Kennedy C.G., Mather M.E., Smith J.M., Finn J.T., Deegan L.A..  2016.  Discontinuities concentrate mobile predators: Quantifying organism-environment interactions at a seascape scale. Ecosphere. 7

Smith J.M., Mather M.E..  2013.  Beaver dams maintain native fish biodiversity by increasing habitat heterogeneity throughout a low-gradient stream network.. Freshwater Biology. 58:1523-1538.

Smith J.M., Wells S.P., Mather M.E., Muth R.M..  2013.  Fish biodiversity sampling in stream ecosystems: a process for evaluating the appropriate types and amount of gear.. Aquatic Conservation: Marine and Freshwater Ecosystems. 

Mather M.E., Finn J.T., Kennedy C.G., Deegan L.A., Smith J.M..  2013.  What happens in an estuary doesn?t stay there: patterns of biotic connectivity resulting from long term ecological research. . Oceanography. 26:168-179.

Mather M.E., Frank H.J., Smith J.M., Cormier R.D., Muth R.M., Finn J.T..  2012.  Assessing freshwater habitat of adult anadromous alewives at multiple scales: a common challenge for fish and watershed restoration. . Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science. 4:188-200.

Dodds W.K., Robinson C.T., Gaiser E.E., Hansen G.J.A., Powell H., Smith J.M., Morse N.B., Johnson S., Gregory S.V., Bell T. et al..  2012.  Surprises and insights from long term aquatic datasets and experiments.. Bioscience. 62:709-721.

Smith J.M..  2011.  Beaver dams maintain native fish biodiversity via altered habitat heterogeneity in a coastal stream network: evaluating gear, quantifying fish assemblages, and testing ecological hypotheses with empirical data.. Ph.D.

Smith J.M., Mather M.E..  2011.  Using assemblage data in ecological indicators: a comparison and evaluation of commonly available statistical tools. Ecological Indicators. 13:253-262.

Frank H.J., Mather M.E., Muth R.M., Pautzke S.M., Smith J.M., Finn J.T..  2009.  The Adopt-a-Herring Program as a Fisheries Conservation Tool. Fisheries. 34:496-507.

Frank H., Mather M.E., Muth R.M., Pautzke S.M., Smith J.M., Finn J.T., McCormick S.D..  2009.  What is 'fallback': metrics needed to assess telemetry tag effects on anadromous fish behaviour. Hydrobiologia. 35:237-249.