Rogers, David A. 2011. Fifty years of change in southern Wisconsin forests: patterns of species loss and homogenization. Ph.D. dissertation.
Klionsky, S., K. Amatangelo, and D.M. Waller. 2011. Above- and below-ground impacts of European buckthorn (Rhamnus cathartica L.) on four native forbs. Restoration Ecology. doi: 10.1111/j.1526-100X.2010.00727.x
Amatangelo, K.L, M.R. Fulton, D.A. Rogers, and D.M. Waller. 2010. Convergence in forest community composition along an edaphic gradient threatens landscape-level diversity. Diversity and Distributions 17: 201–213.
Mudrak, E.L., S.E. Johnson, and D.M. Waller. 2009. Forty-seven year changes in vegetation at the Apostle Islands: Effects of deer on the forest understory In press, Nat. Areas J.
Rogers, D.A., T.P. Rooney, T. Hawbaker, V. Radeloff, and D.M. Waller. 2009. Paying the extinction debt: The increasing influence of patch size and landscape factors on vegetation community composition and dynamics in southern Wisconsin upland forests. In press, Conservation Biology.
Mills, J. 2008. Fifty years of change in wisconsin cedar glades. American Midland Naturalist, 159(1), 214-224.
Rogers, D. A., T. P. Rooney, D. Olson, and D. M. Waller. 2008. Shifts in southern Wisconsin forest canopy and understory richness, composition , and heterogeneity. Ecology 89(9). 2482-2492.
Rooney, T. P. 2008. Comparison of co-occurrence structure of temperate forest herb-layer communities in 1949 and 2000. Acta Oecologica.
Kraszewski, S. E. and D. M. Waller. 2008. Fifty-five year changes in species composition on dry prairie remnants in south-central Wisconsin. Journal of the Torrey Botanical Society 135(2), 235-243.
Johnson, S. E., E. L. Mudrak, E. A. Beever, S. Sanders and D. M. Waller. 2008. Comparing power among three sampling methods for monitoring forest vegetation. Canadian Journal of Forest Research. 38: 143-156.
Mills, J.E. 2008. Fifty Years of Change in Wisconsin Cedar Glades. American Midland Naturalist. 159: 214-224.
Hale, B., E. M. Alsum & M. Adams. 2008. Changes in the Floodplain Forest Vegetation of the Lower Wisconsin River over the Last Fifty Years. American Midland Naturalist. 160: 454-476.
Milbauer, M. L. and M. K. Leach. 2007. Influence of species pool, fire history, and woody canopy on plant species density and composition in tallgrass prairie. Journal of the Torrey Botanical Society. 134: 53-62
Olden, J.D. and T.P. Rooney. 2006. On defining and quantifying biotic homogenization. Global Ecology and Biogeography. 15: 113-120.
Waller, D.M. 2006. Re-Visioning Conservation. Conservation Biology. 20: 587-588.
Weigmann, S.M. and D.M. Waller. 2006. Fifty years of change in in northern upland forest understories: Identity and traits of "winners" and "loser" plant species. Biological Conservation. 129:109-123.
Waller, D.M. 2005. Tracking plant diversity across forest landscapes: Indicators and drivers. Invited paper, UNESCO conference Biodiversity-Science and Governance, Paris, Jan. 2005.