Jones, J.A., Creed, I.F., Hatcher, K.L., and others. 2012. Ecosystem Processes and Human Influences Regulate Streamflow Response to Climate Change at Long-Term Ecological Research Sites. BioScience, 62, 390-404.
Rice, J.M., C.B. Halpern, J.A. Antos, J.A. Jones. 2012. Spatio-temporal patterns of establishment are indicative of biotic interactions during early tree invasion of a montane meadow. Plant Ecology. DOI 10.1007/s11258-012-0021.
Creed, I.F., G.Z. Sass, J.M. Buttle, J.A. Jones. 2011. Hydrological principles for sustainable management of forest ecosystems. Hydrological Processes, 10.1002/hyp.8056.
Jones, J.A., 2011. Hydrologic responses to climate change: considering geographic context and alternative hypotheses. Hydrological Processes, 10.1002/hyp.8004.
Yu, J, W-K. Wong, T. Dietterich, J.A. Jones, M. Betts, S. Frey, S. Shirley, J. Miller, M. White. 2011. Multi-label Classification for Multi-Species Distribution Modeling. Proceedings of the 28th International Conference on Machine Learning, Bellevue, WA, USA, 2011.
Moore, G.W., J.A. Jones, and B.J. Bond. 2011. How soil moisture mediates the influence of transpiration on streamflow at hourly to interannual scales in a forested catchment. Hydrological Processes, 10.1002/hyp.8095.
Jones, J.A., and R.M. Perkins, 2010. Extreme flood sensitivity to snow and forest harvest, western Cascades, Oregon, United States. Water Resour. Res., 46, W12512, doi:10.1029/2009WR008632.
Pallister, J.S., J.J. Major, T.C. Pierson, R.P. Hoblitt, J.B. Lowenstern, J.C. Eichelberger, L. Lara, H. Moreno, J. Muñoz, J.M. Castro, A. Iroumé, A. Andreoli, J. Jones, F. Swanson, C. Crisafulli. 2010. Interdisciplinary Studies of Eruption at Chaitén Volcano, Chile. EOS, 91(42)381-392. Supplement.
Jones, J.A., G.L. Achterman, L.A. Augustine, I.F. Creed, P.F Folliott, L. MacDonald, and B.C. Wemple. 2009. Hydrologic effects of a changing forested landscape--challenges for the hydrological sciences. Hydrological Processes, 23, 2699-2704.
National Research Council (J. Jones, vice-chair). 2008. Hydrologic Effects of a Changing Forest Landscape. Committee on Hydrologic Impacts of Forest Management, Water Science and Technology Board, Division on Earth and Life Studies (2008, 00 pp.; ISBN 0-309-12104-3).
Perkins, R.M. and J.A. Jones. 2008. Climate variability, snow and physiographic controls on storm hydrographs in small forested basins, western Cascades, Oregon. Hydrological Processes. 22, 4949-4964.
Czarnomski, N.M., D.M. Dreher, K.U. Snyder, J.A. Jones and F.J. Swanson. 2008. Landscape-scale dynamics of wood in stream networks of the western Cascades, Oregon. Canadian Journal of Forest Research. 38: 2236-2248.
Muhs, D.R., J. Budahn, D.L. Johnson, M. Reheis, J. Beann, G. Skipp, E. Fisher and J.A. Jones. 2008. Geochemical evidence for airborne dust additions to soils in Channel Islands National Park, California, U.S.A. GSA Bulletin, v. 120; no. 1/2; p. 106-126; doi: 10-1130/B26218.1.
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.