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Baulch, HM, Stanley EH, Bernhardt ES.  2011.  Can algal uptake stop NO3- pollution? Nature. 477:doi:10.1038/nature10418.
Benda, LE, Poff LN, Tague C, Palmer MA, Pizzuto J, Cooper SD, Stanley E, Moglen G.  2002.  How to avoid train wrecks when using science in environmental problem solving. BioScience. 52:1127-1136.benda_et_al_bioscience_2002.pdf
Boulton, AJ, Findley S, Marmonier P, Stanley EH, Valett HM.  1998.  The functional significance of the hyporheic zone in streams and rivers. Annual Review of Ecology and Systematics. 29:59-81.boulton_et_al_ares_1998.pdf
Boulton, AJ, Stanley EH.  1996.  But the story gets bigger: subsurface invertebrates in stream ecosystems. Trends in Ecology and Evolution . 11:430.
Boulton, AJ, Stanley EH.  1995.   Hyporheic processes during flooding and drying in a Sonoran Desert stream. II. Faunal dynamics. Archiv für Hydrobiologie . 134:27-52.
Boulton, AJ, Sheldon F, Thoms MC, Stanley EH.  2000.  Problems and constraints in managing rivers with contrasting flow regimes.. Global perspectives on river conservation: science, policy, and practice.. :415-430.
Buffam, I, Turner MG, Desai AR, Hanson PC, Rusak JA, Lottig NR, Stanley EH, Carpenter SR.  2011.  Integrating aquatic and terrestrial components to construct a complete carbon budget for a north temperate lake district. Global Change Biology. 17:1193-1211.buffam_et_al_gbc_2011.pdf