Bakker, J.D., F. Rudebusch, and M.M. Moore. In press. Effects of long-term livestock grazing and habitat on understory vegetation. Western North American Naturalist.

Hagen, E.N., J.D. Bakker, and R.I. Gara. In press. Aerial arthropod communities of native and invaded forests, Robinson Crusoe Island, Chile. Environmental Entomology.

Kane, V.R., J.D. Bakker, R. McGaughey, J.A. Lutz, R. Gersonde, and J.F. Franklin. 2010. Examining conifer canopy structural complexity across forest ages and elevations with LiDAR data. Canadian Journal of Forest Research 40:774-787.

Kane, V.R., R.J. McGaughey, J.D. Bakker, R.F. Gersonde, J.A. Lutz, and J.F. Franklin. 2010. Comparisons between field- and LiDAR-based measures of stand structural complexity. Canadian Journal of Forest Research 40:761-773.

Davies, G.M., A.A. Smith, A.J. MacDonald, J.D. Bakker, and C.J. Legg. 2010. Fire intensity, fire severity and ecosystem response in heathlands: factors affecting the regeneration of Calluna vulgaris. Journal of Applied Ecology 47:356-365.

Dunwiddie, P.W., S.A. Hall, M.W. Ingraham, J.D. Bakker, K.S. Nelson, R. Fuller, and E. Gray. 2009. Rethinking conservation practice in light of climate change. Ecological Restoration 27(3):320-329.

Sánchez Meador, A.J., M.M. Moore, J.D. Bakker, and P.F. Parysow. 2009. 108 years of change in spatial pattern following selective harvest of a ponderosa pine stand in northern Arizona, USA. Journal of Vegetation Science 20:79-90.

Bakker, J.D. 2008. Increasing the utility of Indicator Species Analysis. Journal of Applied Ecology 45:1829-1835.

Laughlin, D.C., J.D. Bakker, M.L. Daniels, M.M. Moore, C.A. Casey, and J.D. Springer. 2008. Restoring plant species diversity and community composition in a ponderosa pine-bunchgrass ecosystem. Plant Ecology 197:139-151.

MacDougall, A.S., S.D. Wilson, and J.D. Bakker. 2008. Climate variability alters long-term community assembly. Journal of Ecology 96:346-354.

Dyer, J.H., A.J. Sánchez Meador, M.M. Moore, and J.D. Bakker. 2008. Forest structure and tree recruitment changes on a permanent historical Cinder Hills plot over a 130-year period. Pp. 156-161 in S.D. Olberding and M.M. Moore (tech. coords.). Fort Valley Experimental Forest – A Century of Research 1908-2008. Proceedings RMRS-P-55. USDA Forest Service, Rocky Mountain Research Station, Fort Collins, CO.

Bakker, J.D., M.M. Moore, and D.C. Laughlin. 2008. The Hill plots: a rare long-term vegetation study. Pp. 116-123 in S.D. Olberding and M.M. Moore (tech. coords.). Fort Valley Experimental Forest – A Century of Research 1908-2008. Proceedings RMRS-P-55. USDA Forest Service, Rocky Mountain Research Station, Fort Collins, CO.

Bakker, J.D., A.J. Sánchez Meador, P.Z. Fulé, D.W. Huffman, and M.M. Moore. 2008. "Growing trees backwards": description of a stand reconstruction model. Pp. 106-115 in S.D. Olberding and M.M. Moore (tech. coords.). Fort Valley Experimental Forest – A Century of Research 1908-2008. Proceedings RMRS-P-55. USDA Forest Service, Rocky Mountain Research Station, Fort Collins, CO.

Bakker, J.D., and M.M. Moore. 2007. Controls on vegetation structure in southwestern ponderosa pine forests, 1941 and 2004. Ecology 88:2305-2319.

Laughlin, D.C., M.M. Moore, J.D. Bakker, C.A. Casey, J.D. Springer, P.Z. Fule, and W.W. Covington. 2006. Assessing targets for the restoration of herbaceous vegetation in ponderosa pine forests. Restoration Ecology 14:548-560.

Moore, M.M., C.A. Casey, J.D. Bakker, J.D. Springer, P.Z. Fule, W.W. Covington, and D.C. Laughlin. 2006. Herbaceous vegetation responses (1992-2004) to restoration treatments in a ponderosa pine forest. Rangeland Ecology and Management 59:135-144.

Bakker, J.D. 2005. A new, proportional method for reconstructing historical tree diameters. Canadian Journal of Forest Research 35:2515-2520.

Laughlin, D.C., J.D. Bakker, and P.Z. Fule. 2005. Understorey plant community structure in lower montane and subalpine forests, Grand Canyon National Park, USA. Journal of Biogeography 32:2083-2102.

Kooistra, C.M., and J.D. Bakker. 2005. Frozen-stored conifer container stock can be outplanted without thawing. Native Plants Journal 6:267-278.

Bakker, J.D., and S.D. Wilson. 2004. Using ecological restoration to constrain biological invasion. Journal of Applied Ecology 41:1058-1064. Profiled in Botanical Electronic News, issue 340.

Laughlin, D.C., J.D. Bakker, M.T. Stoddard, M.L. Daniels, J.D. Springer, C.N. Gildar, A.M. Green, and W.W. Covington. 2004. Toward reference conditions: effects of wildfire on flora of a remote old-growth ponderosa pine forest. Forest Ecology and Management 199:137-152.

Wilson, S.D., J.D. Bakker, J.M. Christian, X. Li, L.G. Ambrose, and J. Waddington. 2004. Semiarid old-field restoration: is neighbor control needed? Ecological Applications 14:476-484.

Bakker, J.D., S.D. Wilson, J. Christian, X. Li, L. Ambrose, and J. Waddington. 2003. Contingency of prairie restoration success on year, site and competition from introduced grasses. Ecological Applications 13:137-153.

Kooistra, C.M., and J.D. Bakker. 2002. Planting frozen conifer seedlings: warming trends and effects on seedling performance. New Forests 23:225-237.

Bakker, J., and S. Wilson. 2001. Competitive abilities of introduced and native grasses. Plant Ecology 157:117-125.

Bakker, J.D., J. Christian, S.D. Wilson, and J. Waddington. 1997. Seeding blue grama in old crested wheatgrass fields in southwestern Saskatchewan. Journal of Range Management 50:156-159.