- Murphy, J.T.; Johnson, M.P.; Viard, F. (2017). A theoretical examination of environmental effects on the life cycle schedule and range limits of the invasive seaweed Undaria pinnatifida. Biological Invasions 19(2): 691-702. https://dx.doi.org/10.1007/s10530-016-1357-1
- Rutterford, L.A.; Simpson, S.D.; Jennings, S.; Johnson, M.P.; Blanchard, J.L.; Schön, P.-J.; Sims, D.W.; Tinker, J.; Genner, M.J. (2015). Future fish distributions constrained by depth in warming seas. Nat. Clim. Chang. 5(6): 569–573. http://dx.doi.org/10.1038/nclimate2607
- Johnson, M.L.; Johnson, M.P. (2013). Nephrops norvegicus: Introduction to the Issue, in: Johnson, M.L. et al. Adv. Mar. Biol. 64: The ecology and biology of Nephrops norvegicus. Advances in Marine Biology, 64: pp. xiii-xvi. https://dx.doi.org/10.1016/B978-0-12-410466-2.10000-7
- Johnson, M.L.; Johnson, M.P. (Ed.) (2013). Adv. Mar. Biol. 64: The ecology and biology of Nephrops norvegicus. Advances in Marine Biology, 64. Academic Press: London. ISBN 978-0-12-410466-2. XXV, 325 pp.
- Rae, M.; Folch, H.; Moniz, M.B.J.; Wolff, C.W.; McCormack, G.P.; Rindi, F.; Johnson, M.P. (2013). Marine bioactivity in Irish waters. Phytochemistry Reviews 12(3): 555-565. https://dx.doi.org/10.1007/s11101-012-9227-7
- Simpson, S.D.; Jennings, S.; Johnson, M.P.; Blanchard, J.L.; Schön, P.-J.; Sims, D.W.; Genner, M.J. (2011). Continental shelf-wide response of a fish assemblage to rapid warming of the sea. Curr. Biol. 21(18): 1565-1570. dx.doi.org/10.1016/j.cub.2011.08.016
- Allcock, A.L.; Strugnell, J.M.; Johnson, M.P. (2008). How useful are the recommended counts and indices in the systematics of the Octopodidae (Mollusca: Cephalopoda). Biol. J. Linn. Soc. 95(1): 205-218. https://dx.doi.org/10.1111/j.1095-8312.2008.01031.x
- Mineur, F.; Johnson, M.P.; Maggs, C.A.; Stegenga, H. (2007). Hull fouling on commercial ships as a vector of macroalgal introduction. Mar. Biol. (Berl.) 151(4): 1299-1307. http://dx.doi.org/10.1007/s00227-006-0567-y
- Johnson, M.P. (2006). Vertical mixing in Lough Hyne during stratification. J. Mar. Biol. Ass. U.K. 86(5): 947-948. https://dx.doi.org/10.1017/S0025315406013907
- Johnson, M.P.; Edwards, M.; Bunker, F.; Maggs, C.A. (2005). Algal epiphytes of Zostera marina: variation in assemblage structure from individual leaves to regional scale. Aquat. Bot. 82(1): 12-26. https://dx.doi.org/10.1016/j.aquabot.2005.02.003
- Johnson, M.P. (2000). Physical control of plankton population abundance and dynamics in intertidal rock pools. Hydrobiologia 440(1-3): 145-152. https://dx.doi.org/10.1023/A:1004106808213
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- Johnson, M.P. (2006). Rocky intertidal invertebrates: the potential for metapopulations within and among shores, in: Kritzer, J.P. et al. (Ed.) Marine metapopulations. pp. 247-270
 Johnson, M.P. (2005). Projections from population and community models of rocky shores, in: Wilson, J.G. (Ed.) The intertidal ecosystem: the value of Ireland’s shores. pp. 134-146- Johnson, M.P. (2004). Challenges in the analysis and simulation of benthic community patterns, in: Seuront, L. et al. (Ed.) Handbook of scaling methods in aquatic ecology: measurement, analysis, simulation. pp. 229-243
- Johnson, M.P. (2000). Physical control of plankton population abundance and dynamics in intertidal rock pools, in: Jones, M.B. et al. Island, Ocean and Deep-Sea Biology: Proceedings of the 34th European Marine Biology Symposium, held in Ponta Delgada (Azores), Portugal, 13-17 September 1999. Developments in Hydrobiology, 152: pp. 145-152. https://dx.doi.org/10.1007/978-94-017-1982-7_14
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