- Wernberg, T., Thomsen, M.S., Stæhr, P.A. (1998). Invasion af butblærret Sargassotang i Danmark - status anno 1998 (In Danish; ‘The invasion of Sargassum muticum in Denmark’). Urt (Danish Botanical Journal) 4: 128-132.
- Stæhr, P.A., Pedersen, M.F., Thomsen, M.S., Wernberg, T., Krause-Jensen, D. (2000). The Invasion of Sargassum muticum in Limfjorden (Denmark) and its possible impact on the indigenous macroalgal community. Marine Ecology Progress Series 207: 79-88.
- Wernberg, T., Thomsen, M.S., Stæhr, P.A., Pedersen, M.F. (2001). Comparative phenology of Sargassum muticum and Halidrys siliquosa (Phaeophycae: Fucales) in Limfjorden, Denmark. Botanica Marina 44: 31-49.
- Wernberg, T., Coleman, M., Fairhead, A., Miller, S., Thomsen, M.S. (2003). Morphology of Ecklonia radiata (C. Ag.) J. Agardh. along its geographic distribution in Southwestern Australia and Australasia. Marine Biology 143: 47-55.
- Thomsen, M.S., Wernberg, T., Kendrick, G. (2004). The effect of thallus size, life stage, aggregation, wave exposure and substrate conditions on the forces required to break or dislodge the small kelp Ecklonia radiata. Botanica Marina 47: 454-460.
- Thomsen, M.S. (2004). Species, thallus size and substrate determine macroalgal break forces and break places in a low energy soft bottom lagoon. Aquatic Botany 80: 153-161.
- Wernberg, T., Thomsen, M.S., Stæhr, P.A., Pedersen, M.F. (2004). Epibiota communities of the introduced and indigenous macroalgal relatives Sargassum muticum and Halidrys siliquosa in Limfjorden (Denmark). Helgoland Marine Research 58: 154-161.
- Thomsen, M.S., Wernberg, T. (2005). Minireview: What affects the forces required to break or dislodge macroalgae? European Journal of Phycology 40: 1-10.
- Thomsen, M.S., McGlathery, K. (2005). Facilitation of macroalgae by the sedimentary tube forming polychaete Diopatra cuprea. Estuarine, Coastal and Shelf Science 62: 63-73.
- Wernberg, T., Thomsen, M.S. (2005). The effect of wave exposure on the morphology of Ecklonia radiata in southwestern Australia. Aquatic Botany 83: 61-70.
- Pedersen, M.F., Stæhr, P.A., Wernberg, T., Thomsen, M.S. (2005). Biomass dynamics of exotic Sargassum muticum and native Halidrys siliquosa in Limfjorden, Denmark - implications of species replacements on turnover rates. Aquatic Botany 83: 31-47.
- Thomsen, M.S., Krause-Jensen, D., Wernberg, T., Stæhr, P.A, Risgaard, N.P. (2005). Fremmede tangarter i Danmark: Hvilke, hvornår og hvor udbredte? (In Danish; ‘Alien seaweeds in Denmark: which, when and how abundant?’). Urt (Danish Botanical Journal) 29: 110-115.
- Thomsen, M.S., McGlathery, K.J., Tyler, A.C. (2006). Macroalgal distribution pattern in a shallow, soft-bottom lagoon, with emphasis on the nonnative Gracilaria vermiculophylla and Codium fragile. Estuaries and Coasts 29: 465-473.
- Thomsen, M.S., Wernberg, T., Stæhr, P.A., Pedersen, M.F. (2006). Spatio-temporal distribution patterns of the invasive macroalga Sargassum muticum within a Danish Sargassum-bed. Helgoland Marine Research 60: 50-58.
- Thomsen, M.S., McGlathery, K.J. (2006). Effects of accumulations of sediments and drift algae on recruitment of sessile organisms associated with oyster reefs. Journal of Experimental Marine Biology and Ecology 328: 22-34.
- Thomsen, M.S., Gurgel, C.F.D., Fredericq, S., McGlathery, K.J. (2006). Gracilaria vermiculophylla (Rhodophyta, Gracilariales) in Hog Island Bay, Virginia: a cryptic alien and invasive macroalgae and taxonomic corrections. Journal of Phycology 42: 139-141.
- Thomsen, M.S., Staehr, P.A., Wernberg, T. (2007). First Symposium on Danish Marine Bioinvasions, Copenhagen: PDF Abstract Book - With Introduction & Summery. 18 pp.
- Thomsen, M.S., Josefson, A, Wernberg, T. (2007). Indførte bundlevende marine invertebrater: hvor almindelige er de i Danmark? (In Danish; ‘Introduced benthic marine invertebrates: how abundant are they in Denmark?’) Vand og Jord (Danish Environmental Journal) 2: 44-48.
- Thomsen, M.S., McGlathery, K.J. (2007). Stress tolerance of the invasive macroalgae Codium fragile and Gracilaria vermiculophylla in a soft-bottom turbid lagoon. Biological Invasions 9: 1-12.
- Thomsen, M.S., Stæhr, P., Nyberg, C., Krause-Jensen, D., Schwærter, S., Silliman, B. (2007). Gracilaria vermiculophylla in northern Europe, with focus on Denmark, and what to expect in the future. Aquatic Invasions 2: 83-94.
- Thomsen, M.S., Wernberg, T., Stæhr, P.A., Krause-Jensen, D. Risgaard-Petersen, N., Silliman, B.R. (2007). Alien macroalgae in Denmark – a broad-scale national perspective. Marine Biology Research 3: 61 - 72.
- Thomsen, M.S., Silliman, B.R., McGlathery, K.J. (2007). Spatial variation in recruitment of native and invasive sessile species onto oyster reefs in a temperate soft-bottom lagoon. Estuarine, Coastal and Shelf Science 72: 89-101.
- Tuya, F., Wernberg, T., Thomsen, M.S. (2008). Testing the 'abundant centre' hypothesis on endemic reef fishes in south-western Australia. Marine Ecology Progress Series 372: 225–230.
- Thomsen, M.S., Wernberg, T., Stæhr, P.A., Silliman, B.R., Josefson, A.B., Krause-Jensen, D., Risgaard-Petersen, N. (2008). Status and trends of non-indigenous macro-benthic marine species in Denmark. Aquatic Invasions 3: 133-139.
- Tuya, F., Wernberg, T., Thomsen, M.S. (2008). The spatial arrangement of reefs alters the ecological patterns of fauna between interspersed algal habitats. Estuarine, Coastal and Shelf Science 78: 774–782.
- Wernberg, T., Thomsen, M.S., McMahon, K. (2008). Determining seagrass depth distribution in the Swan River – a test of the dumpy level method with recommendations for alternatives. Report prepared for the Water Science Branch, Department of Water. Report no 2008-2 from the Centre for Marine Ecosystems Research, Edith Cowan University, Perth, Australia. Pp. 18.
- Thomsen, M.S., Wernberg, T., Staerh, P., Krause-Jensen, D., Josefson, A., Tendal, O. (2008). Introducerede dyr og planter i Danmark – terminologi, mekanismer og effekter (In Danish; ’Introduced animals and plants in Denmark – terminology, mechanisms and effects’). Naturens Verden (Danish Nature Journal) 6:10-18.
- Tuya, F., Wernberg, T., Thomsen, M.S. (2009). Severity of disturbances to algal canopies does not affect the colonization of gastropods on subtidal reefs. Journal of Molluscan Studies 75: 27–33.
- Thomsen, M.S., Wernberg, B., Silliman, B.R., Tuya, F. (In press). Evidence for impacts of non-indigenous macroalgae: a meta-analysis of experimental field studies. Journal of Phycology.
- Silliman, B.R., Bertness, M.D., Thomsen, M.S. (In press). Trophic cascades and climate change in southern US marshes: Will the over-harvesting of blue crabs and drought stress trigger massive die-off of southern salt marshes? In Anthropogenic Modification of North American Salt Marshes (eds. B.R. Silliman, M.D. Bertness, D. Strong). Cambridge University Press.
- Thomsen, M.S., Adam, P., Silliman, B.R. (In press). Anthropogenic threats to Australasian coastal salt marshes. In Anthropogenic Modification of North American Salt Marshes (eds. B.R. Silliman, M.D. Bertness, D. Strong). Cambridge University Press.
- Thomsen, M.S., McGlathery, K.J., Schartschild, A., Silliman, R.D. (In press). Distribution and ecological role of the non-native macroalgae Gracilaria vermiculophylla in Virginia salt marshes. Biological Invasions.
- Thomsen, M.S., Wernberg, T., Josefson, A., Silliman, B.R. (In press). Broad-scale patterns of abundance of non-indigenous soft-bottom invertebrates in Denmark. Helgoland Marine Research.
- Nyberg, C., Thomsen, M.S., Wallentinus, I. (In press). Species associated with the introduced red alga Gracilaria vermiculophylla. European Journal of Phycology.
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