PIE LTER Publications
Acinas, S. G., K. Klepac-Ceraj, D. E. Hunt, C. Pharino, C. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554  
Agnew, A. M., D. H. Shull, and R. N. Buchsbaum. 2003. Growth of a salt marsh invertebrate on several species of marsh grass detritus. Biological Bulletin 205:238-239  
Agrawal, A. 2001. Uncertainty analysis of land-use change modeling in GIS. MS Thesis. Clark University, Worcester.
Aldrich, S. 2002. Water quality as a function of land use. Honors, BS Thesis. Clark University, Worcester.
Aldwaik, S., and R. G. Pontius Jr. In review. Intensity Analysis to Unify Measurements of Size and Stationarity of Land Changes by Interval, Category, and Transition. Landscape and Urban Planning  
Alexander, R. B., J. F. Bohlke, E. W. Boyer, M. David, J. W. Harvey, P. J. Mulholland, S. P. Seitzinger, C. R. Tobias, C. Tonitto, and W. M. Wollheim. 2009. Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes. Biogeochemistry 93:91-116  DOI 10.1007/s10533-008-9274-8.
Allee, R. J., M. Dethier, D. Brown, L. Deegan, R. G. Ford, T. F. Hourigan, J. Maragos, C. Schoch, K. Sealey, R. Twilley, M. P. Weinstein, and M. Yoklavich. 2000. Marine and Estuarine Ecosystem and Habitat Classification. NOAA Technical Memorandum NMFS-FSPO-43, US Department of Commerce, National Oceanic and Atmospheric Administration, National marine Fisheries Service.
Alpern, J. 2010. How to tell when map difference indicates land change. M.S. Thesis. Clark University, Worcester, MA.
Bahr, M., B. C. Crump, V. Klepac-Ceraj, A. P. Teske, M. L. Sogin, and J. E. Hobbie. 2005. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environmental Microbiology 7:1175-1185  10.1111/j.1462-2920.2005.00796.x.
Bain, D., M. B. Green, J. Campbell, J. Chamblee, J. Fraterrigo, S. S. Kaushal, S. Martin, T. Jordan, A. Parolari, W. V. Sobczak, D. E. Weller, W. M. Wollheim, E. Boose, J. Duncan, G. Gettel, B. Hall, P. Kumar, J. Thompson, J. Vose, E. Elliott, and D. Leigh. In press. Legacies in material flux: structural catchment changes pre-date long-term studies. Bioscience  
Battin, T. J., L. Kaplan, S. Findlay, C. Hopkinson, E. Marti, A. Packman, J. D. Newbold, and F. Sabater. 2008. Biophysical controls on organic carbon fluxes in fluvial networks. Nature Geoscience 1:95-100  doi: 10.1038/ngeo101.
Beaulieu, J. J., J. L. Tank, S. K. Hamilton, W. Wollheim, R. Hall, P. Mulholland, B. Peterson, L. Ashkenas, L. Cooper, C. Dahm, W. Dodds, N. Grimm, S. Johnson, W. McDowell, G. Poole, H. Valett, C. Arango, M. Bernot, A. Burgin, C. Crenshaw, A. Helton, L. Johnson, J. O'Brien, J. Potter, D. Sheibley, D. Sobota, and S. Thomas. 2011. Nitrous oxide emission from denitrification in stream and river networks. Proceedings of the National Academy of Science 108:214-219  doi: 210.1073/pnas.1011464108.
Bernhard, A., T. M. Donn, A. E. Giblin, and D. A. Stahl. 2005. Loss of Diversity of Ammonia-Oxidizing Bacteria Correlates with Increasing Salinity in an Estuary System. Environmental Microbiology 7:1289-1297  10.1111/j.1462-2920.2005.00808.x.
Bernhard, A., Z. C. Landry, A. Blevins, J. R. de al Torre, A. E. Giblin, and D. A. Stahl. 2010. Abundance of ammonia-oxidizing Archaea and Bacteria along an estuarine salinity gradient in relationship to potential nitrification rates. Applied and Environmental Microbiology 76:1285-1289  doi:10.1128/AEM.02018-09.
Bernhard, A. E., J. Tucker, A. E. Giblin, and D. A. Stahl. 2007. Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient. Environmental Microbiology 9:1439-1447  10.1111/j.1462-2920.2007.01260.x.
Bernot, M. J., R. J. Bernot, and J. T. Morris. 2009. Nutrient cycling relative to δ15N and δ13C natural abundance in a coastal wetland with long-term nutrient additions. Aquatic Ecology  doi:10.1007/s10452-008-9221-8.
Blanchard, S. 2010. Implications of using fine versus coarse spatial resolution data in LUCCThesis. Clark University, Worcester, MA.
Bouillon, S., and H. T. S. Boschker. 2006. Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers. Biogeosciences 3:175-185  
Bowen, J. L., B. C. Crump, L. A. Deegan, and J. E. Hobbie. 2009. Increased supply of ambient nitrogen has minimal effect on salt marsh bacterial production. Limnology and Oceanography 54:713 - 722  
Bowen, J. L., B. C. Crump, L. A. Deegan, and J. E. Hobbie. 2009. Salt marsh sediment bacteria: their distribution and response to external nutrient inputs. The ISME Journal 3:924 - 934  doi:10.1038/ismej.2009.44.
Bowen, J. L., B. B. Ward, H. G. Morrison, J. E. Hobbie, I. Valiela, L. A. Deegan, and M. L. Sogin. 2011. Microbial community composition in salt marsh sediments resists perturbation by nutrient enrichment. The ISME Journal 5:1540-1548  doi:10.1038/ismej.2011.22.
Briggs, M. A., M. N. Gooseff, C. D. Arp, and M. A. Baker. 2009. A method for estimating surface transient storage parameters for streams with concurrent hyporheic storage. Water Resources Research 45  doi:10.1029/2008WR006959.
Briggs, M. A., M. N. Gooseff, B. J. Peterson, K. Morkeski, W. M. Wollheim, and C. S. Hopkinson. 2010. Surface and hyporheic transient storage dynamics throughout a coastal stream network. Water Resources Research 46  doi: 06510.01029/02009WR008222.
Broo, S. 2009. Sensitivity Analysis for Scenarios of Water Withdrawal in Massachusetts. MS Thesis. Clark University, Worcester, MA.
Buchsbaum, R. 2000. A Symposium Report: Marine Monitoring in Massachusetts - Water quality monitoring and related activities at Plum Island Sound. Massachusetts Office of Coastal Zone Managment, Boston, MA.
Buchsbaum, R. 2009. Striped bass: the coastal connection. pp 9-11. In Sanctuary.
Buchsbaum, R., E. H. Catena, and M. J. James-Pirri. 2006. Changes in salt marsh vegetation, Phragmites australis, and nekton in response to increased tidal flushing in a New England salt marsh. Wetlands 26:544-557  
Buchsbaum, R., A. Cooper, and J. LeBlanc. 1998. The Plum Island Sound/River ecosystem: Current status and future management. Plum Island Sound Minibay Project, Massachusetts Bays Program.
Buchsbaum, R., A. Cooper, and J. LeBlanc. 1999. Conserving the Plum Island Sound/Rivers Ecosystem - A research report and management plan. Produced for the Massachusetts Bays Program and the Towns of Ipswich, Rowley and Newbury by Massachusetts Audubon: North Shore Conservation Advocacy.
Buchsbaum, R., L. Deegan, and R. Garritt. 2002. Changes in the fish comunity of Plum Island Sound from 1965 through 1994. In: In: The marine resources of the Parker River-Plum Island Sound estuary: An update after 30 years.  R. Buchsbaum, T. Purinton, and B. e. Magnusson (eds.),  pp MCZM publications.
Buchsbaum, R., and J. C. Powell. 2008. Symposium Review: Long term shifts in faunal assemblages in North American estuaries: A review of a workshop held at the biennial meeting of the Coastal and Estuarine Research Federation (CERF), November 2007, Providence, Rhode Island. Reviews in Fisheries Biology and Fisheries 18:447-450  DOI 10.1007/s11160-008-9086-x.
Buchsbaum, R., T. Purinton, and B. Magnusson. 2002. The marine resources of the Parker River-Plum Island Sound estuary: An update after 30 years. Massachusetts Office of Coastal Zone Management, Massachusetts Executive Office of Environmental Affairs, Boston, MA.
Buchsbaum, R. N., L. A. Deegan, J. Horowitz, R. H. Garritt, J. P. Ludlam, and D. H. Shull. 2009. Effects of regular salt marsh haying on marsh plants, algae, invertebrates and birds at Plum Island Sound, Massachusetts. Wetlands Ecology and Management 17:469-487  DOI 10.1007/s11273-008-9125-3.
Buchsbaum, R. N., and C. A. Wigand. In press. Chapter 14: Adaptive management and monitoring as fundamental tools to effective salt marsh restoration. In: Restoring Tidal Flow to Salt Marshes: A Synthesis of Science and Management in New England (USA).  C. Roman and D. Burdick (eds.),  pp Island Press.
Burak, M. 2011. Developing standardized metrics to quantify the temporal distribution of migrating anadromous herring: comparing adult returns across coastal rivers. M.S. Thesis. University of Massachusetts, Amherst.
Burak, M., M. E. Mather, J. T. Finn, J. B. Kim, and R. M. Muth. In review. How standardized metrics that quantify the temporal distribution of migrating anadromous herring can facilitate comparisons of adult returns across coastal rivers.   
Burdick, D., R. Buchsbaum, and E. Holt. 2001. Variation in soil salinity associated with the expansion of Phragmites australis in salt marshes. Environmental and Experimental Botany 46:247-261  
Burgess, P. 1999. Conservation and development in conflict. MS Thesis. Clark University.
Canfield, S., L. Claessens, C. S. Hopkinson, E. Rastetter, and J. Vallino. 1999. Long-term effect of municipal water use on the water budget of the Ipswich River basin. Biological Bulletin 197:295-297  
Cavatorta, J., M. Johnston, C. S. Hopkinson, and V. Valentine. 2003. Patterns of sedimentation in a salt marsh-dominated estuary. Biological Bulletin 205:239-241  
Charles, H. 2007. Effects of Warming and Altered Precipitation on Plant and Nutrient Dynamics of a New England Salt Marsh. MS Thesis. University of Massachusetts, Boston, MA.
Chaudhury, R. 2011. Developing web-based "Interval, Category, and Transition Application". M.A. Thesis. Clark University, Worcester, MA.
Chen, H., and R. G. Pontius Jr. 2010. Diagnostic tools to evaluate a spatial land change projection along a gradient of an explanatory variable. Landscape Ecology 25:1319-1331  
Chen, H., and R. G. Pontius Jr. 2011. Sensitivity of a land change model to pixel resolution and precision of the independent variable. Environmental Modeling & Assessment 16:37-52  
Chowdhury, R., K. Larson, M. Grove, C. Polsky, E. Cook, J. Onsted, and L. Ogden. 2011. A Multi-Scalar Approach to Theorizing Socio-Ecological Dynamics of Urban Residential Landscapes. Cities and the Environment 4  
Claessens, L., C. Hopkinson, E. Rastetter, and J. Vallino. 2006. Effect of historical changes in land use and climate on the water budget of an urbanizing watershed. Water Resources Research 42  doi:10.1029/2005WR004131.
Clement, J., R. M. Holmes, B. J. Peterson, and G. Pinlay. 2004. Isotopic investigation of nitrogen retention in a riparian ecosystem. Journal of Applied Ecology 40:1035-1048  
Crump, B. C., and J. E. Hobbie. 2005. Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnology and Oceanography 50:1718-1729  
Crump, B. C., C. S. Hopkinson, M. L. Sogin, and J. H. Hobbie. 2004. Microbial biogeography along an estuarine salinity gradient: the combined influences of bacterial growth and residence time. Applied and Environmental Microbiology 70:1494-1505  DOI: 10.1128/AEM.70.3.1494–1505.2004.
Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. T. Roman. 2011. Use of computed tomography imaging for quantifying coarse roots, rhizomes, peat, and particle densities in marsh soils. Ecological Applications 21:2156-2171  
Day, J. W., R. R. Christian, D. M. Boesch, A. Yáñez-Arancibia, J. T. Morris, R. R. Twilley, L. Naylor, L. Schaffner, and C. Stevenson. 2008. Consequences of climate change on the ecogeomorphology of coastal wetlands. Estuaries and Coasts 31:477-491  DOI 10.1007/s12237-008-9047-6.
Deegan, L., L. A. Wright, J. Hughes, and E. Boynton. 1999. Establishing the Food Web Links between Estuaries and Nearshore Fisheries of New England. Final Report NA 76 FD 0106, NOAA.
Deegan, L. A. 2002. Lessons learned: the effects of nutrient enrichment on the support of nekton by seagrass and saltmarsh ecosystems. Estuaries 25:585-600  
Deegan, L. A. In prep. Trouble on the edge: plant lodging, creek cracks, toupee effects, etc.   
Deegan, L. A., J. L. Bowen, D. C. Drake, J. W. Fleeger, C. T. Friedrichs, K. A. Galvan, J. E. Hobbie, C. Hopkinson, D. S. Johnson, J. M. Johnson, L. E. LeMay, E. E. Miller, B. J. Peterson, C. Picard, S. Sheldon, M. Sutherland, J. Vallino, and R. S. Warren. 2007. Susceptibility of salt marshes to nutrient enrichment and predator removal. Ecological Applications 17:S-42-S63  
Deegan, L. A., and R. Buchsbaum. 2005. The effect of habitat loss and degradation on fisheries. In: The Decline of Fisheries Resources in New England: Evaluating the Impact of Overfishing, Contamination, and Habitat Degradation.  R. Buchsbaum, J. Pederson, and W. E. Robinson (eds.),  pp 67-96. University of Massachusetts Press.
Deegan, L. A., and C. o. E. E. o. Fishing. 2002. Effects of trawling and dredging on seafloor habitat. In: (eds.),  pp 107 pp. Washington, DC, National Academy Press.
Deegan, L. A., J. E. Hughes, and R. A. Rountree. 2000. Salt marsh ecosystem support of marine transient species. In: Concepts and Controversies in Tidal Marsh Ecology.  M. Weinstein and J. Kreeger (eds.),  pp 333-365. Kluwer Academic Publisher, The Netherlands.
Deegan, L. A., J. Kremer, T. Webler, and J. Brawley. 2001. The use of models in integrated resource management in the coastal zone. In: Science and Integrated Coastal Management.  B. V. Bodungen and R. K. Turner (eds.),  pp Berlin, Dahlem University Press.
Dodds, W. K., C. T. Robinson, E. E. Gaiser, G. J. A. Hansen, H. Powell, J. M. Smith, N. B. Morse, S. Johnson, S. V. Gregory, T. Bell, T. K. Kratz, and W. H. McDowell. In review. Surprises and insights from long term aquatic datasets and experiments.   
Drake, D. C., B. J. Peterson, L. A. Deegan, L. A. Harris, E. E. Miller, and R. S. Warren. 2008. Plant nitrogen dynamics in fertilized and natural New England saltmarshes: a paired 15N tracer study. Marine Ecology Progress Series 354:35-46  doi: 10.3354/meps07170.
Drake, D. C., B. J. Peterson, K. A. Galván, L. A. Deegan, J. W. Fleeger, C. Hopkinson, J. M. Johnson, K. Koop-Jakobsen, L. E. Lemay, E. E. Miller, C. Picard, and R. S. Warren. 2009. Salt marsh ecosystem biogeochemical responses to nutrient enrichment: A paired 15N tracer study. Ecology 90:2535-2546  
Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castor, C. Cronan, C. Goodale, P. Groffman, K. Lambert, G. Lawrence, C. Hopkinson, and S. Ollinger. 2002. Nitrogen Pollution: From sources to the sea. Science Links - Hubbard Brook Research Foundation, Hanover, NH.
Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castro, C. Cronan, C. Goodale, P. Groffman, C. Hopkinson, K. Lambert, G. Lawrence, and S. Ollinger. 2003. Nitrogen pollution in the northeastern United States: Sources, effects and managment options. BioSciences 53:357-374  
Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castro, C. Cronan, C. Goodale, P. Groffman, C. Hopkinson, K. Lambert, G. Lawrence, and S. Ollinger. 2003. Nitrogen pollution: Sources and consequences in the U.S. Northeast. Environment:8-22  
El Fantroussi, S., H. Urakawa, A. E. Bernhard, J. J. Kelly, P. A. Noble, and D. A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal RNAs hybridized to oligonucleotide microarrays. Applied Environmental Microbiology 69:2377-2382  
Emeis, K. C., J. R. Benoit, L. Deegan, A. J. Gilbert, V. Lee, J. M. Glade, M. Meybeck, S. B. Olsen, and B. V. Bodungen. 2001. Group 4: Unifying concepts for integrated coastal management. In: Science and Integrated Coastal Management.  B. V. Bodungen and R. K. Turner (eds.),  pp Berlin, Dahlem University Press.
Fagherazzi, S., D. M. FitzGerald, R. W. Fulweiler, Z. Hughes, P. L. Wiberg, K. J. McGlathery, J. T. Morris, T. J. Tolhurst, L. A. Deegan, and D. S. Johnson. In press. Ecogeomorphology of Salt Marshes. In: Treatise on Geomorphology.  J. Shroder, D. Butler, and C. Hubb (eds.),  pp Elsevier.
Fagherazzi, S., D. M. FitzGerald, R. W. Fulweiler, Z. Hughes, P. L. Wiberg, K. J. McGlathery, J. T. Morris, T. J. Tolhurst, L. A. Deegan, and D. S. Johnson. In press. Ecogeomorphology of Tidal Flats. In: Treatise on Geomorphology.  J. Shroder, D. Butler, and C. Hubb (eds.),  pp Elsevier.
Fagherazzi, S., R. Torres, C. Hopkinson, and D. vanProosdij. 2004. The Salt Marsh Geomorphology: Physical and Ecological Effects on Landform. pp 57-58. In AGU Chapman Conference. EOS, Halifax, Nova Scotia, Canada.
Farber, S., D. Costanza, D. Childers, J. Erikson, K. Gross, M. Grove, C. Hopkinson, J. Kahn, S. Pincetl, A. Troy, P. Warren, and M. Wilson. 2006. Linking ecology and economics for ecosystem management. BioScience 56:121-134  
Fedorko, E. J., R. G. Pontius, Jr., S. P. Aldrich, L. Claessens, C. Hopkinson, and W. M. Wollheim. 2005. Spatial distribution of land type in regression models of pollutant loading. Journal of Spatial Hydrology 5:60-80  
Fennel, K., D. Brady, D. DiToro, R. W. Fulweiler, W. S. Gardner, A. Giblin, M. J. McCarthy, A. Rao, S. Seitzinger, M. Thouvenot-Korppoo, and C. Tobias. 2009. Modeling denitrification in aquatic sediments. Biogeochemistry 93:159-178  DOI 10.1007/s10533-008-9270-z.
Ferry, K. 2003. Factors driving distribution of migratory striped bass across Massachusetts estuaries: predator-prey interactions and implications for multispecies management. MS Thesis. University of Natural Resources.
Ferry, K. H., and M. E. Mather. In press. "Spatial and temporal diet patterns of young adult and subadult striped bass feeding in Massachusetts estuaries: trends across scales." Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 
Filoso, S., J. J. Vallino, C. Hopkinson, E. Rastetter, and L. Claessens. 2004. Modeling Nitrogen Transport in the Ipswich River Basin, Massachusetts, Using HSPF. Journal of the American Water Resources Association 40:1365-1384  
Finn, J. T., M. E. Mather, M. K. Burak, R. M. Muth, and J. B. Kim. In review. Evaluating new approaches to modeling data sets with many zeros: an example using upriver counts of a schooling anadromous fish.   
Fisher, T. R., D. Correll, R. Costanza, J. Hollibaugh, C. Hopkinson, R. Howarth, N. Rabalais, J. Richey, C. Vorosmarty, and R. Wiegert. 2000. Synthesizing drainage basin inputs to coastal systems. In: Estuarine Science: A Synthetic Approach to Research and Practice.  J. Hobbie (eds.),  pp 81-105. Washington, DC, Island Press.
Fleeger, J. W., D. S. Johnson, K. A. Galván, and L. A. Deegan. 2008. Top-down and bottom-up control of infauna varies across the saltmarsh landscape. Journal of Experimental Marine Biology and Ecology 357:20-34  doi:10.1016/j.jembe.2007.12.003.
Frank, H., M. E. Mather, R. M. Muth, S. M. Pautzke, J. M. Smith, J. T. Finn, and S. D. McCormick. 2009. What is 'fallback': metrics needed to assess telemetry tag effects on anadromaous fish behaviour. Hydrobiologia 35:237 - 249  
Frank, H. F., M. E. Mather, J. M. Smith, R. M. Muth, and J. T. Finn. 2011. Role of origin and release location in pre-spawning movements of anadromous alewives. Fisheries Management and Ecology 18:12-14  
Frank, H. J. 2009. Improving Strategies for Coastal River Restoration: Tracking Anadromous River Herring in a Coastal Massachusetts Stream. MS Thesis. University of Massachusetts, Amherst, MA.
Frank, H. J., M. E. Mather, R. M. Muth, S. M. Pautzke, J. M. Smith, and J. T. Finn. 2009. The Adopt-a-Herring Program as a Fisheries Conservation Tool. Fisheries 34:496-507  
Freeman, C. J., H. Haas, S. Warren, L. A. Deegan, and J. Logan. 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. In New England Estuarine Research Society (NEERS), Burlington, Vermont.
Fry, B., M. Cieri, J. Hughes, C. Tobias, L. A. Deegan, and B. Peterson. 2008. Stable isotope monitoring of benthic-pelagic coupling with salt marsh fish. Marine Ecology Progress Series 369:193-204  doi: 10.3354/meps07644.
Fry, B., C. Hopkinson, A. Nolin, and S. Wainright. 1998. 13C/12C composition of marine dissolved organic carbon. Chemical Geology 152:113 - 118  
Galvan, K., J. W. Fleeger, and B. Fry. 2008. Stable isotope addition reveals dietary importance of phytoplankton and microphytobenthos to saltmarsh infauna. Marine Ecology Progress Series 359:37-49  
Galván, K., J. W. Fleeger, B. Peterson, D. Drake, L. A. Deegan, and D. S. Johnson. 2011. Natural abundance stable isotopes and dual isotope tracer additions help to resolve resources supporting a saltmarsh food web. Journal of Experimental Marine Biology and Ecology 410:1-11  
Galván, K., J. W. Fleeger, B. Peterson, D. Drake, L. A. Deegan, D. S. Johnson, M. Johnson, and C. Picard. In prep. The diets of infauna:  A dual isotope (13C and 15N) addition study in a New England saltmarsh.   
Galván, K., J. W. Fleeger, B. Peterson, D. Drake, L. A. Deegan, D. S. Johnson, M. Johnson, and C. Picard. In review. Trophic plasticity and spatiotemporal variation revealed in a New England saltmarsh food web. Hydrobiologia  
Galvan, K. A. 2008. The diet of saltmarsh invertebrates. Ph.D. Thesis. Louisiana State University, Baton Rouge, LA.
Gardner, L. R., and E. F. Gaines. 2008. A method for estimating pore water drainage from marsh soils using rainfall and well records. Estuarine, Coastal and Shelf Science 79:51-58  doi:10.1016/j.ecss.2008.03.014.
Geyer, W. R., J. Morris, F. Prahl, and D. Jay. 2000. Interaction between physical processes and ecosystem structure: A comparative approach. In: Estuarine Science: A Synthetic Approach to Research and Practice.  J. Hobbie (eds.),  pp 177-206. Washington, DC, Island Press.
Giblin, A. E., and J. Vallino. 2003. The Role of Models in Addressing Coastal Eutrophication Problems. In: The Role of Models in Ecosystems Science.  C. D. Canham, J. J. Cole, and W. K. Lauenroth (eds.),  pp 327-343. Princeton University Press.
Giblin, A. E., N. B. Weston, G. T. Banta, J. Tucker, and C. S. Hopkinson. 2010. The effects of salinity on nitrogen losses from an oligohaline estuarine sediment. Estuaries and Coasts 33:1054-1068  
Giner, N., C. Polsky, R. G. Pontius, and D. Runfola. Submitted. A High-Resolution Spatial Statistical Analysis in Suburban Boston, Massachusetts. Landscape and Urban Planning  
Gober, P., K. L. Larson, R. Quay, C. Polsky, H. Chang, and V. Shandas. In review. Why Land Planners and Water Managers Don't Talk to One Another and Why They Should! Society and Natural Resources  
Gooseff, M., D. A. Benson, M. A. Briggs, M. Weaver, W. M. Wollheim, B. J. Peterson, and C. S. Hopkinson. 2011. Residence time distribution in surface transient storage zones in streams: Estimation via signal deconvolution. Water Resources Research 47:7 pp  doi:10.1029/2010WR009959.
Green, M., W. M. Wollheim, N. Basu, G. M. Gettel, P. Rao, N. Morse, and R. Stewart. 2009. Effective denitrification scales predictably with water residence time across diverse systems. Nature Precedings  hdl:10101/npre.2009.3520.1.
Green, M. B., W. M. Wollheim, N. Basu, G. Gettel, N. Morse, R. Stewart, and P. Rao. In review. Universal scaling of denitrification rate constants with water residence time. PloS One  
Green, P. A., C. J. Vorosmarty, M. Meybeck, J. N. Galloway, B. J. Peterson, and E. W. Boyer. 2003. Pre-industrial and contemporary fluxes of nitrogen through rivers: A global assessment based on typology. Biogeochemistry 68:1-35  
Greenbaum, A., and A. Giblin. 2000. Differences in properties of salt marsh sediment between hayed and reference sites. Biological Bulletin 199:225-226  
Greenbaum, A. H. 2001. Long-term fate of heavy metals in sediments of a Massachusetts salt marsh. Honors, BS Thesis. Wellesley College, Wellesley, MA.
Grimm, N., D. Foster, P. Groffman, M. Grove, C. Hopkinson, K. Nadelhoffer, D. Pataki, and D. Peters. 2008. Land change: Ecosystem responses to urbanization and pollution across climatic and societal gradients. Frontiers in Ecology and Environment 6:264-272  doi:10.1890/070147.
Grubaugh, C. 2010. Top-down and bottom-up benthic macroinvertebrate communities in salt marsh ditches. B.S. Thesis. Middlebury College, Middlebury, VT.
Guha, A. 2009. Adapting to Suburbanization-Induced Water Stress in Eastern Massachusetts: Opportunities and Constraints for Integrated Land-Use and Water Resource Management. M.A. Thesis. Clark University, Worcester.
Haas, H. L., C. J. Freeman, J. M. Logan, L. Deegan, and E. F. Gaines. 2009. Examining mummichog growth and movement: Are some individuals making intra-season migrations to optimize growth? Journal of Experimental Marine Biology and Ecology 369:8-16  doi:10.1016/j.jembe.2008.09.027.
Haines, J. 2001. The feeding ecology of mummichog and Atlantic silversides in the Rowley River. BS Thesis. Conneticut College.
Hamill, T. 2010. Visualizing and computing land cover proportions. B.S. Thesis. Clark University, Worcester, MA.
Hamill, T. 2011. Spatial methods to predict land cover. M.A. Thesis. Clark University, Worcester, MA.
Harris, E. M., D. G. Martin, C. Polsky, L. Denhardt, and A. Nehring. In press. Beyond 'Lawn People': The role of emotions in suburban yard management practices. The Professional Geographer  
Harris, L. A., C. M. Duarte, and S. W. Nixon. 2006. Allometric laws and prediction in estuarine and coastal ecology (Invited essay Perspectives section). Estuaries and Coasts 29:340-344  
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Head, J. 2002. Identifying impermeable surface from remotely sensed images. MS Thesis. Clark University, Worcester.
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Hopkinson, C. S., A. E. Giblin, and J. Tucker. 2001. Benthic metabolism and nutrient regeneration on the continental shelf off eastern Massachusetts, USA. Marine Ecology Progress Series 224:1-19  
Hopkinson, C. S., A. E. Giblin, J. Tucker, and R. H. Garritt. 1999. Benthic metabolism and nutrient cycling along an estuarine salinity gradient. Estuaries 22:825-843  
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Huang, X., and J. T. Morris. 2005. Distribution of phosphatase activity in marsh sediments along an estuarine salinity gradient. Marine Ecological Progress Series 292:75-83  
Huffaker, D. 2003. The scale at which land change models are accurate. High Honors, BS Thesis. Clark University, Worcester.
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Hughes, J. E., L. A. Deegan, B. J. Peterson, R. M. Holmes, and B. Fry. 2000. Nitrogen flow through the food web in the oligohaline zone of a New England estuary. Ecology 81:433-452  
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Johnson, D. S., and J. W. Fleeger. 2009. Weak response of saltmarsh infauna to ecosystem-wide nutrient enrichment and fish predator reduction: A four-year study. Journal of Experimental Marine Biology and Ecology 373:35-44  doi:10.1016/j.jembe.2009.03.003.
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Johnson, D. S., J. W. Fleeger, K. A. Galván, and K. Lockfield. In prep. Omnivory disrupts a trophic cascade in the marine benthos.   
Johnson, D. S., J. W. Fleeger, K. A. Galvan, and E. B. Moser. 2007. Worm holes and their space-time continuum: Spatial and temporal variability of macroinfaunal annelids in a northern New England salt marsh. Estuaries and Coasts 30:226-237  
Johnson, D. S., and B. J. Jessen. 2008. Do spur-throated grasshoppers, Melanoplus spp. (Orthoptera: Acrididae), exert top-down control on smooth cordgrass Spartina alterniflora in northern New England? Estuaries and Coasts 31:912-919  DOI 10.1007/s12237-008-9074-3.
Johnson, D. S., and M. Short. In review. Effect of fertilization on the mudsnail I. obsoleta. Estuaries and Coasts  
Johnston, M. E., J. R. Cavatorta, C. S. Hopkinson, and V. Valentine. 2003. Importance of metabolism in the development of salt marsh ponds. Biological Bulletin 205:248-249  
Kerry, J., D. Boorse, and R. Buchsbaum. 2004. The effect of nutrient enrichment  and salinity on salt marsh invertebrates in the Plum Island Estuary. Biological Bulletin 207:174  
Kiehn, W. M., and J. T. Morris. 2009. Relationships between smooth cord-grass Spartina alterniflora (Loisel.) and the periwinkle snail Littorina irrorata (Say) in a South Carolina salt marsh. Wetlands 29:818-825  
Kiehn, W. M., and J. T. Morris. 2010. Variability in dimethylsulfoniopropionate (DMSP) in Spartina alterniflora and its effect on Littoraria irrorata. Marine Ecology Progress Series 406:47-55  doi: 10.3354/meps08548.
Kirkby, R., L. Claessens, J. Hopkinson, C., E. Rastetter, and J. Vallino. 2000. Modeling the effects of land-use change on nitrogen biogeochemistry in the Ipswich watershed, Massachusetts. Biological Bulletin 199:218-219  
Kirwan, M. L., G. R. Guntenspergen, A. D'Alpaos, J. T. Morris, S. M. Mudd, and S. Temmerman. 2010. Limits on the adaptability of coastal marshes to rising sea level. Geophysical Research Letters 37  doi:10.1029/2010GL045489.
Kirwan, M. L., G. R. Guntenspergen, and J. T. Morris. 2009. Latitudinal trends in Spartina alterniflora productivity and the response of coastal marshes to global change. Global Change Biology  doi: 10.1111/j.1365-2486.2008.01834.x.
Klepac-Ceraj, V., M. Bahr, B. C. Crump, A. P. Teske, J. E. Hobbie, and M. F. Poltz. 2004. High overall diversity and dominance of microdiverse relationships in salt marsh sulfate-reducing bacteria. Environmental Microbiology 6:686-698  doi:10.1111/j.1462-2920.2004.00600.x.
Komarow, S., T. Young, L. Deegan, and R. Garritt. 1999. Influence of marsh flooding on the abundance and growth of Fundulus heteroclitus in salt marsh creeks. Biological Bulletin 197:299-300  
Koop-Jakobsen, K. 2003. Ammonium dynamics in tidal salt marshes - an experimental study of ammonium adsorption, tidal flushing and ammonium volatilization. MS Thesis. Roskilde University.
Koop-Jakobsen, K. 2008. The impact of increased Nitrogen Loading on Gaseous Loss of Nitrogen from Salt Marsh Seciments. Ph.D. Thesis. Boston University, Boston, MA.
Koop-Jakobsen, K., and A. E. Giblin. 2002. Tidal flushing of ammonium from intertidal salt marsh sediments - the relative importance of adsorbed ammonium. Biological Bulletin 203:258-259  
Koop-Jakobsen, K., and A. E. Giblin. 2009. Anammox in tidal marsh sediments: The role of salinity, nitrogen loading, and marsh vegetation. Estuaries and Coasts 32:238-245  DOI 10.1007/s12237-008-9131-y.
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Krest, J. M., W. S. Moore, L. R. Gardner, and J. T. Morris. 2000. Marsh nutrient export supplied by ground water discharge: Evidence from radium measurements. Global Biogeochemical Cycles 14:167-176  
LaMontange, M. G., A. E. Giblin, and I. Valiela. 2002. Denitrification and the stoichiometery of nutrient regeneration in Waquoit Bay, MA. Estuaries 25:272-281  
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Luciano, K. E. 2007. Investigation into the relationship between morphology and tidal flux in ditched and non-ditched salt marsh creek systems, Rowley, Massachusetts. B.S. Thesis. Virginia Institute of Marine Science, Gloucester Point, VA.
Ludlam, J. P., D. H. Shull, and R. Buchsbaum. 2002. Effects of haying on salt marsh surface invertebrates. Biological Bulletin 203:250-251  
Lunsford, T. L. 2002. Comparison of the fate of dissolved organic matter in two coastal systems: Hog Island Bay, VA (USA) and Plum Island Sound, MA (USA). MS Thesis. The College of William and Mary, Williamsburg, VA.
Machas, R. 1999. Analise isotopica da cadeia alimentar da Ria Formosa: Conribuicao relitiva dos produtores primaries. MS Thesis. University of Coimbra, Coimbra, Portugal.
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Mather, M. E., H. J. Frank, J. M. Smith, R. D. Cormier, R. M. Muth, and J. T. Finn. Accepted. Assessing freshwater habitat of adult anadromous alewives at multiple scales: a common challenge for fish and watershed restoration. Coastal and Marine Fisheries.  
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Menard, S. 1999. Land-use change and regional growth in the Ipswich watershed basin. BS Thesis. Clark University, Worcester.
Mendelssohn, I. A., and J. T. Morris. 2000. Ecophysiological controls on the growth of Spartina alterniflora. In: Concepts and Controversies in Tidal Marsh Ecology.  M. P. Weinstein and D. A. Kreeger (eds.),  pp 59-80. Dordredt, the Netherlands., Kluwer Academic Publishers.
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Mondrup, T. 2000. Salinity effects on tolerance and adaptation of estuarine nitrifying bacteria investigated by a plug-flux method. MS Thesis. Roskilde University (Denmark).
Moore, N. 2002. A leakage detection model for determining the value of conservation. MS Thesis. Clark University, Worcester.
Morris, J., P. V. Sundareshwar, C. T. Nietch, B. Kjerfve, and D. R. Cahoon. 2002. Responses of coastal wetlands to rising sea level. Ecology 83:2869-2877  
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Morris, J. T., R. R. Christian, and R. E. Ulanowicz. 2005. Analysis of size and complexity of randomly constructed food webs by information theoretic metrics. In: Aquatic Food Webs: an Ecosystem Approach.  A. Belgrano, U. M. Scharler, J. Dunne, and R. E. Ulanowicz (eds.),  pp 73-85. Oxford University Press.
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Moseman-Valtierra, A., R. Gonzalez, K. D. Kroeger, J. Tang, W. C. Chao, J. Crusius, J. Bratton, A. Green, and J. Shelton. 2011. Short-term nitrogen additions can shift a coastal wetland from a sink to a source of N2O. Atmospheric Envrionment 45:4390-4397  
Mudd, S. M., A. D'Alpaos, and J. T. Morris. 2010. How does vegetation affect sedimentation on tidal marshes?  Investigating particle capture and hydrodynamic controls on biologically mediated sedimentation. Journal of Geophysical Research 115  doi:10.1029/2009JF001566.
Mudd, S. M., S. Fagherazzi, J. T. Morris, and D. J. Furbish. 2004. Flow, sedimentation, and biomass production on a vegetated salt marsh in South Carolina: toward a predictive model of marsh morphologic and ecologic evolution. In: The Ecogeomorphology of Tidal Marshes.  S. Fagherazzi, A. Marani, and L. K. Blum (eds.),  pp 165-187. Washington, D.C., American Geophysical Union.
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Nelson, A. 2001. Quantifying the effectivness of conservation projects. MS Thesis. Clark University, Worcester.
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Parker, D. 2002. A method to produce hydrologically corrected DEMs. MS Thesis. Clark University, Worcester.
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Pellerin, B. A. 2004. The influence of urbanization on runoff generation and stream chemistry in Massachusetts watersheds. PhD. Thesis. University of New Hampshire, Durham, NH.
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