Jones, J.A. 2007. Does an Earth system perspective provide fundamental insights into ecology? Book review, Transactions in Ecology and Evolution, 22,6, 288-289.

Watterson, N. and J.A. Jones. 2006. Flood and debris flow interactions with roads promote the invasion of exotic plants along steep mountain streams, western Oregon.  Geomorphology 78, 107 ­ 123

J.A. Jones and D.A. Post. 2004. Seasonal and successional streamflow response to forest cutting and regrowth in the northwest and eastern United States. Water Resources Research, 40, W05203, doi:10.1029/2003WR002952.

G.W.Moore, B.J. Bond, J.A. Jones, N.Phillips, and F.C. Meinzer. 2004. Structural and compositional controls on transpiration in a 40- and 450-yr-old riparian forest in western Oregon, USA. Tree Physiology 24: 481-491.

D. Greenland, F. Bierlmaier, M. Harmon, J. Jones, A. McKee, J. Means, F. Swanson, C. Whitlock. Pp. 393-410 in Greenland, D., D.G. Goodin, and R.C. Smith, eds. 2003. Climate variability and ecosystem response at the H. J. Andrews Long-Term Ecological Research site. In Climate variability and ecosystem response at long-term ecological research sites. Oxford, New York.

B.C. Wemple and J.A. Jones. 2003. Runoff production on forest roads in a steep, mountain catchment. Water Resources Research 39, doi:10.1029/2002WR001744.

J. Faustini and J.A. Jones. 2003. Influence of large woody debris on channel morphology and dynamics in steep, boulder-rich mountain streams, western Cascades, Oregon. Geomorphology 51(1-3): 187 - 205.

T.A. Spies, D.E. Hibbs, J.A. Ohmann, G.H. Reeves, R.J. Pabst, F.J. Swanson, C. Whitlock, J.A. Jones, B.C. Wemple, L.A. Parendes, and B. Schrader. pp. 31-67 in S.D. Hobbs, J.P. Hayes, R.L. Johnson, G.H. Reeves, T.A. Spies, J.C. Tappeiner, and G.E. Wells, eds. 2003 . The ecological basis of forest ecosystem management in the Oregon Coast Range. Forest and stream management in the Oregon Coast Range, Oregon State University Press, Corvallis.

Forman, R.T.T., D. Sperling, J.A. Bissonette, A.P. Clevenger, C.D. Cutshall, V.H. Dale, L. Fahrig, R. France, C.R. Goldman, K. Heanue, J.A. Jones, F.J. Swanson, T. Turrentine, and T.C. Winter. 2003 .Road ecology: science and solutions. Island Press, Washington, DC.

Aaron Arthur, MS, 2007, Thirty-five years of forest succession in southwest Oregon: Vegetation response to three distinct logging treatments

Barbara Geren, MS 2006, Predicting sediment delivery from small catchments in the western Cascades of Oregon using the disturbed WEPP model

Samantha Sheehy, MS 2006, Exotic Plant Species Dynamics from 1994 to 2005 on Road Networks in Forested Landscapes of Western Oregon.

Sam Littlefield, MS 2005, Patterns of Chronic Wind Mortality in a Small, Old-growth Pseudotsuga menziesii Forest in the Western Cascades, Oregon

Michele Punke, PhD 2005, Paleoenvironmental Reconstruction of an Active Margin Coast from the Pleistocene to the Present: Examples from Southwestern Oregon

Lisa Vannatta, MS 2005, Forest Harvest Patterns on Private Land in Western Oregon from 1972 to 2002

Danielle Robbins, MS Forest Resources, Temporal and Spatial Variability of Historic Fire Frequency in the Southern Willamette Valley Foothills of Oregon.

Sheryl Giglia, MS, 2004, "Spatial and Temporal Patterns of "Super-old" Douglas-fir Trees of the Central Western Cascades, Oregon"

Nicholas Watterson MS, 2004. Exotic plant invasion from roads to stream networks in steep forested landscapes of western Oregon.

Georgianne Moore, PhD, 2003. Drivers of Variability in Transpiration and Implications for Stream Flow in Forests of Western Oregon.

Nicole Czarnomski MS, 2003. Effects of Harvest and Roads on In-stream Wood Abundance in the Blue River Basin, Western Cascades, Oregon.

Deana Pennington, PhD, 2002. Structural and Functional Comparison of Human-Impacted and Natural Forest Landscapes in the Western Cascades of Oregon.

IGERT: Ecosystem Informatics (J.A. Jones, PI; B. D’Ambrosio, T. Dietterich, M. Harmon, and E. Waymire, co-PIs). 10/03-9/08. $3,900,000.

Long-term ecological research at the H.J. Andrews Experimental Forest LTER: LTER5 (M. Harmon, PI; B.J. Bond, S.L. Johnson, J.A. Jones, F.J. Swanson, co-PIs). 12/02-11/08. $4,200,000.

A spatially-distributed GIS-based model of temperatures in a stream network. (Jones and S.L. Johnson, co-PIs). National Science Foundation, Geography and Regional Sciences. 9/99-8/02. $130,000.

Long-term Ecological Research at the H.J. Andrews Experimental Forest: LTER4. (co-PI). National Science Foundation, Division of Environmental Biology. 10/96-9/'02. $3,200,000. Jones manages portion for hydrology and small watershed synthesis, $40,000/yr.