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.