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Estuarine and Great Lakes (EaGLe) Coastal Initiative

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Estuarine and Great Lakes (EaGLe)
Coastal Initiative

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(research was funded by a STAR EaGLe grant)

Manuscript count: 270

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Niemi,G., D. Wardrop, R. Brooks, S. Anderson, V. Brady, H. Paerl, C. Rakocinski, M. Brouwer, B. Levinson, M. McDonald. 2004. Rationale for a new generation of indicators for coastal waters. Environmental Health Perspectives 112(9): 979-986.

Acker, J.G., L.W. Harding, G. Leptoukh, T. Zhu, and S. Shen. 2005. Remotely-sensed chl a at the Chesapeake Bay mouth is correlated with annual freshwater flow to Chesapeake Bay. Geophys. Res. Lett. 32. (ACE INC)

Adams, A.D., R.A. Lehr, D.L. Swackhamer, S.A. Diamond, D.R. Mount, M.F. Simcik. Measuring attenuation of ultraviolet-A radiation in Great Lakes coastal ecosystems: implications for photo activation of polycyclic aromatic hydrocarbons. Journal of Great Lakes Research. (GLEI) In preparation

Adolf, J.E., C.L. Jordan, W.D. Miller, M.E. Mallonee, and L.W. Harding, Jr. 2006. Phytoplankton floral composition, biomass, and primary productivity in Chesapeake Bay. Estuar. Coast. Shelf Sci. 67, 108-122. (ACE INC)

Adolf, J.E., L.W. Harding, Jr., M.E. Mallonee. The relationship of floral composition and primary productivity in Chesapeake Bay. Marine Ecological Progress Series. (ACE INC). Submitted.

Adolf, J.E., L.W. Harding, Jr., and M.E. Mallonee. Environmental forcing of phytoplankton floral composition, biomass,and primary productivity in Chesapeake Bay, USA. Limnology and Oceanography (ACE INC). Submitted.

Allen, J.C., R.M. Nisbet, K. Taulbee, H.M. Page. Dynamic energy budget models for stable isotopes. (PEEIR). In preparation.

Arrieta, D.E., B.W. Wilson, P. Flint, K. Trust, C. Seger, D. Tsao, E. Sheetenhelm, A.K. Miles. A micro-EROD assay method suitable for biopsies of wildlife. (PEEIR) In preparation.

Axler, R., J. Henneck, A. Kireta, J. Sgro and J. Kingston. Surrogate water quality indicators for use in monitoring the Great Lakes coastal zone. Environmental Monitoring and Assessment. (GLEI) In preparation.

Baker, M.E., D. E. Weller, and T. E. Jordan. Improved methods for quantifying regional patterns of riparian buffers. Landscape Ecology (ASC) In review.

Baker, M.E., D. E. Weller, and T. E. Jordan. 2005. Mapping watershed boundaries using digital elevation data: implications for land cover analysis of nutrient discharge. Photogrammetric Engineering & Remote Sensing (ASC) In press.

Bhagat, Y., J.J.H.Ciborowski, L.B. Johnson, D. Uzarski, T.M. Burton, S.T.A. Timmermans, M.J. Cooper. 2007. Testing a fish index of biotic integrity for responses to different stressors in Great Lakes coastal wetlands. Journal of Great Lakes Res. 33(SI3):224-235. (GLEI)

Biber, P.D. Hydroponic Versus Rooted Growth of Zostera marina L. (Eelgrass). Estuaries (ACE INC) Submitted.

Biber, P.D., S.C. Snedaker. Measuring the Effects of Salinity Stress in the Red Mangrove, Rhizophora Mangle L. JEMBE. (ACE INC) Submitted

Biber, P.D., H.W. Paerl, C.L. Gallegos. 2005. Evaluating Indicators of Seagrass Stress to Light. Chapter 13 in S.A. Bortone (ed) Estuarine Indicators. Boca Raton, CRC Press, pp. 193-209. (ACE INC & ASC)

Biber, P.D., and E.A. Irlandi. Temporal and Spatial Dynamics of Macroalgal Communities Influenced by an Anthropogenic Salinity Gradient. Aquatic Botany (ACE INC) Accepted.

Bilkovic, D.M., C.H. Hershner, M.R. Berman, K.J. Havens and D.M. Stanhope. 2004. Evaluating nearshore communities as indicators of ecosystem health. In Estuarine Indicators, Stephen Bortone (ed.). CRC Press, Inc., Washington, DC, pp. 365-379. (ASC)

Bilkovic, D.M., M. Roggero, C.H. Hershner and K.H. Havens. Influence of land use on macrobenthic communities in nearshore estuarine habitats. Estuaries (ASC) In review.

Boicourt, W.C. 2005. Physical response of Chesapeake Bay to hurricanes moving to the wrong side. In: K.G. Sellner (ed.), Hurricane Isabel in Perspective. Chesapeake Research Consortium, CRC Publication 05-160, Edgewater, Maryland, p. 39-48. (ACE INC)

Boers, A.M., C.B. Frieswyk, Jos T.A. Verhoeven, J.B. Zedler. In press. Contrasting approaches to the restoration of diverse vegetation in herbaceous wetlands. In: J.T.A. Verhoeven, B. Beltman, R. Bobbink, D.F. Whigham. Wetlands as a natural resource, Volume 1. Wetlands and natural resource management. Springer-Verlag, Berlin, Germany. (GLEI)

Boers, A.M., Rachel L.D. Veltman, and Joy B. Zedler. 2007. Typha x glauca dominance and extended hydroperiod constrain restoration of wetland diversity. Ecological Engineering 29:232-244. (GLEI)

Boers, A.M., J. B. Zedler. Internal eutrophication: A proposed mechanism for increased invasion by Typha x glauca. Wetlands. (GLEI) In review.

Borisova, T., J. S. Shortle, R.D. Horan, and D.G. Abler. 2005. The value of information for water quality protection. Water Resources Research 41(6). (ASC)

Bourdaghs, M., C.A. Johnston, and R.R. Regal. 2006. Properties and Performance of the Floristic Quality Index in Great Lakes coastal wetlands. Wetlands 16:718-735. (GLEI)

Brady, V., J. Ciborowski, J. Holland, N. Danz, L. Johnson, D. Breneman, J. Gathman, T. Hrabik, J. Schuldt. Optimizing fishing time: One vs. two-night fyke net sets in Great Lakes coastal systems. J. Great Lakes Research 33(SI3):236-244. (GLEI)

Brady, V., L. Johnson, J. Ciborowski, D. Breneman, J. Olker. Explaining patterns of variation in
wetland macrobenthos across coastal areas of the Great Lakes. Journal of Great Lakes Research. (GLEI) In preparation.

Brazner, J.C., N.P. Danz, G.J. Niemi, R.R. Regal, Trebitz, A.S., R.W. Howe, J.M. Hanowski, L.B. Johnson, J.J.H. Ciborowski, C.A. Johnston, E.D. Reavie, V.J. Brady, G.V. Sgro. Evaluation of geographic, geomorphic, and human influences on Great Lakes wetland indicators: a multiassemblage approach. Ecological Indicators. (GLEI) Submitted.

Brazner, J.C., N.P. Danz, G.J. Niemi, R.R.Regal, T. Hollenhorst, G. Host, T. Brown, A.S. Trebitz, R.W. Howe, J.M. Hanowski, L.B. Johnson, J.J.H. Ciborowski, C. Johnston, E. Reavie, G. Sgro. Responsiveness of Great Lakes wetland indicators to human disturbances at multiple spatial scales: a multi-assemblage assessment. Journal of Great Lakes Research 33(SI3):42-66. (GLEI)

Breitburg, D.L., A. Adamack, K.A. Rose, S.E. Kolesar, M.B. Decker, J.E. Purcell, J.E. Keister, JH. Cowan. 2003. The pattern and influence of low dissolved oxygen in the Patuxent River, a seasonally hypoxic estuary. Estuaries 26(2A): 280-297. (CEER-GOM)

Brouwer, M., P. Larkin, N. Brown-Peterson, C. King, S. Manning, N. Denslow. 2004. Effects of hypoxia on gene and protein expression in the blue crab, Callinectes sapidus. Marine Environmental Research. (CEER-GOM). In press.

Brouwer, M., N.J. Brown-Peterson, P. Larkin, S. Manning, N. Denslow and K. Rose. 2005. Molecular and organismal indicators of chronic and intermittent hypoxia in marine crustacean. In S. Bortone, ed., Estuarine Indicators, CRC Press, Boca Raton, FL, pp. 261-276. (CEER-GOM)

Brouwer, M., N.J. Brown-Peterson, P. Larkin, V. Patel, N. Denslow, S. Manning, and T. Hoexum-Brouwer. 2006. Molecular and whole-animal responses of grass shrimp, Palaemonetes pugio, exposed to chronic hypoxia. J. Exp. Mar. Bio. Ecol. (CEER-GOM)

Brown-Peterson, N.J., P. Larkin, N. Denslow, C. King, S. Manning and M. Brouwer. 2005. Molecular indicators of hypoxia in Blue crab, Callinectes sapidus. Marine Ecology Progress Series 286:203-215. (CEER-GOM).

Buzzelli, C.P., S. P. Powers, R. A. Luettich Jr., J. E McNinch, C.H. Petereson, J.L. Pinckney and H.W. Paerl. 2002. Estimating the spatial extent of bottom water hypoxia and benthic fishery habitat degradation in the Neuse River Estuary, NC. Mar. Ecol. Progr. Ser. 230:103-112. (ACE INC)

Buzzelli, C.P., J.R. Ramus, H.W. Paerl. 2003 Ferry-based monitoring of surface water quality in North Carolina estuaries. Estuaries 26:975-984. (ACE INC)

Cavatorta, J., M. Johnston, C. Hopkinson, and V. Valentine. 2003. Patterns of sedimentation in a salt marsh-dominated estuary. Biological Bulletin 205: 239-241. (ACE INC)

Cherr, G.N. 2002. Can we develop and utilize indicators of ecological integrity to successfully manage ecosystems? In: C.O. Qualset, D.J. Rapport, D. Ralston, B. Lasley, eds. Managing for Ecosystem Health. Third International Congress on Ecosystem Health, CRC Press, pp 227-229. (PEEIR).

Christian, R.R., J.E. O’Neal, B. Peierls, L. Valdes, H.W. Paerl. 2004. Episodic nutrient loading impacts on eutrophication of the southern Pamlico Sound: The effects of the 1999 hurricanes. Report. UNC Water Resources Research Institute Report No. 349, Raleigh, NC 63p. (ACE INC).

Ciborowski, J.J.H., J. Schuldt, L. Johnson, G. Host, C. Richards and T. Hollenhorst. Reference conditions, degraded areas, stressors, and impaired beneficial uses: conceptual integration of approaches to evaluating human-related environmental pressures. Ecological Applications or Environmental Monitoring and Assessment. (GLEI) In preparation.

Crane, J.L., C. Richards, D. Breneman, S. Lozano, J.A. Schuldt. 2005. Evaluating methods for assessing sediment quality in a Great Lakes embayment. Journal of Aquatic Ecosystem Heath and Management 8(3):323-349. (GLEI)

Danz, N.P., R.R. Regal, G.J. Niemi, V.J. Brady, T. Hollenhorst, L.B. Johnson, G.E. Host, J.M. Hanowski, C. Johnston, T. Brown, J. Kingston, J.R. Kelly. 2005. Environmentally stratified sampling design for the development of Great Lakes ecological indicators. Environmental Monitoring and Assessment 102:41-65. (GLEI).

Danz, N.P., G.J. Niemi, R.R. Regal, T. Hollenhorst, L.B. Johnson, J.M. Hanowski, R. Axler, J.J.H. Ciborowski, T. Hrabik, V.J. Brady, J.R. Kelly, J.C. Brazner, R.W. Howe, C.A. Johnston, G.E. Host. 2007. Integrated gradients of anthropogenic stress in the U.S. Great Lakes basin. Environmental Management 39(5):631-647. (GLEI).

Danz, N.P., M.F. Simcik, D.L. Swackhamer, G.J. Niemi, R.R. Regal, A. Adams, R. Lehr, T. Hollenhorst. Sampling design to capture contaminant gradients in the coastal Great Lakes. Journal of Great Lakes Research. (GLEI). In preparation.

DeLuca, W.V., C.E. Studds, L.L. Rockwood, and P.P. Marra. 2004. Influence of land use on the integrity of marsh bird communities of Chesapeake Bay, USA. Wetlands 24: 837-847. (ASC)

Ector L., J.C. Kingston, D.F. Charles, L. Denys, M.S.V. Douglas, K. Manoylov, N. Michelutti, F. Rimet, J.P. Smol, R.J. Stevenson, J.G. 2004. Workshop report. Freshwater diatoms and their roles as ecological indicators. Proceedings of the 17th International Diatom Symposium 2002, Ottawa, Canada (M. Poulin, ed.), pp.469-480, Biopress Limited, Bristol. (GLEI)

El Fantroussi, S., H. Urakawa, A.E. Bernhard, J.J. Kelly, H. Smidt, G.M. Yershov, P.A. Noble, D.A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal RNAs hybridized to oligonucleotide microarrays. Applied and Environmental Microbiology 69:2377-2382. (CEER-GOM)

Fan, T.W-M., A.N. Lane, R.M. Higashi. An electrophoretic profiling method for thiol-rich phytochelatins and metallothioneins. Phytochemical Analysis. (PEEIR). In press.

Fan, T.W-M., A.N. Lane, Chekmenev, Wittebort, and R.M. Higashi. 2004. Synthesis and physical properties of peptides in soil humic substances. Journal of Peptide Research 63:253-264 (PEEIR)

Farber, S., R. 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: 117-129. (ACE INC)

Fear, J., T. Gallo, N. Hall, J. Loftin and H. Paerl. 2004. Predicting benthic microalgal oxygen and nutrient flux responses to a nutrient reduction management strategy for the eutrophic Neuse River Estuary, North Carolina, USA. Estuarine and Coastal Shelf Science 61:491-506. (ACE INC)

Ferguson, H. and C. Rakocinski. 2008. Tracking marsh restoration using macrobenthic metrics: implementing a functional approach. Wetlands Ecology and Management (CEER-GOM) In press.

Field, K.G., E.C. Chern, L.K. Dick, J. Fuhrman, J. Griffith, P.A. Holden, M.G. LaMontagne, J. Le, B. Olson, M.T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health 1:181-194. (PEEIR)

Fleming, E. Mack, P. Green and D. Nelson. 2006. Mercury-methylation from unexpected sources: molybdate-inhibited freshwater sediments and an iron-reducing bacterium. Applied & Environmental Microbiology. (PEEIR) In press.

Foley, C., D. Breneman, J.J.H. Ciborowski, J.P. Gathman, V.J. Brady, L.B. Johnson., and C. Richards. The associations between larval Odonata and habitat structure as indicators of anthropogenic stress in Great Lakes coastal margin wetlands: a structural equation evaluation. (GLEI) In preparation.

Fries, J.S., Characklis, G.W., Paerl, H.W., and Noble, R.T., submitted. Particle suspensions in the Neuse River Estuary: Identifying contributions of resuspension, runoff, and phytoplankton. Estuaries.(ACE INC) Submitted.

Frieswyk, Christin B., Carol A. Johnston, and Joy B. Zedler. Measuring dominance among co-occurring plants. Diversity and Distributions. (GLEI). In review.

Frieswyk, C.B., C.A. Johnston, and J.B. Zedler. 2007. Identifying and characterizing dominant plants as an indicator of community condition. Journal of Great Lakes Research 33(SI3):125-135. (GLEI)

Frieswyk, C.B., J.B. Zedler. Do seed banks confer resilience to coastal wetlands invaded by Typha x glauca? Canadian Journal of Botany. (GLEI) In review.

Frieswyk, C.B., J.B. Zedler. 2007. Vegetation change in Great Lakes coastal wetlands: Deviation from the historical cycle. Journal of Great Lakes Research 33:366-380 (GLEI)

Fuiman, L.A., K.A. Rose, J.H. Cowan, and E.P. Smith. Survival skills required for predator evasion by fish larvae and their relationship to laboratory measures of performance. Animal Behaviour. (CEER-GOM) Submitted.

Fujiwara, M., B.E. Kendall, R.M. Nisbet. 2004. Growth autocorrelation and animal size variation. Ecology Letters 7:106-113 (PEEIR)

Fujiwara, M., B. Kendall, R. Nisbet, and W. Bennett. 2006. Analysis of size trajectory data using an energetic-based growth model in contaminated environments. Ecology. (PEEIR) In press.

Gallegos, C.L., Biber, P.D., 2004. Diagnostic tool sets water quality targets for restoring submerged aquatic vegetation in Chesapeake Bay. Ecological Restoration 22:296-297. (ACE INC & ASC)

Gallegos, C.L. and P.D. Biber. 2004. Setting Water Quality Targets for Restoration of Submerged Aquatic Vegetation. Ecological Restoration 22(4). (ACE INC)

Gallegos, C.L., Jordan, T.E., Hines, A.H., Weller, D.E., 2005. Temporal variability of optical properties in a shallow, eutrophic estuary: Seasonal and interannual variability. Estuarine, Coastal and Shelf Science 64: 156-170. (ASC)

Grandmaison, D.D., G.J. Niemi. Landscape influence on Red-winged Blackbird (Agelaius phoeniceus) nest success in Great Lakes coastal wetlands. The Auk. (GLEI) Submitted.

Grigorovich, I.A., E.L. Mills, C.B. Richards, D. Breneman, J.J.H. Ciborowski. 2005. European valve snail Valvata piscinalis (Muller) in the Great Lakes basin: Cryptic occurrence and spread. Journal of Great Lakes Research 31:135-143. (GLEI).

Grigorovich, I.A., M. Kang, and J.J.H. Ciborowski. 2005. Establishment of the invasive amphipod Gammarus tigrinus Sexton in Saginaw Bay, Lake Huron. Journal of Great Lakes Research. (GLEI) Accepted with minor revisions.

Groffman, P., J. Baron, T. Blett, A. Gold, I. Goodman, L. Gunderson, B. Levinson, M. Palmer, H. Paerl, G. Peterson, N. Poff, D. Rejeski, J. Reynolds, M. Turner, K. Weathers, J. Wiens. 2006. Ecological thresholds: The key to successful environmental management or an important concept with no practical application? Ecosystems 9:1-13. (ACE INC)

Gurney, W.S.C., R.M. Nisbet. Resource allocation, hyperphagia and compensatory growth. Bulletin of Mathematical Biology 66:1731-1753. (PEEIR partial funding)

Han, L. 2005. Estimating chlorophyll-a concentration using first derivative spectra in coastal water. International Journal of Remote Sensing 26(23): 5235-5244. (CEER-GOM)

Han, L. and K. Jordan. 2005. Measuring algal chlorophyll concentration in Pensacola Bay, Florida using Landsat ETM+ data. International Journal of Remote Sensing 26(23): 5245-5254. (CEER-GOM)

Hanowski, J., R. Howe, R. Regal, G. Niemi, N. Danz. 2007. Considerations for monitoring breeding birds in Great Lakes coastal wetlands. Journal of Great Lakes Res. 33(SI3):245-252. (GLEI)

Hanowski, J., N. Danz, R. Howe, G. Niemi, R. Regal. 2007. Considerations of geography and wetland geomorphic type in the development of Great Lakes coastal wetland bird indicators. EcoHealth. (GLEI)

Hanowski et al. Species-specific sampling effectiveness of calling anuran surveys in Lake Superior wetlands. Copeia. (GLEI). Submitted

Harding, L.W., Jr., M.E. Mallonee, E.S. Perry. 2002. Toward a predictive understanding of primary productivity in a temperate, partially stratified estuary. Estuarine and Coastal Shelf Science 55:47-46. (ACE INC).

Harding, L. W., Jr., A. Magnuson, A., and M. E. Mallonee. 2005. SeaWiFS retrievals of chlorophyll in Chesapeake Bay and the mid-Atlantic bight. Estuarine Coastal Shelf Science 62:75-94. (ACE INC)

Havens, K., C. Hershner, D.M. Bilkovic and D.H. Wardrop. Assessment of Chesapeake Bay Program selection and use of indicators. EcoHealth (ASC) In review.

Hechinger, R., and K. Lafferty. 2005. Host diversity begets parasite diversity: bird final hosts and trematodes in snail intermediate hosts. Proceedings of the Royal Society of London, Biology 272: 1059-1066. (PEEIR)

Hershner, C., K. Havens, D.H. Wardrop and D.M. Bilkovic. A practical concept for developing indicators of aquatic ecosystem health. EcoHealth (ASC) In review.

Higashi, R.M., T.A. Cassel, P.G. Green, T.W-M. Fan.13C-tracer studies of soil humic substructures that reduce heavy metal leaching. ACS Symposium Books (PEEIR). Submitted (peer-reviewed).

Hill, B.J., C.M. Elonen, T.M. Jicha, A.M. Cotter, A.S. Trebitz, N.P. Danz. Sediment microbial enzyme activity in Great Lakes coastal wetlands. Freshwater Biology. (GLEI) In preparation.

Holland, J., J.J.H. Ciborowski, L.B. Johnson, and T. Hollenhorst. Determining the spatial scale at which Great Lakes nearshore fishes respond to anthropogenic stress. (GLEI) In preparation.

Hollenhorst, T.P., T.N. Brown, L.B. Johnson, J.J.H. Ciborowski, and G.E. Host. 2007. Methods for generating multi-scale watershed delineations for indicator development in Great Lakes coastal ecosystems. Journal of Great Lakes 33(SI3): 13-26. (GLEI)

Horan, R., and J. Shortle. 2005. When two wrongs make a right: second best point-nonpoint trading. American Journal of Agricultural Economics 87(2):340-352. (ASC)

Horan, R., J. Shortle and D Abler. 2004. Point-nonpoint trading programs and agri-environmental policies. Agricultural and Resource Economics Review 33 (1): 61-78. (ASC)

Host, G., J.A. Schuldt, J.H. Ciborowski, L.B. Johnson, T.P. Hollenhorst, C. Richards. 2005. Use of GIS and remotely-sensed data for a priori identification of reference areas for Great Lakes coastal ecosystems. International Journal of Remote Sensing 26(23):5325-5342. (GLEI)

Howe, R.W., R. R. Regal, G.J. Niemi, N.P. Danz, J.M. Hanowski. 2007. A probability-based indicator of ecological condition. Ecological Indicators 7:793-806. (GLEI)

Howe, R.W., R.R. Regal, J. Hanowski, G.J. Niemi, N.P. Danz, and C.R. Smith. 2007. An index of ecological condition based on bird assemblages in Great Lakes coastal wetlands. Journal of Great Lakes Research 33(SI3):93-105 (GLEI)

Hsieh, J., Fries, J.S., and Noble, R.T., in revision. Vibrio and phytoplankton dynamics in a eutrophying estuary. Ecol. Applications. (ACE INC) In revision.

Huspeni, T.C., R.F. Hechinger, K. D. Lafferty. 2005. Trematode parasites as estuarine indicators: Applications and opportunities. In S.A. Bortone, ed., Estuarine Indicators, CRC Press, Boca Raton, pp. 297-314. (PEEIR)

Huspeni, T.C., K.D. Lafferty. 2004. Using larval trematodes that parasitize snails to evaluate a salt-marsh restoration project. Ecological Applications 14:795-804. (PEEIR)

Hwang, H., P. Green, and T. Young. 2006. Tidal salt marsh sediment in California, USA: 1) Occurence and sources of organic contaminants. Chemosphere. (PEEIR) In press.

Hwang, H., P. Green, R. Higashi, and T. Young. 2006. Tidal salt marsh sediment in Californai, USA: 2) Occurence and anthropogenic input of trace metals. Chemosphere. (PEEIR) In press.

Irlandi, E.A., B.A. Orlando, and P.D. Biber. 2004. Drift Algae-Epiphyte-Seagrass Interactions in a Subtropical Thalassia testudinum Meadow. Marine Ecological Progress Series 279:81-91. (ACE INC)

Jensen, J.R., G. Olsen, S. R. Schill, D. E. Porter, J. Morris. 2002. Remote sensing of biomass, leaf-area-index and chlorophyll a and b content in the ACE basin and National Estuarine Research Reserve using sub-meter digital camera imagery. Geocarto International 17:1-10. (ACE INC).

Johnson, L., V. Brady, et al. Contrasting fish and invertebrate coastal margin habitat between reference and non-reference areas. (GLEI) In preparation.

Johnson, L., V. Brady, et al. Relationships between coastal margin fish and invertebrate habitat and landscape stressors. (GLEI) In preparation.

Johnston, C.A., P. Meysembourg. 2002. Comparison of Wisconsin and National Wetlands Inventories. Wetlands 22(2): 386-405. (GLEI).

Johnston, C.A., B. Bedford, M. Bourdaghs, T. Brown, C.B. Frieswyk, M. Tulbure, L. Vaccaro, J.B. Zedler. 2007. Plant species indicators of physical environment in Great Lakes coastal wetlands. Journal of Great Lakes Research 33(SI3):106-124. (GLEI)

Johnston, C.A., T. Brown, T. Hollenhorst, P. Wolter, N. Danz, G. Niemi. 2006. GIS in support of ecological indicator development. Manual of geographic information systems. American Society for Photogrammetry and Remote Sensing, Bethesda, MD. (GLEI) In press.

Johnston, C.A., T. Watson, and P.T. Wolter. 2007. Sixty-three years of land alteration in Erie Township. Journal of Great Lakes Res. 33(SI3):253-268. (GLEI)

Johnston, C.A., D. Ghioca, M. Tulbure, B. Bedford, M. Bourdaghs, C. B. Frieswyk, L. Vaccaro, and J. B. Zedler. 2008. Partitioning Vegetation Response to Anthropogenic Stress to Develop Multi-taxa Wetland Indicators. Ecological Applications 18:983-1001. (GLEI)

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. (ACE INC)

Jung, S. and E. D. Houde. 2004. Production of bay anchovy Anchoa mitchilli in Chesapeake Bay: application of size-based theory. Mar. Ecol. Prog. Ser. 281: 217-232. (ACE INC)

Jung, S., E.D. Houde. 2005. Fish biomass size spectra in Chesapeake Bay. Marine Ecological Progress Series 28:226-240. (ACE INC)

Kang, M., J.J.H. Ciborowski, and L.B. Johnson. 2007. The influence of anthropogenic disturbance and environmental suitability on the distribution of the nonidigenous amphipod, Echinogammarus ischnus, at Laurentian Great Lakes coastal margins. Journal of Great Lakes Research 33(SI3):198-210 (GLEI)

Kelly, D. M. Kang, I.A. Grigorovich, J.J.H. Ciborowski and H.J. MacIsaac. In preparation. Distribution and probable European origin of Gammarus tigrinus, a new Great Lakes invader native to eastern North American brackish waters. Canadian Journal of Fisheries and Aquatic Sciences. (GLEI) In preparation.

Kelly, J.J., S. Siripong, J. McCormack, L.R. Janus, H. Urakawa, S. ElFantroussi, P.A. Noble, L. Sappelsa, B.E. Rittmann, and D.A. Strahl. 2005. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research 39:3229-3238. (CEER-GOM)

Kemp, W. M., W. R. Boynton, J. E. Adolf, D. F. Boesch, W. C. Boicourt, G. Brush, J. C. Cornwell, T. R. Fisher, P. M. Glibert, J. D. Hagy, L. W. Harding, E.D. Houde, D.G. Kimmel, W.D. Miller, R.I.E. Newell, M. R. Roman, E.M. Smith, J.C. Stevenson. 2005. Eutrophication of Chesapeake Bay: Historical trends and ecological interactions. Marine Ecololgical Progress Series 303:1-29. (ACE INC).

Kendall, B.E., M. Fujiwara, R.M. Nisbet,. Projecting population-level implications of sublethal stress in selected wetland fish species. (PEEIR). In preparation.

Kendall, B.E., P. Vitt, K. Havens. Individual growth rate variability can increase the population growth rate of annual plants. Ecology Letters. (PEEIR). In preparation.

Kercher, S.M., C.B. Frieswyk, J.B. Zedler. 2003. Quality control approaches reveal effects of sampling teams and estimation methods for assessing plant cover in temperate herbaceous wetlands. Journal of Vegetation Science 14:899-906. (GLEI).

Kimmel, D.G., M.R. Roman. 2004. Long-term trends in mesozooplankton abundance and community composition in the Chesapeake Bay USA: Influence of freshwater input. Marine Ecological Progress Series 267:71-83. (ACE INC)

Kimmel, D.G., M.R. Roman, and X. Zhang. 2005. Spatial and temporal variability affecting mesozooplankton dynamics in Chesapeake Bay: evidence from biomass size spectra. Limnology and Oceanography 51:131-141. (ACE INC)

Kimmel, D.G. and M.R. Roman. 2005. Regional scale climatic forcing of mesozooplankton dynamics in Chesapeake Bay. Estuaries. (ACE INC) In press.

King, R.S., C.J. Richardson. 2003. Integrating bioassessment and ecological risk assessment: An approach to developing numerical water-quality criteria. Environmental Management 31:795-809. (ASC).

King, R. S., A. H. Hines, F. D.Craige, and S. Grap. 2005. Regional, watershed, and local correlates of blue crab and bivalve abundances in subestuaries of Chesapeake Bay, USA. Journal of Experimental Marine Biology and Ecology 319:101-116. (ASC)

King, R. S., J. R. Beaman, D. F. Whigham, A.H. Hines, M.E. Baker, and D.E. Weller. 2004. Watershed land use is strongly linked to PCBs in white perch in Chesapeake Bay subestuaries. Environmental Science and Technology 38: 6546-6552. (ASC)

King, R.S., M.E. Baker, D.F. Whigham, D.E. Weller, T.E. Jordan, M.K. Hurd, and P.F. Kazyak. 2005. Spatial considerations for linking watershed landcover to ecological indicators in streams. Invited manuscript for Ecological Applications 15:137-153 (ASC).

Kireta, A., E.D. Reavie, N.P. Danz, R.P. Axler, G.V. Sgro, J.C. Kingston, T.N. Brown, T. Hollenhorst. 2007. Coastal geomorphic and lake variability in the Laurentian Great Lakes: Implications for a diatom-based monitoring tool. Journal of Great Lakes Research 33(SI3):136-153 (GLEI)

Lafferty, K.D. Assessing estuarine biota in southern California. In: Planning for Biodiversity. Symposium Proceedings. US Forest Service Technical Report Series. (PEEIR). In press.

Lafferty, K.D. 2003. Is disease increasing or decreasing, and does it impact or maintain biodiversity? Journal of Parasitology 89:S101-S105. (PEEIR)

Lafferty, K.D., R. D. Holt. 2003. How should environmental stress affect the population dynamics of disease? Ecology Letters 6:654-664. (PEEIR)

Lafferty, K.D. and Dunham. 2005. Trematodes in snails near raccoon latrines suggest a final host role for this mammal in California salt marshes. Journal of Parasitology 91:474-476. (PEEIR)

Lafferty, K,, R. Hechinger, J. Lorda, and L. Soler. 2005. Trematodes associated with mangrove habitat in Puerto Rican salt marshes. Journal of Parasitology 91: 697-699. (PEEIR)

Lafferty, K., R. Hechinger, J. Shaw, K. Whitney and A. Kuris. 2006. Food webs and parasites in a solt marsh ecosystem. In S. Collinge and C. Ray, eds., Disease Ecology: Community Structure and Pathogen Dynamics. Oxford University Press, Oxford. (PEEIR) In press.

LaMontagne, M.G., P.A. Holden. 2002. Comparison of free-living and particle-associated bacterial communities in a coastal lagoon. Microbial Ecology 46:228-237. (PEEIR)

LaMontagne, M.G., Liefer, Bergmann, Van de Werfhorst, and P.A. Holden. 2004. Assessment of the effect of marine oil seeps on sediment bacterial diversity and community structure by PCR-TRFLP. Environmental Microbiology 6:799-808. (PEEIR)

Landry, C.A., S.L. Steele, S. Manning, and A.O. Cheek. Hypoxia suppresses reproductive function in Gulf killifish, Fundulus grandis. Environmental Science and Technology. (CEER-GOM) Submitted.

Lehr, R.A., Adams, A., Simcik, M., Ankley, G., Swackhamer, D.L. Effects of carrier solvent selection on the Vitellogenin (Vtg) mRNA response in male fathead minnows (Pimephales promelas). (GLEI) In preparation.

Lehr, R.A., Adams, A., Simcik, M., Ankley, G., Swackhamer, D.L. Linking exposure and effect for environmental estrogens: the exposure-effect paradox. (GLEI) In preparation.

Lehr, R.A., Adams, A., Simcik, M., Ankley, G., Swackhamer, D.L. Managing environmental estrogens in aquatic ecosystems. (GLEI) In preparation.

Lewitus, A.J., D.L. White, R.G. Tymowski, M.E. Geesey, S.N. Hymel, and P.A. Noble. 2005. Adapting the CHEMTAX method for assessing phytoplankton community composition in southeastern U.S. estuaries. Estuaries 28: 160-172. (CEER-GOM)

Li, L., S. Ustin and M. Lay. 2006. Mapping coastal salt marsh species with multiple endmember spectral mixture analysis (MESMA) of hperspectral AVIRIS imagery. IEEE Geoscience & Remote Sensing. (PEEIR) In press.

Li, T., and M. Brouwer. Hypoxia inducible factor, gsHIF, of the grass shrimp Palaemonetes pugio Holthuis 1949. Molecular characterization and response to hypoxia. Comp. Biochem. Physiol. (CEER-GOM) In press.

Luettich, R.A., S.D. Carr, J.V. Reynolds-Fleming, C.W. Fulcher, J.E. McNinch. 2002. Semi-diurnal seiching in a shallow, micro-tidal lagoonal estuary. Continental Shelf Research 22:1669-1681. (ACE INC)

Magnuson, A., L.W. Harding, Jr., M.E. Mallonee. 2004. Bio-optical and remote sensing observations in Chesapeake Bay. Estuarine and Coastal Shelf Science 61:403-424 (ACE INC)

Marshall, E. and J. Shortle. 2005. Using DEA and VEA to evaluate quality of life in the mid- Atlantic states. Agriculture and Resource Economics Review 34(2):185-203. (ASC)

Marshall, E., and J. Shortle. 2005. Urban development impacts on ecosystems. In S. Goetz, J. Shortle, and J. Bergstrom (eds.), Land Use Problems and Conflicts: Causes, Consequences and Solutions. Routledge Publishing, New York. (ASC)

Marshall, H.L. and Morris, J.T. 2005. Detection of Pigment Changes due to Variations in Nitrogen and Phosphorus in Spartina alterniflora (Loisel) and Spartina patens (Ait.) Muhl, at Plum Island Estuary (MA). Development of a xanthophyll pigment reflectance index. (ACE INC) In preparation.

Martinez, M.L., C. Landry, R. Boehm, S. Manning, A.O. Cheek, and B.B. Rees. 2006. Effects of long-term hypoxia on enzymes of carbohydrate metabolism in the Gulf killifish, Fundulus grandis. J. Experimental Biology 209:3851-3861. (CEER-GOM)

McElfish, J. M., Jr. and L. M. Varnell. 2005. Designing environmental indicators for use in public decisions. Columbia Journal of Environmental Law 31 (1) (ASC) In press.

Millie, D.F., G.R. Weckman, H.W. Paerl, J.L. Pinckney, B.J. Bendis, R.J. Pigg, G.L. Fahnenstiel. 2006. Neural net modeling of estuarine indicators: Hindcasting phytoplankton biomass and net ecosystem production in the Neuse (North Carolina) and Trout (Florida) Rivers, USA. Ecological Indicators (ACE INC) In press.

Miller, C.M., G.J. Niemi, J.M. Hanowski, R.R. Regal. Effects of anthropogenic development on breeding bird abundance and communities. Auk. (GLEI). In preparation.

Miller, W.D., D.G. Kimmel, and L.W. Harding, Jr. 2006. Predicting spring discharge of the Susquehanna River from a winter synoptic climatology for the eastern United States. Water Resources Research. (ACE INC) In press.

Miller, W.D., L.W. Harding Jr., and J.E. Adolf. 2005. The Influence of Hurricane Isabel on Chesapeake Bay Phytoplankton Dynamics, In: Sellner, K.G. (ed.) Proceedings from the Symposium on Hurricane Isabel. Chesapeake Research Consortium, Baltimore, Maryland. (ACE INC) In press.

Montane, J.M., R. Torres. Accuracy of LiDAR in a Salt Marsh Environment. Remote Sensing of the Environment. (ACE INC). Submitted.

Morgan, S., S. Spilseth, H. Page, A. Brooks and E. Grosholz. 2006. Spatial and temporal movements of the lined shore crab (Pachygrapsus crassipes) in salt marshes and itsutility as an indicator of habitat condition. Marine Ecology Progress Series. (PEEIR) In press.

Morrice, J., N.P. Danz, R.R. Regal, J. Kelly, R. Axler, E. Reavie, et al. Landscape characteristics as predictors of water quality in Great Lakes coastal wetlands. (GLEI) In preparation.

Morris, J.T., P.V. Sundareshwar, C.T. Nietch, B. Kjerfve, D.R. Cahoon. 2002. Responses of coastal wetlands to rising sea level. Ecology 83:2869-2877. (ACE INC).

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. (ACE INC)

Morris, J.T. 2006. Effects of changes in sea level and productivity on the stability of intertidal marshes. In UNESCO Proceeding Series on Lagoons and Coastal Wetlands in the Global Change Context: Impacts and Management Issues. (ACE INC) In press.

Morris, J.T. 2006. Competition among marsh macrophytes by means of geomorphological displacement in the intertidal zone. Estuarine Coastal and Shelf Science (ACE INC) In press.

Morris, J.T. 2006. Ecological engineering in the intertidal zone. Hydrobiologia (ACE INC) In press.

Morris, J.T. Scale-dependent responses of coastal wetlands to rising sea level. Estuarine and Coastal Marine Science (ACE INC) Submitted.

Morris, J.T. Responses of tidal salt marshes to changes in mean sea level. Third International Conference on Invasive Spartina Proceedings. (ACE INC) Submitted.

Morris, J.T. D. Porter, M. Neet, P. Noble, and J. Jensen. LIDAR-derived elevational distributions of salt and brackish marshes at North Inlet, SC and land-use classification by artificial neural network. International Journal of Remote Sensing. (CEER-GOM) Submitted.

Moss, J.A., A. Nocker, J.E. Lepo, and R.A. Snyder. 2006. Stability and change in estuarine biofilm bacterial community diversity. Appl. Environ. Microbiol. 72: 5679-5688. (CEER-GOM)

Moss, J.A., A. Nocker, J.E. Lepo, and R.A. Snyder. Incorporating DNA sequence comparisons in measures of prokaryotic community diversity using the taxonomic distinctness concept. Appl. Environ. Microbiol. (CEER-GOM) In preparation.

Mulitsch, M., S. Ustin, and L. Li. 2004. Effects of global climate change on San Francisco Bay estuary communities. Proceedings of the 13th Earth Science Airborne Workshop. (PEEIR)

Muller, E.B., R.M. Nisbet, H. Berkley. Sublethal effects of toxic compounds on dynamic energy budgets; theory and applications. (PEEIR partial funding). In preparation.

Murphy, C.A., K.A. Rose, and P. Thomas. Modeling vitellogenesis in female fish exposed to environmental stressors: predicting the effects of endocrine disturbance due to exposure to a PCB mixture and cadmium. Reproductive Toxicology. (CEER-GOM) Submitted.

Mwamba, M.J., R. Torres. 2002. Rainfall effects on marsh sediment redistribution, North Inlet, SC. Marine Geology 189:267. (ACE INC).

Niemi, G.J., J.M. Hanowski, N. Danz, R. Howe, M. Jones, J. Lind, D. Mladenoff. 2004. Hierarchical scales in landscape responses by forest birds, landscape ecology and wildlife habitat evaluation: Critical information for ecological risk assessment, land-use management activities, and biodiversity enhancement practices, ASTM STP 1458, L.A. Kapustka, H. Gilbraith, M. Luxon, and G.R. Biddinger, eds. American Society for Testing and Materials, West Conshohocken, PA, 2004. (GLEI).

Niemi, G.J. and M.E. McDonald. 2004. Application of Ecological Indicators. Annual Review of Ecology and Systematics 35: 89-111. (GLEI).

Niemi, G.J., D. Wardrop, R. Brooks, S. Anderson, V. Brady, H. Paerl, C. Rakocinski, M. Brouwer, B. Levinson, M. McDonald. 2004. Rationale for a new generation of ecological indicators for coastal waters. Environmental Health Perspectives 112(9): 979-986. (GLEI, ACE INC, ASC, PEEIR, CEER-GOM).

Niemi, G.J., J.R. Kelly, and N.P. Danz. 2007. Environmental indicators for the coastal region of the North American Great Lakes: Introduction and prospectus. Journal of Great Lakes Research 33(SI3): 1-12. (GLEI)

Nisbet, R.M., E. McCauley, W.S.C. Gurney, W.W. Murdoch, S.N. Wood. Formulating and testing a partially specified dynamic energy budget model. Ecology 85:3132-3139. (PEEIR partial funding).

Noble, P.A., R.G. Tymowski, J.T. Morris, M. Fletcher, A.J. Lewitus. 2003. Comparing phytoplankton community pigment composition in two US southeastern salt marsh estuaries differing in freshwater drainage. Applied and Environmental Microbiology 69:4129-4143. (CEER-GOM)

Noble, P.A., and E. Tribou. 2005. Neuroet: an easy-to-use artificial neural network for ecological and biological modelling. Ecological Modelling. (CEER-GOM) In press.

Nocker A., J. E. Lepo, and R. A. Snyder. 2004. Diversity of microbial biofilm communities associated with an oyster reef and an adjacent muddy-sand bottom habitat. Appl. Environ. Microbiol. (CEER-GOM) In press.

Nocker, A., J.E. Lepo, L.L. Martin, and R.A. Snyder. Effect of dissolved oxygen on the development of microbial heterotrophic community of an estuarine biofilm with particular regard to sulfate reducing prokaryotes. Appl. Environ. Microbiol. (CEER-GOM) In preparation.

Nocker A., J. E. Lepo, L.M. Proctor,and R. A. Snyder. 2004. Molecular characterization of the bacterial biofilm community in an estuarine bay comprising a seagrass and a sandflat habitat. Microbiol Ecology (CEER-GOM) In preparation.

Novakowski, K.I., R. Torres. 2004. Geomorphic analysis of tidal creek networks. Water Resources Research 40(5) (ACE INC)

Paerl, H. W. 2002. Primary Productivity and Producers. Pp. 329-341, In C. J. Hurst (ed.) Manual of Environmental Microbiology (2nd Ed.). ASM Press, Washington, DC. (ACE INC)

Paerl, H.W. 2002. Connecting atmospheric deposition to coastal eutrophication. Environmental Science and Technology 36(15):323A-326A. (ACE INC)

Paerl, H.W, R.L. Dennis, D.R. Whitall. 2002. Atmospheric deposition of nitrogen: Implications for nutrient over-enrichment of coastal waters. Estuaries 25:677-693. (ACE INC)

Paerl, H.W., J. Dyble, L. Twomey, J.L. Pinckney, J. Nelson, L. Kerkhof. 2002. Characterizing man-made and natural modifications of microbial diversity and activity in coastal ecosystems. Antonie van Leeuwenhoek 81:487-507. (ACE INC).

Paerl, H.W. and J. Kuparinen. 2002. Microbial aggregates and consortia. In: G. Bitton (Ed). Encyclopedia of Environmental Microbiology, Vol. 1, p. 160-181. John Wiley and Sons, Inc. New York, NY.

Paerl, H., J. Dyble, P. Moisander, R. Noble, M. Piehler, J. Pinckney, T. Steppe, L. Twomey, L. Valdes. 2003. Microbial indicators of aquatic ecosystem change: Current applications to eutrophication studies. In L. Giuliano, Conrad, eds. Proceedings of the Eighth Society of Aquatic Microbiology Ecology meetings. FEMS Microbiology Ecology 46:233-246. (ACE INC).

Paerl, H.W., L.M. Valdes, J.L. Pinckney, M.F. Piehler, J. Dyble, P.H. Moisander. 2003. Phytoplankton photopigments as indicators of estuarine and coastal eutrophication. BioScience 53(10):953-964. (ACE INC).

Paerl, H.W. and T.F. Steppe 2003. Scaling up: The next challenge in environmental microbiology. Environmental Microbiology 5(11): 1025-1038. (ACE INC)

Paerl, H.W., T.F. Steppe, K.C. Buchan, M. Potts. 2003. Hypersaline cyanobacterial mats as indicators of elevated tropical hurricane activity and associated climate change. Ambio 32:87-90. (ACE INC)

Paerl, H.W. 2004. Estuarine eutrophication, hypoxia and anoxia dynamics: Causes, consequences and controls. Pp. 35-56 In Rupp, G.L. and M. D. White, eds. Proceedings of the 7th International Symposium on Fish Physiology, Toxicology and Water Quality. May 12-15, 2003, Tallinn, Estonia. U.S. Environmental Protection Agency Office of Research and Development, Ecosystems Research Division, Athens, Georgia, USA. EPA/600/R-04/049. (ACE INC)

Paerl, H.W., L.M. Valdes, A.R. Joyner, M.F. Piehler and M.E. Lebo. 2004. Solving problems resulting from solutions: The evolution of a dual nutrient management strategy for the eutrophying Neuse River Estuary, North Carolina, USA. Environmental Science and Technology 38:3068-3073 (ACE INC)

Paerl, H.W. 2005. Ecological effects of a recent rise in Atlantic hurricane activity on North Carolina’s Pamlico Sound System: Putting Hurricane Isabel in perspective. P. 3-18, In, K.G. Sellner (ed.), Hurricane Isabel in Perspective. Chesapeake research Consortium, CRC Publications 05-160, Edgewater, MD. (ACE INC)

Paerl, H.W. 2005. Assessing and managing nutrient-enhanced eutrophication in estuarine and coastal waters: Interactive effects of human and climatic perturbations. Ecological Engineering 26:40-54. (ACE INC)

Paerl, H.W., J. Dyble, J.L. Pinckney, LM. Valdes, D.F. Millie, P.H. Moisander, J.T. Morris, B. Bendis, and M.F. Piehler. 2005. Using microalgal indicators to assess human and climatically induced ecological change in estuaries. S.A. Bortone (ed.). Estuarine Indicators. CRC Press. Boca Raton, Florida, pp.145-174. (ACE INC)

Paerl, H.W., M.F. Piehler, L.M. Valdes, J. Dyble, P.H. Moisander, J.L. Pickney and T.S. Steppe. 2005. Determining anthropogenic and climatically-induced change in aquatic ecosystems using microbial indicators: An integrative approach. Verh. Internat. Verein. Limnol. 29:89-133. (ACE INC)

Paerl, H.W., L.M. Valdes, M.F. Piehler and C. A. Stow. 2006. Assessing the effects of nutrient management in an estuary experiencing climatic change: the Neuse River Estuary, NC, USA. Environmental Management (ACE INC) In press.

Paerl, H.W., L.M. Valdes, J. Adolf, B.L. Peierls and L.W. Harding Jr. 2006. Anthropogenic and climatic influences on the eutrophication of large estuarine ecosystems. Limnology and Oceanography 51:448-462 (ACE INC)

Paerl, H.W. et al. 2006. Ecological response to hurricane events in the Pamlico Sound System, NC and implications for assessment and management in a regime of increased frequency. Estuaries. (ACE INC) In revision.

Paerl, H.W., L.M. Valdes and M.F. Piehler. Evaluating long-term estuarine water quality trends in the Neuse River Estuary, NC USA to differentiate nutrient management from climatic change. Environmental Management (ACE INC). Submitted.

Paerl, H.W. Interactive impacts of human activities and storm events on coastal nutrient loading and eutrophication. In: P. Wassman, J. Ohli, P. Nos, eds. Drainage basin nutrient inputs and eutrophication: An integrated approach. European Union/EEC Press. (ACE INC). In preparation.

Paerl, H.W., L.M. Valdes-Weaver, A.R. Joyner, and V. Winkelmann. 2007. Phytoplankton indicators of ecological change in the eutrophying Pamlico Sound system, North Carolina. Ecological Applications 17(5) Supplement: S88-S101. (ACE INC)

Patil, G.P., R.P. Brooks, W.L. Myers, D.J. Rapport, C. Taillie. 2001. Ecosystem health and its measurement at the landscape scale: Towards the next generation of quantitative assessments. Ecosystem Health 7(4):307-316. (ASC)

Patil, G. P., J. Bishop, W.L. Myers, C. Taillie, R. Vraney, and D. H. Wardrop. 2004. Detection and delineation of critical areas using echelons and spatial scan statistics with synoptic cellular data. Environmental and Ecological Statistics 11 (2): 139 – 164. (ASC)

Patil, G.P., R.P. Brooks, W.L. Myers, C. Taillie. 2002. Multiscale advanced raster map analysis system for measuring ecosystem health at the landscape scale: A novel synergistic consortium initiative. In: D. Rapport, W. Lasley, D. Rolston, O. Nielsen, C. Qualset, A. Damania, eds. Managing for Healthy Ecosystems. CRC Press/Lewis Publishers, Boca Raton, FL, pp. 567-576. (ASC)

Pawley, A., S. Detwiler, C. Christian. 2002. A brief overview of historical data sources for the San Francisco Bay Estuary. Bay Institute. (PEEIR)

Pawley, A. 2006. Tidal marsh indicators: a progress report with emphasis on the San Francisco Estuary. Ecohealth. (PEEIR) In press.

Peierls, B.L., R.R. Christian and H.W. Paerl. 2003. Water Quality and phytoplankton as indicators of hurricane impacts on a large estuarine ecosystem. Estuaries 26:1329-1343. (ACE INC)

Pengra, B.W., C.A. Johnston, T.R. Loveland. 2007. Remote sensing of Phragmites australis with the EO-1 Hyperion Sensor. Remote Sensing of Environment 108:74-81. (GLEI)

Peterson, A.C. and G.J. Niemi. 2007. Evaluation of the Ohio Rapid Assessment Method for wetlands in the western Great Lakes: An analysis using bird communities. Journal of Great Lakes Res. 33(SI3):280-291. (GLEI)

Peterson, G.S., M.E. Sierszen, P.M. Yurista, and J.R. Kelly. 2007. Stable nitrogen isotopes of plankton and benthos reflect a landscape-level influence on Great Lakes coastal ecosystems. Journal of Great Lakes Res. 33(SI3): 27-41 (GLEI)

Piehler, M.F., J. Dyble, P.H. Moisander, J.L. Pinckney, H.W. Paerl. 2002. Effects of modified nutrient concentrations and ratios on the structure and function of the native phytoplankton community in the Neuse River Estuary, North Carolina USA. Aquatic Ecology 36: 371-385. (ACE INC)

Piehler, M.F., L.J. Twomey, N.S. Hall and H.W. Paerl. 2004. Impacts of inorganic nutrient enrichment on the phytoplankton community structure and function in Pamlico Sound, NC USA. Estuarine, Coastal and Shelf Science 61:197-207. (ACE INC)

Pillai, M.C., C.A. Vines, A.H. Wikramanayake and G.N. Cherr. 2003. Polycyclic aromatic hydrocarbons disrupt axial development in sea urchin embryos through a -Catenin dependent pathway. Toxicology 186: 93-108. (PEEIR)

Pozhitkov, A., B. Chernov, G. Yershov, and P.A. Noble. 2005. Evaluation of gel-pad oligonucleotide microarray technology using artificial neural networks. Applied and Environmental Microbiology 71:8663-8676. (CEER-GOM)

Pozhitkov, A., P.A. Noble, T. Domazet-Loso, A.W. Nolte, R. Sonnenbert, P. Staehler, M. Beier, and D. Tautz. 2006. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research 34: e66. (CEER-GOM)

Pozhitkov, A. and P.A. Noble. 2006. Revision of the nonequilibrium dissociation approach for identifying mixed microbial communities using oligonucleotide DNA arrays. Nucleic Acids Research (CEER-GOM) In review.

Pozhitkov, A., K.D. Bailey, and P.A. Noble. Statistically robust quantification and identification of microorganisms by analysis of hybridization patterns using oligonucleotide microarrays. BMC Genomics (CEER-GOM) Accepted.

Price, S.J., D.R. Marks, R.W. Howe, J. Hanowski, G.J. Niemi. 2004. The importance of spatial scale for conservation and assessment of anuran populations in coastal wetlands of the western Great Lakes. Landscape Ecology 20:441-454. (GLEI)

Price, S.J., R.W. Howe, J.M. Hanowski, R.R. Regal, G.J. Niemi, and C.R. Smith. 2007. Are Anurans of Great Lakes coastal wetlands reliable indicators of ecological condition? Journal of Great Lakes Res. 33(SI3):211-223 (GLEI)

Rakocinski, C.F. and G.A. Zapfe. 2005. Chapter 20. Macrobenthic process indicators of estuarine condition. In S.A. Bortone, ed., Estuarine Indicators. CRC Press. Boca Raton, FL, pp. 315-331. (CEER-GOM)

Rakocinski, C.F. and J.A. McLelland. Macrofauna. Chapter TBA. In M.S. Peterson, G.L. Waggy, and M. Woodrey, eds., The Grand Bay National Estuarine Research Reserve Site Profile, Biloxi, Mississippi. (CEER-GOM) In press.

Reavie, Euan D., Richard P. Axler, Gerald V. Sgro, Nicholas P. Danz, John C. Kingston, Amy R. Kireta, Terry N. Brown, Thomas P. Hollenhorst, Michael J. Ferguson. 2006. Diatom-based weighted averaging transfer functions for Great Lakes coastal water quality: relationships to watershed characteristics. Journal of Great Lakes Research. (GLEI) In press.

Reavie, E.D. 2006. Diatom indicator solutions for any budget. Ecohealth. (GLEI) In review.

Reavie, E.D., R.P. Axler, G.V. Sgro, N.P. Danz, J.C. Kingston, A.R. Kireta, T.N. Brown, T.P. Hollenhorst. 2006. Diatom-based multimetric index of disturbance for Great Lakes coastlines. Environmental Bioindicators (GLEI) In preparation.

Reavie, E.D. 2007. A diatom-based water quality model for Great Lakes coastlines. Journal of Great Lakes Research 33(SI3):86-92. (GLEI)

Reynolds-Fleming, J.V., J.G. Fleming, R.A. Luettich. 2002. Portable, autonomous vertical profiler for estuarine applications. Estuaries 25(1):142-147. (ACE INC)

Reynolds-Fleming, J.V., R.A. Luettich, Jr. 2004. Wind-driven lateral variability in a partially mixed estuary. Estuarine, Coastal, and Shelf Science 60:395-407. (ACE INC)

Reynolds-Fleming, J.V., R.A. Luettich, Jr. Lateral variability of dissolved oxygen and density in a shallow, partially mixed estuary. Estuaries. (ACE INC). In preparation.

Reynolds-Fleming, J.V. R.A. Luettich, Jr. Simulation of lateral salinity variability in a shallow, wind-driven estuary affected by fish kills. Ocean Dynamics. (ACE INC). In preparation.

Rheinhardt, R., M. Brinson, M. McKenney-Easterling, J. Rubbo, R. Brooks, J. Hite, and B. Armstrong. Applying indicators of riparian condition to reach and watershed assessments: a case study for three coastal plain watersheds in North Carolina. Ecological Indicators (ASC) In review.

Rheinhardt, R., M. Brinson, R. Christian, K. Miller, G. Meyer, C. Bason, and E. Hardison. 2005. Development of Ecological Assessments for Planning Coastal Plain Stream Restoration in Coastal North Carolina. Report presented to the North Carolina Ecosystem Enhancement Program. (ASC)

Richmond, C.E., D.L. Breitburg, and K.A. Rose. The effect of stress tolerance on the relationship between species richness and system function. Ecological Modelling. (CEER-GOM). Submitted.

Roepke, T.A., M. J. Snyder, and G. N. Cherr. Estrogens and estrogen mimics adversely affect development of sea urchin embryos at environmentally relevant concentrations. Aquatic Toxicology. In review. (PEEIR)

Roman, M.R., J.E. Adolf, J. Bichy, W.C. Boicourt, L.W. Harding, Jr., E.D. Houde, S. Jung, D.G. Kimmel, W.D. Miller, and X. Zhang. 2005. Stimulation of plankton and fish abundance in Chesapeake Bay by Hurricane Isabel. EOS, Transactions, American Geophysical Union 86: 261-265. (ACE INC)

Rose, K.A., C.A. Murphy, S.L. Diamond, L.A. Fuiman, and P. Thomas. 2003. Using nested models and laboratory data for predicting population effects of contaminants on fish: a step towards a bottom-up approach for establishing causality in field studies. Human and Ecological Risk Assessment 9:231-257. (CEER-GOM)

Rose, K.A. Lack of relationship between fish population responses and their life history traits: inaccurate models, incorrect analyses, or importance of site-specific factors. Canadian Journal of Fisheries and Aquatic Sciences. (CEER-GOM) Submitted.

Rose, W.L., Hobbs, R. Nisbet, Green, G. Cherr, and S. Anderson. 2005. Validation of otolith growth rate using Cadmium-exposed larval topsmelt (Atherinops affinis). Environmental Toxicology and Chemistry 24(10):192-200. (PEEIR)

Rosso, P., J. Pushnik, M. Lay, and S. Ustin. 2005. Reflectance properties and physiological responses of Salicornia virginica to heavy metal and petroleum contamination. Environmental Pollution 137 (2): 241-252. (PEEIR)

Rosso, P., S. Ustin and A. Hastings. 2006. Mapping marshland vegetation of San Francisco Bay, California, using hyperspectral data. IEEE Geoscience & Remote Sensing. (PEEIR) In press.

Sgro G.V., Ketterer M.E., Johansen J.R. 2005. Ecology and assessment of the diatom communities of four Lake Erie estuaries using Lange-Bertalot Tolerence Values. Hydrobiologia. (GLEI) Accepted.

Sgro, G.V., E.D. Reavie, J.C. Kingston, A.R. Kireta, M.J. Ferguson, N.P. Danz, J.R. Johansen. Development of a habitat quality index from a diatom-based TP inference model. (GLEI) In preparation.

Roman, M.R., J.E. Adolf, J. Bichy, W.C. Boicourt, L.W. Harding, Jr., E.D. Houde, S. Jung, D.G. Kimmel, W.D. Miller, X. Zhang. 2005. Stimulation of plankton and fish abundance in Chesapeake Bay by Hurricane Isabel. EOS. (ACE INC) In press.

Smith, E. 2002. Tomales Bay water quality status and trends report. Smith & Associates. (PEEIR)

Snyder, R.A., M.A. Lewis, A. Nocker. J.E. Lepo. 2005. Microbial Biofilms as Integrative Sensors of Environmental Quality. In S. Bartone, ed., Estuarine Indicators, CRC press, Boca Raton, FL, pp. 111-126. (CEER-GOM)

Spilseth, S. and S. Morgan. 2006. Evaluation of internal elastomer tags for small, mature crabs. Crustaceana: International Journal of Crustacean Research. (PEEIR) In press.

Steets, B., P.A. Holden. 2003. A mechanistic model of runoff-associated fecal coliform fate and transport through a coastal lagoon. Water Research 37: 589-608. (PEEIR)

Stoermer, E.F., N.A. Andresen. 2006. Atypical Tabularia in coastal Lake Erie, USA. In N. Ognjanova-Rumenova and K. Manoylov, eds. Fossil and Recent Phycological Studies pp. 9-16. Pensoft Publishers, Moscow. (GLEI)

Swackhamer, D.L., H.W. Paerl, S.J. Eisenreich, J. Hurley, K.C. Hornbuckle, M. McLachlan, D. Mount, D. Muir, and D. Schindler. 2004. Impacts of atmospheric pollutant on aquatic ecosystems. Issues in Ecology 12, Ecological Society of America, Washington, DC. (ACE INC & GLEI)

Thomas, P., M.S. Rahman, J.A. Kummer and S. Lawson. 2006. Reproductive endocrine dysfunction in ATlantic croaker exposed to hypoxia. Marine Environmental Research 62:249-253. (CEER-GOM)

Torres, R., M.J. Mwamba, M.A. Goni. 2003. Properties of intertidal sediment mobilized by rainfall. Limnology and Oceanography 48(3) 1245-1253. (ACE INC).

Torres, R., M.A. Goni, G.V. Voulgaris. 2003. Rainfall Effects on Saltmarsh Ecology. In: S. Fagherazzi, L. Blum, M. Marani, eds. Ecogeomorphology of Saltmarshes. AGU Monograph pp. 93-114. (ACE INC)

Torres, R., R. Styles. Effects of Salt Marsh Topography on Tidal Asymmetry. Estuarine Coastal and Shelf Science. (ACE INC) Submitted.

Trebitz, A., J. Brazner, V. Brady and D. Tanner. 2007. Turbidity tolerances of Great Lakes coastal wetland fishes. North American Journal of Fisheries Management 27:619-633. (GLEI)

Trebitz, A.S., J.C. Brazner, A.M. Cotter, M.L. Knuth, J.A. Morrice, G.S. Peterson, M.E. Sierszen, J.A. Thompson, and J.R. Kelly. 2007. Water quality in Great Lakes coastal wetalnds: basin-wide patterns and responses to an anthropogenic disturbance gradient. Journal of Great Lakes Research 33(SI3):67-85. (GLEI)

Tulbure, M.G., C.A. Johnston, and D.L. Auger. 2007. Rapid invasion of a Great Lakes coastal wetland by non-native Phragmites australis and Typha. Journal of Great Lakes Res. 33(SI3):269-279 (GLEI)

Twomey, L.J., M.F. Piehler and H.W. Paerl. 2005. Phytoplankton uptake of ammonium, nitrate and urea in the Neuse River Estuary, NC, USA. Hydrobiologia 533:123-134. (ACE INC)

Tzortziou, M., J.R. Herman, C.L. Gallegos, P.J. Neale, A. Subramaniam, L.W. Harding, Jr., and Z. Ahmad. 2006. Bio-optics of Chesapeake Bay from measurements and radiative transfer calculations. Estuar. Coast. Shelf Sci. (ACE INC) In press.

Urakawa, H., S. El Fantroussi, P.A. Noble, J.J. Kelly, D.A. Stahl. 2003. Single-base-pair mismatch discrimination using oligonucleotide DNA microarrays and melting profiles. Applied and Environmental Microbiology 69:2848-2856. (CEER-GOM)

Ustin, S., M. Lay, and L. Li. 2004. Remote sensing of wetland conditions in West Coast salt marshes. International Symposium on Optical Science and Technology. (PEEIR)

Vähätalo, A. V., R.G. Wetzel and H.W. Paerl. 2005. Light adsorption by phytoplankton and chromatophoric dissolved organic matter in the drainage basin and estuary of the Neuse River, North Carolina (USA). Freshwater Biology 50:477-493. (ACE INC)

Valdes, L.M. and H.W. Paerl. Annual, seasonal and spatial trends in phytoplankton community structure along the Neuse River Estuary-Pamlico Sound continuum, NC (1994-2002). (ACE INC). In preparation.

Valdes, L.M. and H.W. Paerl. The importance of large-scale hydrologic disturbances in structuring phytoplankton communities. (ACE INC). In preparation.

Valdes-Weaver, L.M., M.F. Piehler, J.L. Pinckney, K.E. Howe & K. Rossignol. 2006. Long-term temporal and spatial trends in phytoplankton biomass and class-level taxonomic composition in the hydrologically variable Neuse-Pamlico estuarine continuum, NC, USA. Limnology and Oceanography (ACE INC) In press.

Valentine, Vinton, Charles S. Hopkinson, Jr., Thomas L. Millette, Christopher D. Hayward, Corey Lawrence, and Joshua Goldstein. Formation of ponds in marshes of the Plum Island Sound estuary. Estuarine, Coastal and Shelf Science. (ACE INC) Submitted.

Ward and Lafferty. 2004. The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing? PLoS Biol. 2:542-547. (PEEIR)

Wardrop, D.H., C. Hershner, K. Havens, K. Thornton and D.M. Bilkovic. Developing and communicating a taxonomy of ecological indicators: a case study from the Mid-Atlantic. EcoHealth (ASC) In review.

Wardrop, D.H., J.A. Bishop, M. Easterling, K. Hychka, W. Myers, G.P. Patil, C. Taille. 2005. Use of landscape and land use parameters for classification and characterization of watersheds in the Mid-Atlantic across five physiographic provinces. Environmental and Ecological Statistics 12(2):209-233. (ASC).

Whitehead, A., K. Kuivila, J. Orland, G. Kotelevtsev, and S. Anderson. 2004. Genotoxic effects of agricultural runoff in a California native fish. Environmental Toxicology 23:2868-2877. (PEEIR)

Whipple, A.C., R.A. Luettich, Jr., H.E. Seim. Measurements of Reynolds stress in a Wind Driven Lagoonal Estuary. Ocean Dynamics. (ACE INC) Submitted

Wolter, P.T, C.A. Johnston, G.J. Niemi. 2005. Mapping submerged aquatic vegetation in the U.S. Great Lakes using Quickbird satellite data. International Journal of Remote Sensing 26(23):5255-5274. (GLEI)

Wolter, P., C. Johnston, G.J. Niemi. 2006. Land use, land cover change in the U.S. Great Lakes basin 1992-2001. Journal of Great Lakes Research. (GLEI) In press.

Yang, X. 2005. Special issue: Remote Sensing and GIS for Estuarine Ecosystem Analysis. International Journal of Remote Sensing 26(23). (EaGLe)

Yang, X. 2005. Remote sensing and GIS applications for estuarine ecosystem analysis: an overview. International Journal of Remote Sensing 26(23): 5347-5356. (CEER-GOM).

Yang, X. 2006. Estimating Urban Imperviousness with Remotely Sensed Imagery. IEEE Geoscience and Remote Sensing Letters 3(1): 6-9. (CEER-GOM)

Yang, X. and Liu, Z. 2005a. Use of Satellite-Derived Landscape Imperviousness Index to Characterize Urban Spatial Growth. Journal of Computers, Environment and Urban Systems 29: 524-540. (CEER-GOM)

Yang, X. and Liu, Z. 2005b. Using satellite imagery and GIS to characterize land use and land cover changes in an estuarine watershed. International Journal of Remote Sensing 26(23): 5275-5296. (CEER-GOM)

Yang, X. and Liu, Z. 2005c. Quantifying landscape pattern and its change in an estuarine watershed using satellite imagery and landscape metrics. International Journal of Remote Sensing 26(23): 5297-5323. (CEER-GOM)

Yeager, C.L.J., L.W. Harding, Jr., and M.E. Mallonee. 2005. Phytoplankton production, biomass and community structure following a summer nutrient pulse in Chesapeake Bay. Aquat. Ecol. 39, 135-149. (ACE INC)

Yurista, P.M., J.R. Kelly, S.E. Miller. 2003. Evaluation of optically acquired zooplankton size-spectrum data as a potential tool for assessment of conditions in the Great Lakes. Environmental Management. (GLEI). In internal review.

Zedler, J.B. and K.W. Potter. 2005. Southern Wisconsin herbaceous wetlands. In Don Waller and Tom Rooney, eds., Vanishing present. University of Wisconsin Press. (GLEI)

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