Journal Publications for Center:

EAGLES - Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico

Grant Number SU839462

Journal Article (64)
Reference Type Citation Progress Report Year Document Sources
Journal Article Breitburg DL, Adamack A, Rose KA, Kolesar SE, Decker MB, Purcell JE, Keister JE, Cowan JH. The pattern and influence of low dissolved oxygen in the Patuxent River, a seasonally hypoxic estuary. Estuaries 2003;26(2A):280-297.
R829458C009 (2003)
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Journal Article

Brouwer M, Larkin P, Brown-Peterson N, King C, et al. Effects of hypoxia on gene and protein expression in the blue crab, Callinectes sapidus. Marine Environmental Research 2004;58(2-5):787-792.


abstract available     full text available
R829458C003 (2003)
R829458C003 (2004)
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Journal Article Brouwer M, Brown-Peterson NJ, Larkin P, Patel V, Denslow N, Manning S, Brouwer TH. Molecular and whole animal responses of grass shrimp, Palaemonetes pugio, exposed to chronic hypoxia. Journal of Experimental Marine Biology and Ecology 2007;341(1):16-31.
abstract available     full text available
R829458C003 (2005)
Journal Article Brown-Peterson NJ, Larkin P, Denslow N, King C, Manning S, Brouwer M. Molecular indicators of hypoxia in the blue crab Callinectes sapidus. Marine Ecology Progress Series 2005;286:203-215.
abstract available    
R829458C003 (2004)
R829458C003 (2005)
Journal Article

Popular article featuring Cheek & Thomas projects: Janet Raloff. Choked Up: How dead zones affect fish reproduction. Science News 2004;166(20):309.


R829458C005 (2004)
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Journal Article El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Applied and Environmental Microbiology 2003;69(4):2377-2382.
abstract available     full text available
R829458 (2005)
R829458C004 (2003)
Journal Article Ferguson HJ, Rakocinski CF. Tracking marsh restoration using macrobenthic metrics: implementing a functional approach. Wetlands Ecology and Management 2008;16(4):277-289.
abstract available     full text available
R829458 (2005)
Journal Article Fuiman LA, Rose KA, Cowan Jr. JH, Smith EP. Survival skills required for predator evasion by fish larvae and their relation to laboratory measures of performance. Animal Behaviour 2006;71(6):1389-1399.
abstract available    
R829458C009 (2005)
Journal Article Gough HL, Dahl AL, Tribou E, Noble PA, Gaillard J-F, Stahl DA. Elevated sulfate reduction in metal-contaminated freshwater lake sediments. Journal of Geophysical Research: Biogeosciences 2008;113(G4):G04037, doi:10.1029/2008JG000738.
abstract available    
R829458 (2005)
R829458C004 (2003)
R829458C004 (2004)
Journal Article Han LH, Jordan KJ. Estimating and mapping chlorophyll-a concentration in Pensacola Bay, Florida using Landsat ETM+ data. International Journal of Remote Sensing 2005;26(23):5245-5254.
abstract available     full text available
R829458C001 (2004)
R829458C001 (2005)
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Journal Article Han LH. Estimating chlorophyll-a concentration using first-derivative spectra in coastal water. International Journal of Remote Sensing 2005;26(23):5235-5244
abstract available     full text available
R829458C001 (2004)
R829458C001 (2005)
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Journal Article Henneman LRF, Shen H, Liu C, Hu Y, Mulholland JA, Russell AG. Responses in ozone and its production efficiency attributable to recent and future emissions changes in the Eastern United States. Environmental Science & Technology 2017;51(23):13797-13805.
abstract available     full text available
R835880 (2016)
R835880 (2017)
R835880 (2018)
R835880 (Final)
Journal Article Kelly JJ, Siripong S, McCormack J, Janus LR, Urakawa H, El Fantroussi S, Noble PA, Sappelsa L, Rittmann BE, Stahl DA. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research 2005;39(14):3229-3238.
abstract available     full text available
R829458 (2005)
R829458C004 (2005)
Journal Article Landry CA, Steele SL, Manning S, Cheek AO. Long term hypoxia suppresses reproductive capacity in the estuarine fish, Fundulus grandis. Comparative Biochemistry and Physiology-Part A: Molecular & Integrative Physiology 2007;148(2):317-323.
abstract available     full text available
R829458 (2005)
Journal Article Lawal AS, Guan X, Liu C, Henneman LRF, Vasilakos P, Bhogineni V, Weber RJ, Nenes A, Russell AG. Linked response of aerosol acidity and ammonia to SO2 and NOX emissions reductions in the United States. Environmental Science & Technology 2018;52(17):9861-9873.
abstract available     full text available
R835880 (2017)
R835880 (2018)
R835880 (Final)
R835882 (Final)
Journal Article Lewitus AJ, White DL, Tymowski RG, Geesey ME, Hymel SN, Noble PA. Adapting the CHEMTAX method for assessing phytoplankton taxonomic composition in Southeastern U.S. estuaries. Estuaries 2005;28(1):160-172.
abstract available    
R829458 (2005)
R829458C004 (2004)
R829458C004 (2005)
Journal Article Martinez ML, Landry C, Boehm R, Manning S, Cheek AO, Rees BB. Effects of long-term hypoxia on enzymes of carbohydrate metabolism in the Gulf killifish, Fundulus grandis. Journal of Experimental Biology 2006;209(19):3851-3861.
abstract available    
R829458C005 (2005)
Journal Article Morris JT, Porter D, Neet M, Noble PA, Schmidt L, Lapine LA, Jensen JR. Integrating LIDAR elevation data, multi-spectral imagery and neural network modelling for marsh characterization. International Journal of Remote Sensing 2005;26(23):5221-5234.
abstract available     full text available
R828677 (Final)
R828677C003 (2004)
R828677C003 (Final)
R829458 (2005)
R829458C004 (2003)
R829458C004 (2005)
Journal Article Moss JA, Nocker A, Lepo JE, Snyder RA. Stability and change in estuarine biofilm bacterial community diversity. Applied and Environmental Microbiology 2006;72(9):5679-5688.
abstract available     full text available
R829458 (2005)
R829458C002 (2004)
R829458C002 (2005)
Journal Article

Murphy CA, Rose KA, Thomas P. 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 2005;19(3):395-409.


abstract available     full text available
R829458C005 (2003)
R829458C009 (2003)
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Journal Article Murphy CA, Rose KA, Alvarez MC, Fuiman LA. Modeling larval fish behavior:scaling the sublethal effects of methylmercury to population-relevant endpoints. Aquatic Toxicology 2008;86(4):470-484.
abstract available     full text available
R827399 (2001)
R829458 (2005)
Journal Article Niemi G, Wardrop D, Brooks R, Anderson S, Brady V, Paerl H , Rakocinski C, Brouwer M, Levinson B, McDonald M. Rationale for a new generation of indicators for coastal waters. Environmental Health Perspectives 2004;112(9):979-986.
abstract available     full text available
R828675 (2004)
R828675 (Final)
R828677C001 (Final)
R828684 (Final)
R829458C003 (2003)
R829458C008 (2003)
R829458C008 (2004)
Journal Article Noble PA, Tymowski RG, Fletcher M, Morris JT, Lewitus AJ. Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in southeastern United States. Applied and Environmental Microbiology 2003;69(7):4129-4143.
abstract available     full text available
R826944 (2000)
R826944 (Final)
R828677C003 (2003)
R829458 (2005)
R829458C004 (2003)
R829458C004 (2005)
Journal Article Noble PA, Tribou EH. Neuroet: an easy-to-use artificial neural network for ecological and biological modeling. Ecological Modelling 2007;203(1-2):87-98.
abstract available     full text available
R829458 (2005)
R829458C004 (2004)
Journal Article Nocker A, Lepo JE, Snyder RA. Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. Applied and Environmental Microbiology 2004;70(11):6834-6845.
abstract available     full text available
R829458 (2005)
R829458C002 (2003)
R829458C002 (2004)
Journal Article Nocker A, Lepo JE, Martin LL, Snyder RA. Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations. Microbial Ecology 2007;54(3):532-542.
abstract available    
R829458 (2005)
R829458C002 (2004)
Journal Article Pozhitkov AE, Bailey KD, Noble PA. Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays. Journal of Microbiological Methods 2007;70(2):292-300.
abstract available     full text available
R829458 (2005)
Journal Article Pozhitkov AE, Tautz D, Noble PA. Oligonucleotide microarrays: widely applied—poorly understood. Briefings in Functional Genomics and Proteomics 2007;6(2):141-148.
abstract available     full text available
R829458 (2005)
Journal Article Pozhitkov AE, Stedtfeld RD, Hashsham SA, Noble PA. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Research 2007;35(9):e70.
abstract available     full text available
R829458 (2005)
Journal Article Pozhitkov A, Chernov B, Yershov G, Noble PA. Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks. Applied and Environmental Microbiology 2005;71(12):8663-8676.
abstract available     full text available
R829458 (2005)
R829458C004 (2004)
R829458C004 (2005)
Journal Article Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research 2006;34(9):e66.
abstract available     full text available
R829458 (2005)
R829458C004 (2005)
Journal Article Rahman MS, Thomas P. Molecular cloning, characterization and expression of two hypoxia-inducible factor alpha subunits, HIF-1α and HIF-2α, in a hypoxia-tolerant marine teleost, Atlantic croaker (Micropogonias undulatus). Gene 2007;396(2):273-282.
abstract available     full text available
R829458 (2005)
Journal Article Rakocinski CF. Linking allometric macrobenthic processes to hypoxia using the Peters mass balance model. Journal of Experimental Marine Biology and Ecology 2009;381(Suppl 1):S13-S20.
abstract available     full text available
R829458 (2005)
Journal Article Richmond CE, Breitburg DL, Rose KA. The role of environmental generalist species in ecosystem function. Ecological Modelling 2005;188(2-4):279-295.
abstract available     full text available
R829458 (2005)
Journal Article

Richmond CE, Breitburg DL, Rose KA. The effect of stress tolerance on the relationship between species richness and system function. Ecological Modelling.


R829458C009 (2004)
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Journal Article Rose KA, Murphy CA, Diamond SL, Fuiman LA, Thomas P. 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 2003;9(1):231-257.
abstract available     full text available
R829458C009 (2003)
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Journal Article Rose KA. Lack of relationship between simulated fish population responses and their life history traits: inadequate models, incorrect analysis, or site-specific factors?. Canadian Journal of Fisheries and Aquatic Sciences 2005;62(4):886-902
R829458C009 (2003)
R829458C009 (2004)
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Journal Article Thomas P, Rahman MS, Kummer JA, Lawson S. Reproductive endocrine dysfunction in Atlantic croaker exposed to hypoxia. Marine Environmental Research 2006;62(Suppl 1):S249-S252.
abstract available     full text available
R826130 (1999)
R829458C005 (2005)
Journal Article Thomas P, Rahman MS, Khan IA, Kummer JA. Widespread endocrine disruption and reproductive impairment in an estuarine fish population exposed to seasonal hypoxia. Proceedings of The Royal Society B: Biological Sciences 2007;274(1626):2693-2701.
abstract available     full text available
R829458 (2005)
Journal Article Thomas P, Rahman MS. Biomarkers of hypoxia exposure and reproductive function in Atlantic croaker: a review with some preliminary findings from the northern Gulf of Mexico hypoxic zone. Journal of Experimental Marine Biology and Ecology 2009;381(Suppl 1):S38-S50.
abstract available     full text available
R829458 (2005)
Journal Article Thomas P, Rahman MS. Chronic hypoxia impairs gamete maturation in Atlantic croaker induced by progestins through nongenomic mechanisms resulting in reduced reproductive success. Environmental Science & Technology 2009;43(11):4175-4180.
abstract available    
R829458 (2005)
Journal Article Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology 2003;69(5):2848-2856.
abstract available     full text available
R829458 (2005)
R829458C004 (2003)
R829458C004 (2005)
Journal Article Yang X, Liu Z. Quantifying landscape pattern and its change in an estuarine watershed using satellite imagery and landscape metrics. International Journal of Remote Sensing 2005;26(23):5297-5323.
abstract available     full text available
R829458C007 (2004)
R829458C007 (2005)
Journal Article Yang XJ. Remote sensing and GIS applications for estuarine ecosystem analysis:an overview. International Journal of Remote Sensing 2005;26(23):5347-5356.
abstract available     full text available
R829458C007 (2004)
R829458C007 (2005)
Journal Article Yang X. Estimating landscape imperviousness with remotely sensed imagery. IEEE Geoscience and Remote Sensing Letters 2006;3(1):6-9.
abstract available     full text available
R829458C007 (2004)
R829458C007 (2005)
Journal Article Yang X, Lo CP. Using a time series of satellite imagery to detect land use and land cover changes in the Atlanta, Georgia metropolitan area. International Journal of Remote Sensing 2002;23(9):1775-1798
R829458C007 (2003)
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Journal Article

Yang X. Geospatial technologies for coastal and estuarine ecosystem analysis: status and research priorities. Journal of Coastal Research


R829458C007 (2004)
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Journal Article Yang X, Liu Z. Use of satellite-derived landscape imperviousness index to characterize urban spatial growth. Computers, Environment and Urban Systems 2005; 29(5):524-540.
abstract available     full text available
R829458C007 (2003)
R829458C007 (2004)
R829458C007 (2005)
Journal Article Yang X, Liu Z. Using satellite imagery and GIS for land-use and land-cover change mapping in an estuarine watershed. International Journal of Remote Sensing 2005;26(23):5275-5296.
abstract available     full text available
R829458C007 (2005)
Journal Article Yang X, Liu Z. Use of remote sensing and landscape metrics to analyze estuarine landscape changing dynamics. International Journal of Remote Sensing .
R829458C007 (2003)
R829458C007 (2004)
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Journal Article Zhang B, Shen H, Liu P, Guo H, Hu Y, Chen Y, Xie S, Xi Z, Skipper TN, Russell AG. Significant contrasts in aerosol acidity between China and the United States. Atmos Chem Phys 2021;21:8341–56. doi:10.5194/acp-21-8341-2021.
R835880 (Final)
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Journal Article Chen Y, Shen H, Russell AG. Current and Future Responses of Aerosol pH and Composition in the US to Declining SO2 Emissions and Increasing NH3 Emissions. Environmental science & technology 2019;53(16):9646-55.
abstract available    
R835880 (2019)
R835880 (Final)
Journal Article Shen H, Tao S, Chen Y, Odman MT, Zou Y, Huang Y, Chen H, Zhong Q, Zhang Y, Chen Y, Su S. Global Fire Forecasts Using Both Large‐Scale Climate Indices and Local Meteorological Parameters. Global Biogeochemical Cycles 2019;33(8):1129-45.
abstract available    
R835880 (2019)
R835880 (Final)
Journal Article Shen H, Chen Y, Li Y, Russell AG, Hu Y, Henneman LR, Odman MT, Shih JS, Burtraw D, Shao S, Yu H. Relaxing energy policies coupled with climate change will significantly undermine efforts to attain us ozone standards. One Earth 2019;1(2):229-39.
abstract available    
R835880 (2019)
R835880 (Final)
Journal Article Keyes AT, Lambert KF, Burtraw D, Buonocore JJ, Levy JI, Driscoll CT. The Affordable Clean Energy rule and the impact of emissions rebound on carbon dioxide and criteria air pollutant emissions. Environmental Research Letters 2019;14:044018. doi:10.1088/1748-9326/aafe25.
R835880 (Final)
Journal Article Nenes A, Pandis SN, Weber RJ, Russell A. Aerosol pH and liquid water content determine when particulate matter is sensitive to ammonia and nitrate availability. Atmospheric Chemistry and Physics 2020;20:3249–58. doi:10.5194/acp-20-3249-2020.
R835880 (Final)
Journal Article Chen Y, Shen H, Shih J-S, Russell AG, Shao S, Hu Y, Odman MT, Nenes A, Pavur GK, Zou Y, Chen Z, Smith RA, Burtraw D, Driscoll CT. Greater contribution from agricultural sources to future reactive nitrogen deposition in the United States. Earth’s Future 2020;8:e2019EF001453. doi:10.1029/2019EF001453.
R835880 (Final)
Journal Article Shen H, Chen Y, Hu Y, Ran L, Lam SK, Pavur GK, Zhou F, Pleim JE, Russell AG. Intense warming will significantly increase cropland ammonia volatilization threatening food security and ecosystem health. One Earth 2020;3:126–34. doi:10.1016/j.oneear.2020.06.015.
R835880 (Final)
Journal Article Henneman LRF, Shen H, Hogrefe C, Russell AG, Zigler CM. Four decades of United States mobile source pollutants:Spatial–temporal trends assessed by ground-based monitors, air quality models, and satellites. Environmental Science & Technology 2021;55:882–92. doi:10.1021/acs.est.0c07128.
full text available
R835880 (Final)
Journal Article Chen Y, Shen H, Kaiser J, Hu Y, Capps SL, Zhao S, Hakami A, Shih J-S, Pavur GK, Turner MD, Henze DK, Resler J, Nenes A, Napelenok SL, Bash JO, Fahey KM, et al. High-resolution hybrid inversion of IASI ammonia columns to constrain US ammonia emissions using the CMAQ adjoint model. Atmospheric Chemistry and Physics 2021;21:2067–82. doi:10.5194/acp-21-2067-2021.
R835880 (Final)
Journal Article Shen H, Liu B, Chen Y, Zhu X, Yun X, Meng W, Lu C, Shen G, Hu Y, Russell AG, Smith KR, Tao S. Individual and population level protection from particulate matter exposure by wearing facemasks. Environment International 2021;146:106026. doi:10.1016/j.envint.2020.106026.
R835880 (Final)
Journal Article Shen H, Hou W, Zhu Y, Zheng S, Ainiwaer S, Shen G, Chen Y, Cheng H, Hu J, Wan Y, Tao S. Temporal and spatial variation of PM2.5 in indoor air monitored by low-cost sensors. Science of The Total Environment 2021;770:145304. doi:10.1016/j.scitotenv.2021.145304.
R835880 (Final)
Journal Article Qian Y, Henneman LRF, Mulholland JA, Russell AG. Empirical development of ozone isopleths:Applications to Los Angeles. Environmental Science & Technology Letters 2019. doi:10.1021/acs.estlett.9b00160.
R835880 (Final)
Journal Article Shen H, Shen G, Chen Y, Russell AG, Hu Y, Duan X, Meng W, Xu Y, Yun X, Lyu B, Zhao S, Hakami A, Guo J, Tao S, Smith KR. Increased air pollution exposure among the Chinese population during the national quarantine in 2020. Nature Human Behaviour 2021;5:239–46. doi:10.1038/s41562-020-01018-z.
R835880 (Final)