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Crump, B.C. ;Hopkinson, C.S. ;Sogin, M.L. ;Hobbie, J.H. 2004. “Microbial biogeography along an estuarine salinity gradient: the combined influences of bacterial growth and residence time.” 70: 1494-1505. doi:10.1128/AEM.70.3.1494–1505.
Filoso, S. ;Vallino, J.J ;Hopkinson, C. ;Rastetter, E. ;Claessens, L. 2004. “Modeling Nitrogen Transport in the Ipswich River Basin, Massachusetts, Using HSPF.” 40: 1365-1384.
Freeman, C.J. ;Haas, H. ;Warren, S. ;Deegan, L.A. ;Logan, J. 2004. “What makes mummichogs grow? The relationship between growth rates and gut contents of Fundulus heteroclitus held in enclosures along a salinity gradient in a New England salt marsh.”
Hopkinson, C. ;Smith, E.  Williams, P. delGiorgio and P.J.leB. 2004. “Estuarine respiration” : 122-146.
Kerry, J. ;Boorse, D. ;Buchsbaum, R. 2004. “The effect of nutrient enrichment and salinity on salt marsh invertebrates in the Plum Island Estuary.” 207: 174.
Klepac-Ceraj, V. ;Bahr, M. ;Crump, B.C. ;Teske, A.P. ;Hobbie, J.E. ;Poltz, M.F. 2004. “High overall diversity and dominance of microdiverse relationships in salt marsh sulfate-reducing bacteria.” 6: 686-698.
Lee, W. M. 2004. “Factors affecting sedimentation patterns of a tidal marsh in Plum Island Sound Estuary, Massachusetts.”
Mudd, S.M. ;Fagherazzi, S. ;Morris, J.T. ;Furbish, D.J.  Blum, L.K. 2004. “Flow, sedimentation, and biomass production on a vegetated salt marsh in South Carolina: toward a predictive model of marsh morphologic and ecologic evolution.” : 165-187.
Nielsen, J.L. ;Schramm, A. ;Bernhard, A.E. ;EnghG.J., van den ;Stahl, D.A. 2004. “Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries” 70: 7550-7554.
Pellerin, B.A. ;Wollheim, W. ;Hopkinson, C. ;McDowell, W. ;Williams, M. ;Vorosmarty, C. ;Daley, M. 2004. “Role of wetlands and developed land use on dissolved organic nitrogen concentrations and DON / TDN in northeastern U.S. rivers and streams.” 49: 910-918.
Pellerin, B. A. 2004. “The influence of urbanization on runoff generation and stream chemistry in Massachusetts watersheds.”
Pontius Jr., R.G. ;Huffaker, D. ;Denman, K. 2004. “Useful techniques of validation for spatially explicit land-change models.” 179: 445-461.
Raymond, P.A. ;Bauer, J.E. ;Caraco, N.F. ;Cole, J.J. ;Longworth, B. ;Petsch, S.T. 2004. “Controls on the variability of organic matter and dissolved inorganic carbon age in northeast U.S. rivers.” 92: 353-366.
Salgado, J. ;Costa, M-J. ;Cabral, H. ;Deegan, L. 2004. “Comparison of fish assemblages in tidal salt marsh creeks and in adjoining mudflat areas in the Tejo estuary.” 45 (3): 213-224.
Salgado, J. ;Costa, M-J. ;Cabral, H. ;Deegan, L. 2004. “Nekton use of salt marsh creeks in the upper Tejo Estuary.” 27 (5): 818-825.
Versluis, A.J. ;Pontius Jr., R.G. ;Malizia, N.R. 2004. “Visualizing the rate at which the accuracy of a land change prediction decays.”
Williams, M. ;Hopkinson, C. ;Rastetter, E. ;Vallino, J. 2004. “N budgets and aquatic uptake in the Ipswich River basin, northeastern Massachusetts.” 40 (11): 1-12.
Pontius, R.G., Jr. ;Li, X. 2008. “Estimating the land transition matrix based on erroneous maps.”
Green, P.A. ;Vorosmarty, C.J. ;Meybeck, M. ;Galloway, J.N. ;Peterson, B.J. ;Boyer, E.W. 2003. “Pre-industrial and contemporary fluxes of nitrogen through rivers: A global assessment based on typology” 68: 1-35.
Hobbie, J. ;Carpenter, S. ;Grimm, N. ;Gosz, J. ;Seastedt, T. 2003. “The United States Long Term Ecological Research program.” 53: 21-32.