S 2014 Impacts of climate change on marine ecosystem production in societies dependent on fisheries. Nature Climate Change. 6, pp. https://doi.org/10.1038/NCLIMATE2119

Artioli, Y, Blackford, JC, Nondal, G, Bellerby, RGJ, Wakelin, SL, Holt, JT, Butenschon, M and Allen, JI 2014 Heterogeneity of impacts of high CO2 on the North Western European Shelf. Biogeosciences, 11 (3). 601-612. https://doi.org/10.5194/bg-11-601-2014

Polimene, L, Brunet, C, Butenschon, M, Martinez-Vicente, V, Widdicombe, CE, Torres, R and Allen, JI 2014 Modelling a light-driven phytoplankton succession. Journal of Plankton Research, 36 (1). 214-229. https://doi.org/10.1093/plankt/fbt086

Rose, KA and Allen, JI 2013 Modeling marine ecosystem responses to global climate change: Where are we now and where should we be going?. Ecological Modelling, 264. 1-6. https://doi.org/10.1016/j.ecolmodel.2013.04.014

de Mora, L, Butenschon, M and Allen, JI 2013 How should sparse marine in situ measurements be compared to a continuous model: an example. Geoscientific Model Development, 6 (2). 533-548. https://doi.org/10.5194/gmd-6-533-2013

Hirata, T, Saux-Picart, S, Hashioka, T, Aita-Noguchi, M, Sumata, H, Shigemitsu, M, Allen, JI and Yamanaka, Y 2013 A comparison between phytoplankton community structures derived from a global 3D ecosystem model and satellite observation. Journal of Marine Systems, 109-11. 129 - 137. https://doi.org/10.1016/j.jmarsys.2012.01.009

Christensen, A, Butenschon, M, Gurkan, Z and Allen, JI 2013 Towards an integrated forecasting system for fisheries on habitat-bound stocks. Ocean Science. 261 - 279. https://doi.org/10.5194/os-9-261-2013

Blanchard, J, Jennings, S, Holmes, R, Harle, J, Merino, G, Allen, JI, Holt, JT, Dulvy, NK and Barange, M 2012 Potential consequences of climate change for primary production and fish production in large marine ecosystems. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 367. 2979 - 2989. https://doi.org/10.1098/rstb.2012.0231

Merino, G, Barange, M, Blanchard, J, Harle, J, Holmes, R, Allen, JI, Allison, EH, Badjeck, MC, Dulvy, NK, Holt, JT, Jennings, S, Mullon, C and Rodwell, LD 2012 Can marine fisheries and aquaculture meet fish demand from a growing human population in a changing climate?. Global Environmental Change, 22. 795 - 806. https://doi.org/10.1016/j.gloenvcha.2012.03.003

Bruun, JT, Somerfield, PJ and Allen, JI 2012 Applications of Box Jenkins Transfer function methods to identify seasonal and longer term. ICES CM. R:22 - R:22.

Bruun, JT, Somerfield, PJ, Allen, JI, Vichi, M, McKiver, W, Racault, M-FLP, Johannessen, J, Bellerby, RGJ and Waldron, HN 2012 New methodologies to build an integrated global plankton database: the GreenSeas Analysis Framework. ICES CM. R:10 - R:10.

Polimene, L, Archer, SD, Butenschon, M and Allen, JI 2012 A mechanistic explanation of the Sargasso Sea DMS summer paradox. Biogeochemistry, 110. 243 - 255. https://doi.org/10.1007/s10533-011-9674-z

Wakelin, SL, Holt, JT, Blackford, JC, Allen, JI, Butenschon, M and Artioli, Y 2012 Modeling the carbon fluxes of the northwest European continental shelf: Validation and budgets.. Journal of Geophysical Research-Oceans, 117. 0 - 0. https://doi.org/10.1029/2011jc007402

Artioli, Y, Blackford, JC, Butenschon, M, Holt, JT, Wakelin, SL, Thomas, H, Borges, AV and Allen, JI 2012 The carbonate system of the NW European shelf: sensitivity and model validation. Journal of Marine Systems, 102-10. Jan-13. https://doi.org/10.1016/j.jmarsys.2012.04.006

Christensen, A, Butenschon, M, Gurkan, Z and Allen, JI 2012 Towards an integrated forecasting system for pelagic fisheries. Ocean Science Discussions, 9. 1437 - 1479. https://doi.org/10.5194/osd-9-1437-2012

Polimene, L, Brunet, C, Allen, JI, Butenschon, M, White, DA and Llewellyn, CA 2012 Modelling xanthophyll photoprotective activity in phytoplankton. Journal of Plankton Research, 34. 196 - 207. https://doi.org/10.1093/plankt/fbr102

Holt, JT, Butenschon, M, Wakelin, SL, Artioli, Y and Allen, JI 2012 Oceanic controls on the primary production of the northwest European continental shelf: model experiments under recent past conditions and a potential future scenario. Biogeosciences, 9. 97 - 117. https://doi.org/10.5194/bg-9-97-2012

Ciavatta, S, Torres, R, Saux-Picart, S and Allen, JI 2011 Can ocean color assimilation improve biogeochemical hindcasts in shelf seas?. Journal of Geophysical Research-Oceans, 116. Jan-19. https://doi.org/10.1029/2011JC007219

Shutler, J, Smyth, TJ, Saux-Picart, S, Wakelin, SL, Hyder, P, Orekhov, P, Grant, MG, Tilstone, GH and Allen, JI 2011 Evaluating the ability of a hydrodynamic ecosystem model to capture inter- and intra-annual spatial characteristics of chlorophyll-a in the north east Atlantic. Journal of Marine Systems, 88. 169 - 182. https://doi.org/10.1016/j.jmarsys.2011.03.013

Polimene, L, Archer, SD, Butenschon, M and Allen, JI 2011 A mechanistic explanation of the Sargasso Sea DMS summer paradox. Biogeochemistry. Jan-13. https://doi.org/10.1007/s10533-011-9674z

Allen, JI and Polimene, L 2011 Linking physiology to ecology: towards a new generation of plankton models. Journal of Plankton Research, 33. 989 - 997. https://doi.org/10.1093/plankt/fbr032

Vichi, M, Allen, JI, Masina, S and Hardman-Mountford, NJ 2011 The emergence of ocean biogeochemical provinces: A quantitative assessment and a diagnostic for model evaluation. Global Biogeochemical Cycles, 25. 0 - 0. https://doi.org/10.1029/2010GB003867

Glibert, PM, Allen, JI, Bouwman, AF, Brown, CW, Flynn, KJ, Lewitus A, J and Madden, CJ 2010 Modeling of HABs and eutrophication Status advances challenges. Journal of Marine Systems, 83 (3. 262 - 275. https://doi.org/10.1016/j.jmarsys.2010.05.004

Le Clainche, Y, Vezina, A, Levasseur, M, Cropp, R, Gunson, JR, Vallina, SM, Vogt, M, Lancelot, C, Allen, JI, Archer, SD, Bopp, L, Laurent, L, Deal, C, Elliott, S, Jin, MM, Malin, G, Schoemann, V, Simo, F, Six, KD and Stefels, J 2010 A first appraisal of prognostic ocean DMS models and prospects for their use in climate models. Global Biogeochemical Cycles, 24. 0 - 0. https://doi.org/10.1029/2009GB003721

Allen, JI 2010 Marine ecosystem response to multiple climatic and anthropogenic drivers: A modelling approach. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 157. 01-Jan. https://doi.org/10.1016/j.cbpa.2010.06.002

Allen, JI and Fulton, EA 2010 Top-down bottom-up or middle-out? Avoiding extraneous detail and over-generality in marine ecosystem models. Progress in Oceanography, 84 (1-. 129 - 133. https://doi.org/10.1016/j.pocean.2009.09.016

Allen, JI, Aiken, J, Anderson, TR, Buitenhuis, E, Cornell, S, Geider, RJ, Haines, K, Hirata, T, Holt, JT, Le Quere, C, Hardman-Mountford, NJ, Ross, RN, Sinha, B and While, J 2010 Marine ecosystem models for earth systems applications: The MarQUEST experience. Journal of Marine Systems, 81 (1-. 19 - 33. https://doi.org/10.1016/j.jmarsys.2009.12.017

Blackford, JC, Allen, JI, Anderson, TR and Rose, KA 2010 Challenges for a new generation of marine ecosystem models: Overview of the Advances in Marine Ecosystem Modelling Research (AMEMR) Symposium 23-26 June 2008 Plymouth UK Preface. Journal of Marine Systems, 81. 01-Mar. https://doi.org/10.1016/j.jmarsys.2009.12.018

Rose, KA, Allen, JI, Artioli, Y, Barange, M, Blackford, JC, Carlotti, F, Cropp, R, Daewel, U, Flynn, KJ, Hill, SL, Hille Ris Lambers, R, Huse, G, Mackinson, S, Megrey, B, Moll, A, Rivkin, R, Salihoglu, B, Schrum, C, Shannon, L, Shin, Y-J, Smith, SL, Smith, C, Solidoro, C, St John, M and Zhou, M 2010 End-To-End Models for the Analysis of Marine Ecosystems: Challenges Issues and Next Steps. Marine and Coastal Fisheries: Dynamics Management and Ecosystem Science, 2. 115 - 130. https://doi.org/10.1577/C09-059.1

Stromberg, KHP, Smyth, TJ, Allen, JI, Pitois, SG and O'Brien, TD 2009 Estimation of global zooplankton biomass from satellite ocean colour. Journal of Marine Systems, 78. 18 - 27. https://doi.org/10.1016/j.jmarsys.2009.02.004

Lewis, K and Allen, JI 2009 Validation of a hydrodynamic-ecosystem model simulation with time-series data collected in the western English Channel. Journal of Marine Systems, 77. 296 - 311. https://doi.org/10.1016/j.jmarsys.2007.12.013

Holt, JT, Harle, J, Proctor, R, Michel, S, Ashworth, M, Batstone, C, Allen, JI, Holmes, R, Smyth, TJ, Haines, K, Bretherton, D and Smith, GC 2009 Modelling the global coastal ocean. Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical and Engineering Sciences. 939 - 951. https://doi.org/10.1098/rsta.2008.0210

Stow, C, Jolliff, J, McGillicuddy, DJ, Doney, SC, Allen, JI, Friedrichs, MAM, Rose, KA and Wallheadg, P 2009 Skill assessment for coupled biological/physical models of marine systems. Journal of Marine Systems, 01-Feb. Apr-15. https://doi.org/10.1016/j.jmarsys.2008.03.011

Allen, JI and Somerfield, PJ 2009 A multivariate approach to model skill assessment. Journal of Marine Systems, 76. 83 - 94. https://doi.org/10.1016/j.jmarsys.2008.05.009

Fox, C, Harris, RP, Sundby, S, Achterberg, EP, Allen, JI, Allen, J, Baker, AR, Brussaard, CPD, Buckley, P, Cook, E, Dye, S, Edwards, M, Fernand, L, Kershaw, P, Metcalfe, JD, Østerhus, S, Potter, T, Sakshaug, E, Speirs, D, Stenevik, E, St John, M, Thingstad, TF and Wilson, B 2009 Transregional linkages in the North-Eastern Atlantic - An ‘end-to-end ’ analysis of pelagic ecosystems. Oceanography and Marine Biology, 47. 1-75.

Vichi, M, Allen, JI and Hardman-Mountford, NJ 2008 Biogeographic validation of a global ocean biogeochemistry model. Conference Proceedings. 38 - 38.

Allen, JI, Smyth, TJ, Siddorn, JR and Holt, JT 2008 How well can we forecast high biomass algal bloom events in a eutrophic coastal sea?. Harmful Algae, 8(1). 70 - 76. https://doi.org/10.1016/j.hal.2008.08.024

Aveytua-Alcazar, L, Camacho-Ibar, VF, Souza, AJ, Allen, JI and Torres, R 2008 Modelling Zostera marina and Ulva spp. in a coastal lagoon. Ecological Modelling, 218(3-. 354 - 366. https://doi.org/10.1016/j.ecolmodel.2008.07.019

Allen, JI, Holt, JT, Proctor, R and Blackford, JC 2007 Error quantification of a high-resolution coupled hydrodynamic-ecosystem coastal-ocean model: Part 2. Chlorophyll-a nutrients and SPM. Journal of Marine Systems, 68. 381 - 404. https://doi.org/10.1016/j.jmarsys.2007.01.005

Allen, JI and Clarke, KR 2007 Effects of demersal trawling on ecosystem functioning in the North Sea: a modelling study. Marine Ecology Progress Series, 336. 63 - 75. https://doi.org/10.3354/meps336063

Dagnino, A, Allen, JI, Moore, MN and Viarengo, A 2007 Development of an expert system for the integration of biomarker responses in mussels into an animal health index. Biomarkers, 12. 155 - 172. https://doi.org/10.1080/13547500601037171

Siddorn, JR, Allen, JI, Blackford, JC, Gilbert, FJH, Holt, JT, Holt, M, Osbourne, J, Proctor, R and Mills, DK 2007 Modelling the hydrodynamics and ecosystem of the North-West European continental shelf for operational oceanography. Journal of Marine Systems, 65. 417 - 429. https://doi.org/10.1016/j.jmarsys.2006.01.018

Polimene, L, Zavatarelli, M and Allen, JI 2007 A numerical simulation study of dissolved organic carbon accumulation in the northern Adriatic Sea. Journal of Geophysical Research-Oceans, 112 (C (Art. N). https://doi.org/10.1029/2006JC003529

Blackford, JC, Allen, JI and de Young, B 2007 Advances in marine ecosystem modelling research. Journal of Marine Systems, 64. 01-Feb. https://doi.org/10.1016/j.jmarsys.2006.05.001

Moore, MN, Lowe, DM, Allen, JI, McVeigh, A and Somerfield, PJ 2007 Predicting health of the environment - lysosomal biomarker responses in mussels. In: Proceedings of the Workshop on the Med Pol Biological Effects Programme: Acheivements and Future Orientations Alessandria Italy 20 - 21 December 2006. MAP Technical Reports Series No 166 United Nations Environment Programme/Mediterranean Action Plan (UNEP/MAP) Athens greece. Mar-20.

Allen, JI, Somerfield, PJ and Gilbert, FJH 2007 Quantifying uncertainty in high-resolution coupled hydrodynamic-ecosystem models. Journal of Marine Systems, 64. Mar-14. https://doi.org/10.1016/j.jmarsys.2006.02.010

Lewis, K, Allen, JI, Richardson, AJ and Holt, JT 2006 Error quantification of a high resolution coupled hydrodynamic-ecosystem coastal-ocean model: Part3 validation with Continuous Plankton Recorder data. Journal of Marine Systems, 63 (3 - 4). 209 - 224. https://doi.org/10.1016/j.jmarsys.2006.08.001

Moore, MN, Allen, JI and Somerfield, PJ 2006 Autophagy: Role in surviving environmental stress. Marine Environmental Research, 62 Sup. S420 - S425. https://doi.org/10.1016/j.marenvres.2006.04.055

Allen, JI, Archer, SD, Gilbert, FJH, Blackford, JC and Taylor, AH 2006 Changes in DMS production and flux in relation to decadal shifts in ocean circulation. Tellus Series B-Chemical and Physical Meteorology, 58B. 242 - 254. https://doi.org/10.1111/j.1600-0889.2006.00183.x

McVeigh, A, Moore, MN, Allen, JI and Dyke, P 2006 Lysosomal responses to nutritional and contaminant stress in mussel hepatopancreatic digestive cells: A modelling study. Marine Environmental Research, 62 Sup. S433 - S438. https://doi.org/10.1016/j.marenvres.2006.04.021

Moore, MN, Allen, JI, McVeigh, A and Shaw, JP 2006 Lysosomal and autophagic reactions as predictive indicators of environmental impact in aquatic animals. Autophagy, 2. 217 - 220.

Torres, R, Allen, JI and Figueiras, FG 2006 Sequential data assimilation in an upwelling influenced estuary. Journal of Marine Systems. 0 - 0. https://doi.org/10.1016/j.jmarsys.2006.02.001

Moore, MN, Allen, JI and McVeigh, A 2006 Environmental prognostics: An integrated model supporting lysosomal stress responses as predictive biomarkers of animal health status. Marine Environmental Research, 61. 278 - 304. https://doi.org/10.1016/j.marenvres.2005.10.005

Hardman-Mountford, NJ, Allen, JI, Frost, MT, Hawkins, SJ, Kendall, MA, Mieszkowska, N, Richardson, K and Somerfield, PJ 2005 Diagnostic monitoring of a changing environment: An alternative UK perspective. Marine Pollution Bulletin, 50. 1463 - 1471. https://doi.org/10.1016/j.marpolbul.2005.06.022

Holt, JT, Allen, JI, Proctor, R and Gilbert, FJH 2005 Error quantification of a high-resolution coupled hydrodynamic-ecosystem coastal-ocean model: Part 1 model overview and assessment of the hydrodynamics. Journal of Marine Systems, 57. 167 - 188. https://doi.org/10.1016/j.jmarsys.2005.04.008

Blackford, JC, Allen, JI and Gilbert, FJH 2004 Ecosystem dynamics at six contrasting sites: a generic modelling study. Journal of Marine Systems, 52 (1 - 4). 191 - 215. https://doi.org/10.1016/j.jmarsys.2004.02.004

Allen, JI and McVeigh, A 2004 Towards computational models of cells for environmental toxicology. Journal of Molecular Histology, 35(7). 697 - 706.

Allen, JI and Moore, MN 2004 Environmental prognostics: Is the current use of biomarkers appropriate for environmental risk evaluation?. Marine Environmental Research, 58 (2-5). 227 - 232. https://doi.org/10.1016/j.marenvres.2004.03.119

Moore, MN, Allen, JI and McVeigh, A 2004 Ecophysiomics: a systems biology approach to environmental toxico-pathology from the molecular and cellular levels to the ecosystem.. Journal of Histochemistry & Cytochemistry. 12 - 12.

Zubkov, MV, Allen, JI and Fuchs, BM 2004 Coexistence of dominant groups in marine bacterioplankton community - a combination of experimental and modelling approaches. Journal of the Marine Biological Association of the United Kingdom, 84. 519 - 529. https://doi.org/10.1017/S002531540400952Xh

Allen, JI, Blackford, JC, Gilbert, FJH and Siddorn, JR 2004 Turbulence as a control on the microbial loop in a temperate seasonally stratified marine systems model. Journal of Sea Research, 52. 1 - 20. https://doi.org/10.1016/j.seares.2003.09.004

Holt, JT, Proctor, R, Blackford, JC, Allen, JI and Ashworth, M 2004 Advective controls on primary production in the stratified western Irish Sea: An eddy-resolving model study. Journal of Geophysical Research-Oceans, 109 C5. 5024 - 5034. https://doi.org/10.1029/2003JC001951

Archer, SD, Gilbert, FJH, Allen, JI, Blackford, JC and Nightingale, PD 2004 Modelling of the seasonal patterns of dimethylsulphide production and fate during 1989 at a site in the North Sea. Canadian Journal of Fisheries and Aquatic Sciences, 61. 765 - 787. https://doi.org/10.1139/F04-028

McVeigh, A, Allen, JI, Moore, MN, Dyke, P and Noble, D 2004 A carbon and nitrogen flux model of mussel digestive gland epithelial cells and their simulated response to pollutants. Marine Environmental Research, 58. 821 - 827. https://doi.org/10.1016/j.marenvres.2004.03.099

Proctor, R, Holt, JT, Allen, JI and Blackford, JC 2003 Nutrient fluxes and budgets for the North West European Shelf from a three-dimensional model. Science of the Total Environment, 314. 769 - 785. https://doi.org/10.1016/S0048-9697(03)00083-4

Siddorn, JR, Allen, JI and Uncles, RJ 2003 Heat salt and tracer transport in the Plymouth Sound coastal region: a 3-D modelling study. Journal of the Marine Biological Association of the United Kingdom, 83 (4). 673 - 682. https://doi.org/10.1017/S002531540300763Xh

Triantafyllou, G, Petihakis, G and Allen, JI 2003 Assessing the performance of the Cretan Sea ecosystem model with the use of high frequency M3A buoy data set. Annales Geophysicae, 21 (1). 365 - 375.

Allen, JI, Eknes, M and Evensen, G 2003 An Ensemble Kalman Filter with a complex marine ecosystem model: hindcasting phytoplankton in the Cretan Sea. Annales Geophysicae, 21 (1). 399 - 411.

Siddorn, JR and Allen, JI 2003 Surface heat fluxes and ecosystem function in the Cretan Sea (eastern Mediterranean): a modelling study. Annales Geophysicae, 21 (1). 377 - 388.

Hoteit, I, Triantafyllou, G, Petihakis, G and Allen, JI 2003 A singular evolutive extended Kalman filter to assimilate real in situ data in a 1-D marine ecosystem model. Annales Geophysicae, 21 (1). 389 - 397.

Moore, MN and Allen, JI 2002 A computational model of the digestive gland epithelial cell of marine mussels and its simulated responses to oil-derived aromatic hydrocarbons. Marine Environmental Research, 54 (03-May). 579 - 584. https://doi.org/10.1016/S0141-1136(02)00166-6

Allen, JI, Somerfield, PJ and Siddorn, JR 2002 Primary and bacterial production in the Mediterranean Sea: a modelling study. Journal of Marine Systems, 33. 473 - 495. https://doi.org/10.1016/S0924-7963(02)00072-6

Taylor, AH, Allen, JI and Clark, PA 2002 Extraction of a weak climatic signal by an ecosystem. Nature, 416 (6881). 629 - 632. https://doi.org/10.1038/416629a

Allen, JI, Blackford, JC, Holt, JT, Proctor, R, Ashworth, M and Siddorn, JR 2001 A highly spatially resolved ecosystem model for the North West European Continental Shelf. Sarsia, 86 (6). 423 - 440.

Crise, A, Allen, JI, Baretta, J, Crispi, G, Mosetti, R and Solidoro, C 1999 The Mediterranean pelagic ecosystem response to physical forcing. Progress in Oceanography, 44 (01-Mar). 219 - 243. https://doi.org/10.1016/S0079-6611(99)00027-0

Allen, JI, Blackford, JC and Radford, PJ 1998 An 1-D vertically resolved modelling study of the ecosystem dynamics of the middle and southern Adriatic Sea. Journal of Marine Systems, 18 (01-Mar). 265 - 286. https://doi.org/10.1016/S0924-7963(98)00015-3

Allen, JI, Howland, RMH, Bloomer, NJ and Uncles, RJ 1998 Simulating the spring phytoplankton bloom in the Humber plume UK. Marine Pollution Bulletin, 37 (03-Jul). 295 - 305.

Allen, JI 1997 A modelling study of ecosystem dynamics and nutrient cycling in the Humber plume UK. Journal of Sea Research, 38 (03-Apr). 333 - 359. https://doi.org/10.1016/S1385-1101(97)00050-6

Millward, GE, Kitts, HJ, Ebdon, L, Allen, JI and Morris, AW 1997 Arsenic in the Thames Plume UK. Marine Environmental Research, 44 (1). 51 - 67. https://doi.org/10.1016/S0141-1136(96)00102-X

Millward, GE, Allen, JI, Morris, AW and Turner, A 1996 Distributions and fluxes of non-detrital particulate FeMnCuZn in the Humber coastal zone UK. Continental Shelf Research, 16 (7). 967 - 993. https://doi.org/10.1016/0278-4343(95)00040-2

Morris, AW, Allen, JI, Howland, RJM and Wood, RG 1995 The Estuary Plume Zone - Source Or Sink For Land-Derived Nutrient Discharges. Estuarine, Coastal and Shelf Science, 40 (4). 387 - 402. https://doi.org/10.1006/ecss.1995.0027

Huthnance, JM, Allen, JI, Davies, AM, Hydes, DJ, James, ID, Jones, JE, Millward, GE, Prandle, D, Proctor, R, Purdie, DA, Statham, PJ, Tett, PB, Thomson, S and Wood, RG 1993 Towards Water-Quality Models. Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical and Engineering Sciences, 343 (1669). 569 - 584. https://doi.org/10.1098/rsta.1993.0067

Allen, JI Model of interactions between dissolved organic carbon and bacteria in marine systems.

Allen, JI 2011 Marine Environment & Human Health: An Overview. UNSPECIFIED, 0 - 0.

Cazenave, PW, Torres, R and Allen, JI 2016 Offshore Wind Farm Impacts on Seasonally Stratified Seas: An Unstructured Modelling Approach. [Lecture] In: Challenger Coastal Special Interest Group. Met Office. (Unpublished)

Cazenave, PW, Torres, R and Allen, JI 2016 Offshore Wind Farm Impacts on Seasonally Stratified Seas: An Unstructured Modelling Approach. [Lecture] In: Challenger Meeting 2016. National Oceanography Centre, Liverpool. (Unpublished)

Bruggeman, J, Torres, R, Cazenave, P, Artioli, Y and Allen, JI 2016 Coupling FVCOM with FABM - Multiplying the Choice of Marine Ecosystem Models within FVCOM. [Lecture] In: UK FVCOM Workshop. National Oceanography Centre, Liverpool. (Unpublished)

Cazenave, P, Allen, JI, Blackford, JC, Artioli, Y, Torres, R, Hawkins, AJS and Morris, K 2015 Risks and Opportunities for Sustainable Aquaculture. [Poster] In: Aquaculture 2015, Montpellier, France, 24th-26th August 2015.

Cazenave, P, Torres, R and Allen, JI 2015 Offshore wind farm impacts on seasonally stratified seas: an unstructured modelling approach. [Lecture] In: Partnership for Research in Marine Renewable Energy, Univesity of Exeter, Falmouth Campus, 2015/06/16. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2015 Offshore wind farm impacts on seasonally stratified seas: an unstructured modelling approach. [Lecture] In: PML Seminar Series, Plymouth Marine Laboratory, 2014/04/08. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2014 Offshore renewable energy device impacts on seasonally stratified seas around the UK: an unstructured modelling approach. [Lecture] In: National Oceanography Centre, Liverpool, Seminar Series, National Oceanography Centre, Liverpool, 2014/12/10. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2014 Offshore renewable energy device impacts on seasonally stratified seas around the UK: an unstructured modelling approach. [Lecture] In: 5th FVCOM Workshop, SAMS, Oban, Scotland, 2014/11/17. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2014 Offshore renewable energy device impacts on seasonally stratified seas around the UK: an unstructured modelling approach. [Lecture] In: Partnership for Research in Marine Renewable Energy (PRIMaRE), University of Plymouth, 2014/06/04. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2014 Offshore renewable energy device impacts on seasonally stratified seas around the UK: an unstructured modelling approach. [Poster] In: Partnership for Research in Marine Renewable Energy. (Unpublished)

Cazenave, P, Torres, R and Allen, JI 2014 Modelling the coastal and nearshore zones with the FVCOM unstructured model. [Lecture] In: Memori Workshop, Seoul, Korea, 2014/03/18. (Unpublished)

Allen, JI, Blackford, JC, Cheung, W and Fulton, EA 2013 Overview of the third Advances in Marine Ecosystem Modelling Research (AMEMR) Symposium, 27–30 June 2011, Plymouth. [Other] In: Advances in Marine Ecosystem Modelling Research (AMEMR) Symposium, Plymouth, 27 - 30 June 2011. 1-2.

Allen, JI 2002 Simulating the spring phytoplankton bloom in the Humber Plume (UK) with a variable phytoplankton carbon: chlorophyll-a model.. In: 2nd International EuroGOOS Conference, ROME, ITALY, MAR 11-13, 1999. ELSEVIER SCIENCE BV, 497 - 504.

Allen, JI 1997 The importance of high frequency data in ecological modelling.. In: 1st International Conference on EuroGOOS - Operational Oceanography: The Challenge for European Co-Operation, THE HAGUE, NETHERLANDS, OCT 07-11, 1996. ELSEVIER OCEANOGRAPHY SERIES, 499 - 506.