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  • Yvon-Durocher, G., J. M. Caffrey, A. Cescatti, M. Dossena, P. del Giorgio, J.M. Gasol, J.M. Montoya, J. Pumpanen, P.A. Staehr, M. Trimmer, G. Woodward & A.P. Allen. Reconciling differences in the temperature-dependence of ecosystem respiration across time scales and ecosystem types. accepted Nature
  • Mortazavi, B., A.A. Riggs, J.M. Caffrey, H. Genet, and S.W. Phipps. 2012. The contribution of benthic nutrient regeneration to primary production in a shallow eutrophic estuary, Weeks Bay, Alabama. Estuaries and Coasts. 35:862-877.
  • Bagui, S., J. Brown, J. Caffrey, S. Bagui. Designing a relational database for tracking and analysis of atmospheric deposition of mercury and trace metals in the Pensacola Bay Watershed. accepted to Computers and Geosciences
  • Caffrey, J.M., W.M. Landing, S.D. Nolek, K.J. Gosnell, S.S Bagui, and S.C. Bagui. 2010 Atmospheric deposition of mercury and major ions to the Pensacola (Florida) watershed: spatial, seasonal, and inter-annual variability. Atmospheric Chemistry and Physics 10:1-24
  • Landing, W.M., J.M. Caffrey, S.D. Nolek, K.J. Gosnell and W.C. Parker. 2010 Atmospheric deposition of mercury and other trace elements in Pensacola, Florida. Atmospheric Chemistry and Physics 10:4867-4877.
  • Caffrey, J.M., N. Bano, J.T. Hollibaugh and J. Haskins. 2010 The effect of upwellling on short-term variability in sediment biogeochemistry in Elkhorn Slough, CA. In Aquatic Microbial Ecology. 58: 261-271
  • Murrell, M.C., J. Campbell, J.E Hagy, and J.M. Caffrey. 2009 Effects of irradiance on benthic and water column processes in a Gulf of Mexico estuary: Pensacola Bay, Florida, USA. Estuarine Coastal and Shelf Science. 81:501-512
  • Smith, K.A. and J.M. Caffrey.2009 The effects of human activities and extreme meterological events on sediment nitrogen dynamics in an urban estuary, Escambia Bay, Florida, USA. Hydrobiologia.
  • Caffrey, J.M., N. Bano, K. Kalanetra and J. T. Hollibaugh. 2007. Environmental factors controlling ammonia-oxidation by ammonia oxidizing Bacteria and Archaea. ISME Journal 1:660-662.
  • Caffrey, J.M., T.P. Chapin, H.W. Jannasch, and J.C. Haskins. 2007. High nutrient pulses, tidal mixing and biological response in a small California estuary, Elkhorn Slough, CA, USA: variability in nutrient concentrations from hourly to decadal time scales. Estuarine, Coastal and Shelf Science 71:368-380
  • Caffrey, J.M., M.C. Murrell, C. Wigand and R. McKinney. 2007. Effect of nutrient loading on biogeochemical and microbial processes in a New England high salt marsh. Biogeochemistry 82:251-264.
  • DiDonato G.T., E.M. Lores, M.C. Murrell, L.M. Smith, and J.M. Caffrey. 2006. Benthic nutrient flux in a small estuary in northwestern Florida (USA). Gulf and Caribbean Research.
  • Murrell, M.C. and J.M. Caffrey. 2005. High cyanobacterial abundance in three Gulf of Mexico estuaries. Gulf and Caribbean Research. 17:95-106.
  • Chapin, T.P., J.M. Caffrey, H.W. Jannasch, L. Coletti, J.C. Haskins and K. Johnson. 2004. Nitrate sources and sinks in Elkhorn Slough, CA: results from continuous in situ nitrate analyzers. Estuaries 27:882-894
  • Caffrey, J.M. 2004 Factors controlling net ecosystem metabolism in U.S. estuaries. Estuaries 27: 90-101
  • Caffrey, J.M. 2003. Production, Respiration and Net Ecosystem Metabolism in U.S. Estuaries. Environmental Monitoring and Assessment. 81: 207-219.
  • Caffrey, J.M., N.E. Harrington, I. Solem, and B.B. Ward. 2003. Biogeochemical Processes in a Small California Estuary: 2. Nitrification Activity, Community Structure and Role in Nitrogen Budgets. Marine Ecology Progress Series. 248: 27-40.
  • Caffrey, J.M., N.E. Harrington, and B.B. Ward. 2002. Biogeochemical Processes in a Small California Estuary: 1. Benthic Fluxes and Pore Water Constituents Reflect High Nutrient Freshwater Inputs. Marine Ecology Progress Series. 233:39-53.
  • Caffrey, J.M., M. Brown, B. Tyler, M. Silberstein (eds.) 2002. Changes in a California Estuary: an Ecosystem Profile of Elkhorn Slough. Elkhorn Slough Foundation. Moss Landing, CA.
  • Mortazavi B., R.L. Iverson, W. Huang, F.G. Lewis, J.M. Caffrey. 2000. Nitrogen Budget of Apalachicola Bay, a Bar-built Estuary in the Northeastern Gulf of Mexico. Marine Ecology Progress Series. 195:1-14.