Rastetter E., Vallino J..  2015.  Ecosystem's 80th and the Reemergence of Emergence. Ecosystems. 18:735-739.

Zhao L., Chen C., Vallino J., Hopkinson C., Beardsley R.C., Lin H., Lerczak J..  2010.  Wetland-estuarine-shelf interactions in the Plum Island Sound and Merrimack River in the Massachusetts coast. Journal of Geophysical Research. 115:1-13.

Deegan L.A., Bowen J.L., Drake D.C., Fleeger J.W., Friedrichs C.T., Galván K.A., Hobbie J.E., Hopkinson C., Johnson D.S., Johnson J.M. et al..  2007.  Susceptibility of salt marshes to nutrient enrichment and predator removal. Ecological Applications. 17:S-42-S63.

Claessens L., Hopkinson C., Rastetter E., Vallino J..  2006.  Effect of historical changes in land use and climate on the water budget of an urbanizing watershed. Water Resources Research. 42

Hopkinson C.S., Vallino J..  2005.  Efficient export of carbon to the deep ocean through dissolved organic matter.. Nature. 433:142-145.

Vallino J., Hopkinson C.S., Garritt R.H..  2005.  Estimating estuarine gross production, community respiration and net ecosystem production: A nonlinear inverse technique.. Ecological Modeling. 187:281-296.

Wan Z., Vallino J..  2005.  An inverse ecosystem model of year-to-year variations with first order approximation to the annual mean fluxes.. Ecological Modeling. 187:369-388.

Williams M., Hopkinson C., Rastetter E., Vallino J., Claussens L..  2005.  Relationships of land use and streamwater solute concentrations in the Ipswich River basin, northeastern Massachusetts.. Water, Air, and Soil Pollution. 161

Williams M., Hopkinson C., Rastetter E., Vallino J..  2004.  N budgets and aquatic uptake in the Ipswich River basin, northeastern Massachusetts.. Water Resources Research. 40:1-12.

Tobias C.R., Cieri M., Peterson B.J., Deegan L.A., Vallino J., Hughes J..  2003.  Processing watershed-derived nitrogen in a well-flushed New England estuary.. Limnology and Oceanography. 48:1766-1778.

Giblin A.E, Vallino J..  2003.  The Role of Models in Addressing Coastal Eutrophication Problems. The Role of Models in Ecosystems Science. :327-343.

Hopkinson C.S., Vallino J., Nolin A..  2002.  Decomposition of dissolved organic matter from the continental margin. Deep Sea Research II. 49:4461-4478.

Vallino J..  2000.  Improving marine ecosystem models: Use of data assimilation and mesocosm experiments.. Journal of Marine Research. 58:117-164.

Kirkby R., Claessens L., , Rastetter E., Vallino J..  2000.  Modeling the effects of land-use change on nitrogen biogeochemistry in the Ipswich watershed, Massachusetts. Biological Bulletin. 199:218-219.

Pontius, Jr. R.G., Claessens L., Hopkinson C., Marzouk A., Rastetter E.B., Schneider L.C., Vallino J..  2000.  Scenarios of land-use change and nitrogen release in the Ipswich watershed, Massachusetts, USA. Proceedings of the 4th International Conference on Integrating Geographic Information Systems and Environmental Modeling: Problems, prospects, and Needs for Research. 

Perring A., Williams M., C. Jr. H, Rastetter E., Vallino J..  2000.  Solute dynamics in storm flow of the Ipswich River Basin: Effects of land use.. Biological Bulletin. 199:219-221.

Pease K.M, Claessens L., Hopkinson C., Rastetter E., Vallino J., Kilham N..  1999.  Ipswich River nutrient dynamics: Preliminary assessment of a simple nitrogen-processing model. Biological Bulletin. 197:289-290.

Canfield S., Claessens L., Hopkinson C.S., Rastetter E., Vallino J..  1999.  Long-term effect of municipal water use on the water budget of the Ipswich River basin. Biological Bulletin. 197:295-297.

Vallino J., Hopkinson C.S., Garritt R., Tucker J..  1999.  A non-linear inverse technique to estimate estuarine ecosystem metabolism from whole system oxygen measurements.. Proceedings of the 3rd International Symposium on Ecohydraulics. 

Hopkinson C.S, Buffam I., Hobbie J., Vallino J., Perdue M., Eversmeyer B., Prahl F., Covert J., Hodson R., Moran M.A. et al..  1998.  Terrestrial inputs of organic matter to coastal ecosystems: An intercomparison of chemical characteristics and bioavailability. Biogeochemistry. 43:211-234.