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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 

Harrison, J., R. Maranger, R. B. Alexander, J. Cornwell, A. Giblin, P. Jacinthe, E. Mayorga, S. Seitzinger, and W. M. Wollheim. 2009. The regional and global significance of reactive N removal in lakes and reservoirs. Biogeochemistry 93:147-158  DOI 10.1007/s10533-008-9272-x.

Head, J. 2002. Identifying impermeable surface from remotely sensed images. MS Thesis. Clark University, Worcester.

Helton, A. M., G. C. Poole, J. L. Meyer, W. M. Wollheim, B. J. Peterson, P. J. Mulholland, E. S. Bernhardt, J. A. Stanford, C. Arango, L. R. Ashkenas, L. W. Cooper, W. K. Dodds, S. V. Gregory, R. O. Hall, S. K. Hamilton, S. L. Johnson, W. H. McDowell, J. D. Potter, J. L. Tank, S. M. Thomas, H. M. Valett, J. R. Webster, and L. Zeglin. 2011. Thinking outside the channel: Modeling nitrogen cycling in networked river ecosystems. Frontiers in Ecology and Environment 9:229-238 

Hill, T., and C. Polsky. 2005. Adaptation to Drought in the Context of Suburban Sprawl and Abundant Rainfall. Geographical Bulletin 47:85-100 

Hill, T., and C. Polsky. 2007. Development and drought in suburbia: A mixed methods rapid assessment of vulnerability to drought in rainy Massachusetts. Environmental Hazards: Human and Policy Dimensions 7:291-301 

Hobbie, J. 2000. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Hobbie, J., S. Carpenter, N. Grimm, J. Gosz, and T. Seastedt. 2003. The United States Long Term Ecological Research program. BioSciences 53:21-32 

Hobbie, J. E. 2000. Estuarine Science: The key to progress in coastal ecological research. In: Estuarine Science: A Synthetic Approach to Research and Practice.  J. Hobbie (eds.),  pp 1-16. Washington, DC, Island Press.

Hobbie, J. E. 2003. Scientific accomplishments of the Long Term Ecological Research program: an introduction. BioSciences 53:17-20 

Holden, M., C. Lippitt, R. G. Pontius, and C. Williams. 2003. Building a database of historic land cover to detect landscape change. Biological Bulletin 205:257-258 

Holmes, R. M., A. Aminot, R. Kerouel, B. A. Hooker, and B. J. Peterson. 1999. A simple and precise method for measuring ammonium in marine and freshwater ecosystems. Canadian Journal of Fisheries and  Aquatic Science 56:1801-1808 

Holmes, R. M., J. McClelland, D. M. Sigman, B. Fry, and B. J. Peterson. 1998. Measuring 15N-NH4 in marine, estuarine, and freshwaters: an adaptation of the ammonium diffusion method for samples with low ammonium concentrations. Marine Chemistry 60:235-243 

Holmes, R. M., B. J. Peterson, L. Deegan, J. Hughes, and B. Fry. 2000. Nitrogen biogeochemistry in the oligohaline zone of a New England estuary. Ecology 81:416-432 

Holt, E., and R. Buchsbaum. 2000. Bird use of Phragmites australis in coastal marshes of northern Massachusetts. pp 232-240. In J. Pederson, editor. Proceedings of the 1st National Conference on Marine Bioinvasions. MIT Sea Grant, Cambridge, MA.

Hopkinson, C., and A. Giblin. 2008. Salt marsh N cycling. In: Nitrogen in the Marine Environment, 2nd Edition.  R. Capone, D. Bronk, M. Mulholland, and E. Carpenter (eds.),  pp 991-1036. Elsevier Publishers.

Hopkinson, C., and E. Smith. 2004. Estuarine respiration. In: Respiration of Aquatic Ecosystems of the World.  P. d. a. P. J. l. Williams (eds.),  pp 122-146. New York, NY, Academic Press.

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

Hopkinson, C. S., A. E. Giblin, R. H. Garritt, J. Tucker, and M. A. J. Hullar. 1998. The influence of the benthic boundary layer on growth of pelagic bacteria. Aquatic Microbial Ecology 16:109-118 

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 

Hopkinson, C. S., A. E. Lugo, M. Alber, A. Covich, and S. van Bloem. 2008. Understanding and forecasting the effects of sea level rise and intense windstorms on coastal and upland ecosystems: the need for a continental-scale netowrk of observatories. Frontiers in Ecology and Environment 6:255-263  doi:10.1890/070153.

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

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

Horowitz, J. 2001. Stable istopic analysis of food webs in hayed and reference salt marshes. Honors, BS Thesis. Hampshire College.

Howarth, R. W., D. Anderson, T. Church, H. Greening, C. Hopkinson, W. Huber, N. Marcus, R. Naiman, K. Segerson, A. Sharpley, and W. Wiseman. 2000. Clean Coastal Waters: Understanding and reducing the effects of nutrient pollution. National Academy of Sciences, Washington, DC.

Howarth, R. W., D. Anderson, J. Cloern, C. Elfring, C. Hopkinson, B. Lapointe, T. Malone, N. Marcus, K. McGlathery, A. Sharpley, and D. Walker. 2000. Nutrient pollution of coastal rivers, bays and seas. Issues in Ecology:1-15 

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.

Huffaker, D., and R. G. Pontius Jr. 2002. Reconstruction of Historical Land Cover in the Ipswich Watershed. Biological Bulletin 203:253-254 

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 

Johnson, D. S. 2008. Trophic control of saltmarsh invertebrates. Ph.D. Thesis. Louisiana State University, Baton Rouge, LA.

Johnson, D. S. 2011. High-marsh invertebrates are susceptible to eutrophication. Marine Ecological Progress Series 438:142-152 

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.

Johnson, D. S., J. W. Fleeger, and L. A. Deegan. 2009. Large-scale manipulations reveal that top-down and bottom-up controls interact to alter habitat utilization by saltmarsh fauna. Marine Ecology Progress Series 377:33-41  doi: 10.3354/meps07849.

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.

Koop-Jakobsen, K., and A. E. Giblin. 2009. A new approach for measuring denitrification in the rhizosphere of vegetated marsh sediments. Limnology and Oceanography, Methods 7:626 - 637 

Koop-Jakobsen, K., and A. E. Giblin. 2010. The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments. Limnology and Oceanography 55:789-802 

Kratz, T. K., L. A. Deegan, M. E. Harmon, and W. K. Lauenroth. 2003. Understanding Ecological Variability in Space and Time from Long-Term Observations. BioSciences 53:57-67 

Kremer, J., W. Kemp, A. Giblin, I. Valiela, S. Seitzinger, and E. Hoffman. 2000. Linking biogeochemical processes to higher trophic levels. In: Estuarine Science, A Synthetic Approach to Research and Practice.  J. Hobbie (eds.),  pp 299-246. Washington, DC, Island Press.

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 

Leahy, K., and R. Buchsbaum. 1998. Nonpoint source comprehensive implementation program for the Mill River sub-watersheds. Prep. for Mass DEP and US EPA.

Lee, W. M. 2004. Factors affecting sedimentation patterns of a tidal marsh in Plum Island Sound Estuary, Massachusetts. B.S. Thesis. College of William and Mary.

Lemay, L. E. 2007. The impact of drainage ditches on salt marsh flow patterns, sedimentation and morphology:  Rowley River, Massachusetts. M.S. Thesis. Virginia Institute of Marine Science, Gloucester Point, VA.

Levine, U. Y., and B. C. Crump. 2002. Bacteroplankton Community Composition in Flowing Waters of the Ipswich River Watershed. Biological Bulletin 203:251-252 

Lockfield, K. 2011. Population-level responses of the mummichog, Fundulus heteroclitus, to chronic nutrient enrichment in a New England salt marsh. M.S. Thesis. Louisiana State University, Baton Rouge, LA.

Logan, J., H. Hass, L. A. Deegan, and E. Gaines. 2006. Turnover rates of nitrogen stable isotopes in the salt marsh mummichog, Fundulus heteroclitus, following a laboratory diet switch. Oecologia 147:391-395 

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.

Machas, R., and R. Santos. 1999. Sources of organic matter in Ria Formosa revealed by stable isotope analysis. Acta Oecologica 20:463-469 

Machas, R., R. Santos, and B. Peterson. 2003. Tracing the flow of organic matter from primary producers to filter feeders in Ria Formosa Lagoon, Southern Portugal. Estuaries 26:846-856 

Mather, M. E., J. T. Finn, K. H. Ferry, L. A. Deegan, and G. A. Nelson. 2009. Use of non-natal estuaries by migratory striped bass (Morone saxatilis) in summer. Fishery Bulletin 107:329 - 337 

Mather, M. E., J. T. Finn, S. M. Pautzke, D. Fox, T. Savoy, H. M. Brundage III, L. A. Deegan, and R. M. Muth. 2010. Diversity in destinations, routes and timing of small adult and sub-adult striped bass Morone saxatilis on their southward autumn migration. Journal of Fish Biology 77:2326-2337  DOI: 10.1111/j.1095-8649.2010.02811.x.

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. 

McConnell, W. J., J. D. A. Millington, N. J. Reo, M. Alberti, H. Asbjornsen, L. A. Baker, N. Brozović, L. E. Drinkwater, S. A. Drzyzga, J. Fragoso, D. S. Holland, C. A. Jantz, T. A. Kohler, H. D. G. Maschner, M. Monticino, G. Podestá, R. G. Pontius Jr., C. L. Redman, D. Sailor, G. Urquhart, and J. Liu. 2011. Research on coupled human and natural Systems (CHANS): Approach, challenges and strategies. Bulletin of the Ecological Society of America 92:218-228 

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.

Meybeck, M., and C. J. Vorosmarty. 2005. Fluvial filtering of land to ocean fluxes: from Holocene variations to Anthrocene. Compte Rendus 337:107-123 

Miller, E. E. 2006. Experimental nutrient enrichment of a New England salt marsh: plant productivity and community composition responses. M.S. Thesis. Connecticut College, New London, CT.

Millette, T. L., B. Argow, E. Marcano, C. Hayward, C. Hopkinson, and V. Valentine. 2010. Salt marsh geomorphological analyses via integration of multi-temporal multispectral remote sensing with LIDAR and GIS. Journal of Coastal Research 26:809-816 

Mondrup, T. 1999. Salinity effects on nitrogen dynamics in estuarine sediment investigated by a plug-flux method. Biological Bulletin 197:287-288 

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 

Morris, J. T. 2000. Effects of sea level anomalies on estuarine processes. In: Estuarine Science: A Synthetic Approach to Research and Practice.  J. Hobbie (eds.),  pp 107-127. Washington, DC, Island Press.

Morris, J. T. 2005. Effects of changes in sea level and productivity on the stability of intertidal marshes. pp 121-127. In P. Lasserre, P. Viaroli, and C. P., editors. UNESCO Proceeding Series on Lagoons and Coastal Wetlands in the Global Change Context: Impact and Management Issues, Venice.

Morris, J. T. 2006. Competition among marsh macrophytes by means of geomorphological displacement in the intertidal zone. Estuarine and Coastal Shelf Science 69:395-402 

Morris, J. T. 2007. Ecological engineering in intertidal saltmarshes. Hydrobiologia 577:161-168 

Morris, J. T. 2007. Estimating net primary production of salt marsh macrophytes. In: Principles and Standards for Measuring Primary Production.  T. J. Fahey and A. K. Knapp (eds.),  pp 106-119. Oxford University Press.

Morris, J. T. 2010. Competition among marsh macrophytes by means of vertical geomorphological displacement. pp 109-115. In D. R. Ayres, D. W. Kerr, S. D. Ericson, and P. R. Olofson, editors. Third International Conference on Invasive Spartina. San Francisco Estuary Invasive Spartina Project of the California State Coastal Conservance: Oakland, CA, San Francisco, CA.

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.

Morris, J. T., J. Edwards, S. Crooks, and E. Reyes. In press. Assessment of Carbon Sequestration Potential in Coastal Wetlands. In: Recarbonization of the Bioshpere: Ecosystem and Global Carbon Cycle.  R. Lal, K. Lorenz, R. H_?ttl, B. U. Schneider, and J. von Braun (eds.),  pp Springer.

Morris, J. T., D. Porter, M. Neet, P. A. Noble, L. Schmidt, L. A. Lapine, and J. Jensen. 2005. Integrating LIDAR, multispectral imagery and neural network modeling techniques for marsh classification. International Journal of Remote Sensing 26:5221-5234  DOI: 10.1080/01431160500219018.

Morse, N. B. 2010. Impacts of suburbanization on food web stoichiometry of detritus-based streams. M.S. Thesis. University of New Hampshire, Durham, N.H.

Morse, N. B., W. M. Wollheim, J. P. Benstead, and W. H. McDowell. In review. Impacts of suburbanization on food web stoichiometry in detritus-based streams of New England.  

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.

Mudd, S. M., S. Howell, and J. T. Morris. 2009. Impact of the dynamic feedback between sedimentation, sea level rise, and biomass production on near surface marsh stratigraphy and carbon accumulation. Estuarine, Coastal and Shelf Science 82:377-389  doi:10.1016/j.ecss.2009.01.028.

Mulholland, P. J., A. M. Helton, G. C. Poole, J. Hall, R.O., S. K. Hamilton, B. J. Peterson, J. L. Tank, L. R. Ashkenas, L. W. Cooper, C. N. Dahm, W. K. Dodds, S. E. G. Findlay, S. V. Gregory, N. B. Grimm, S. L. Johnson, W. H. McDowell, J. L. Meyer, H. M. Valett, J. R. Webster, C. P. Arango, J. J. Beaulieu, M. J. Bernot, A. J. Burgin, C. L. Crenshaw, L. T. Johnson, B. R. Niederlehner, J. M. OﾒBrien, J. D. Potter, R. W. Sheibley, D. J. Sobota, and S. M. Thomas. 2008. Stream denitrification across biomes and its response to anthropogenic nitrate loading. Nature 452:202-206  doi:10.1038/nature06686.

Neckles, H., M. Dionne, D. Burdick, R. Buchsbaum, T. Diers, E. Hutchins, and C. Roman. 2002. A monitoring protocol to assess tidal restoration of salt marshes on local and regional scales. Restoration Ecology 10:556-563 

Nelson, A. 2001. Quantifying the effectivness of conservation projects. MS Thesis. Clark University, Worcester.

Nguyen, T. 2010. Sensitivity of land cover analysis to category aggregation. M.A. Thesis. Clark University, Worcester, MA.

Nielsen, J. L., A. Schramm, A. E. Bernhard, v. d. EnghG.J., and D. A. Stahl. 2004. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries. Applied and Environmental Microbiology 70:7550-7554 

Oczkowski, A. J., B. A. Pellerin, C. W. Hunt, W. M. Wollheim, C. J. Vorosmarty, and T. C. Loder. 2006. The role of snowmelt and spring rainfall in inorganic nutrient fluxes from a large temperate watershed, the Androscoggin River basin (Maine and New Hampshire). Biogeochemistry 80:217-234 

Parker, D. 2002. A method to produce hydrologically corrected DEMs. MS Thesis. Clark University, Worcester.

Parmentier, B., and R. G. Pontius, Jr. 2007. Improvements in the use of the ROC statistic for landscape ecology. pp 2. In Conference proceedings of the World Congress of the International Association for Landscape Ecology, Wageningen, The Netherlands.

Pascal, P.-Y. In prep. Grazing rates of saltmarsh invertebrates.  

Pascal, P.-Y., and J. W. Fleeger. In review. Diverse dietary responses by saltmarsh consumers to chronic nutrient enrichment. Estuaries and Coasts 

Pascal, P.-Y., J. W. Fleeger, H. T. S. Boschker, H. Mitwally, and D. S. Johnson. In review. Chronic nutrient-enrichment influence on mudflat food web in a New England (USA) estuary. Limnology and Oceanography 

Pautzke, S. M. 2008. Distribution patterns of migratory striped bass in Plum Island estuary, Massachusetts. M.S. Thesis. University of Massachusetts, Amherst, MA.

Pautzke, S. M., M. E. Mather, J. T. Finn, L. A. Deegan, and R. M. Muth. 2010. Seasonal use of a New England estuary by foraging contingents of migratory striped bass. Transactions of the American Fisheries Society 139:257 - 269  DOI: 10.1577/T08-222.1.

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

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.

Pellerin, B. A., J. Saraceno, J. B. Shanley, S. Sebestyn, G. R. Aiken, W. M. Wollheim, and B. A. Bergamaschi. 2011. Taking the pulse of snowmelt: In situ sensors reveal season, event and diurnal patterns of nitrate and dissolved organic matter variability in an upland forest stream. Biogeochemistry  doi:10.1007/s10533-011-9589-8.

Pellerin, B. A., W. Wollheim, C. Hopkinson, W. McDowell, M. Williams, C. Vorosmarty, and M. Daley. 2004. Role of wetlands and developed land use on dissolved organic nitrogen concentrations and DON / TDN in northeastern U.S. rivers and streams. Limnology and Oceanography 49:910-918 

Pellerin, B. A., W. M. Wollheim, X. Feng, and C. J. Vorosmarty. 2007. The application of electrical conductivity as a tracer for hydrograph separation in urban catchments. Hydrological Processes 22:1810-1818  DOI:10.1002/hyp.6786.

Pennings, S., M. Alber, C. Alexander, M. Booth, A. Burd, W.-J. Cai, C. Craft, C. DePratter, D. Di Iorio, C. Hopkinson, S. Joye, C. Meile, W. Moore, B. Silliman, V. Thompson, and J. Wares. In press. South Atlantic Tidal Wetlands.  

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

Peterson, B. J. 1999. Stable isotopes as tracers of organic matter input and transfer in benthic food webs: A review. Acta Oecologia 20:479-487 

Pieri, N. 2001. Quantifying the effectivness of conservation projects. MS Thesis. Clark University, Worcester.

Polsky, C., S. Assefa, K. Del Vecchio, T. Hill, L. Merner, I. Tercero, and G. Pontius. 2009. The Mounting Risk of Drought in a Humid Landscape: Structure and Agency in Suburbanizing Massachusetts. In: Sustainable Communities on a Sustainable Planet: The Human-Environment Regional Observatory Project.  B. Yarnal, C. Polsky, and J. O'Brien (eds.),  pp New York, Cambridge University Press.

Poltz, M. F., S. Bertilsson, S. G. Acinas, and D. Hunt. 2003. A (r)Ray of hope in analysis of function and diversity of microbial communities. Biological Bulletin 204:196-199 

Pontius Jr., R. G. 2000. Quantification error versus location error in comparison of categorical maps. Photogrammetric Engineering & Remote Sensing 66:1011-1016 

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