Gulf Coast Research Laboratory

Research Index

Consortium for Estuarine Ecoindicator Research for the Gulf of Mexico

Publications

Final Report

Neural Net Data Management

Pozhitkov, A. E., P. A. Noble, T. Domazet-Loso, A. Nolte, 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. PDF
Urakawa, H., P. A. Noble, S. El Fantroussi, J. J. Kelly and D. A. Stahl. 2002. Single-base pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Applied and Environmental Microbiology 68: 235-244.
Urakawa, H., S. El Fantroussi, H. Smidt, J.C. Smoot. E.H. Tribou, J. J. Kelly, P. A. Noble, and D. A. Stahl. 2003. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology 69: 2848-2856. PDF
El Fantroussi, S., H. Urakawa, A. E. Bernhard, J. J. Kelly, P. A. Noble, H. Smidt, G. M. Yershov, and D. A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal rRNAs hybridized to oligonucleotide microarrays. Applied and Environmental Microbiology 69: 2377-2382
Noble, P. A., R. G. Tymowski, M. Fletcher, J. T. Morris , and A. J. Lewitus. 2003. Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in Southeastern United States. Applied and Environmental Microbiology 69: 4129-4143. PDF
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 taxonomic composition in southeastern U.S. estuaries. Estuaries. 28:160-172. PDF
Morris, J.T., D. Porter, M. Neet, P.A. Noble, L. Schmidt, L. A. Lapine, and J.R. Jensen. 2005. Integrating LIDAR elevation data, multi-spectral imagery and neural network modeling for marsh characterization. Int. J. Remote Sensing 26:5221-5234. PDF
Noble, P.A. and E.H. Tribou. 2005. Neuroet: an easy-to-use artificial neural network for ecological and biological modeling. Ecol. Modelling. (in press). pdf=Noble(Neuroet)
Pozhitkov, A., B. Chernov, G. Yershov, and P.A. Noble. 2005. Evaluation of Gel-Pad oligonucleotide microarray technology by using artificial neural networks. Appl. Environ. Microbiol. 71:8663-8676. PDF

GIS

Han, L. 2005. Estimating chlorophyll-a concentration using first-derivative spectra in coastal water. International Journal of Remote Sensing 26(23):5235-5244. PDF
Han, L. and K. Jordan. 2005. Estimating and mapping chlorophyll-a concentration in Pensacola Bay, Florida using Landsat ETM+ data. International Journal of Remote Sensing 26(23):5245-5254. PDF

Remote Sensing

Yang, X., 2006. Estimating Landscape Imperviousness Index From Satellite Imagery. IEEE Geoscience and Remote Sensing Letters (in press) PDF
Yang, X. (ed.) 2005. Remote sensing and GIS for estuarine ecosystem analysis. International Journal of Remote Sensing, 26(23):5163-5356.
Yang, X. 2005. Cartographic visualization techniques for coastal watershed assessment. Proceedings of the 22nd International Cartographic Conference, 11-16 July 2005, A Coruna, Spain.
Yang, X. 2005. Remote sensing and GIS applications for estuarine ecosystem analysis: an overview. International Journal of Remote Sensing, 26(23):5347-5356. PDF
Yang, X. and Liu, Z. 2005. Use of satellite-derived landscape imperviousness index to characterize urban spatial growth. Computers, Environment and Urban Systems, 29(5):524-540. PDF
Yang, X. and Liu, Z., 2005. 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. PDF
Yang, X. and Liu, Z., 2005. 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. PDF
Yang, X. 2005. Use of Lidar elevation data to construct a high-resolution digital terrain model for an estuarine marsh area. International Journal of Remote Sensing, 26(23):5163-5166. PDF

Fish

Hiramatsu, N., A. Cheek, C. Sullivan, T. Matsubara & A. Hara. 2005. Vitellogenesis and endocrine disruption. In: T. Mommsen & T. Moon (ed.) Biochemical and Molecular Biology of Fishes: Environmental Toxicology, Elsevier, New York and Amsterdam.
Martinez, M.L., C.A. Landry, R. Boehm, S. Manning, A.O. Cheek, B.B. Rees. Glycolytic enzyme responses to long-term hypoxia in the Gulf killifish, Fundulus grandis. Submitted to Journal of Experimental Biology.
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. (in review)
Murphy, C.A., K.A. Rose, and P. Thomas. 2005. 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 19:395-409. PDF
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 (in review)
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 toward a bottom-up approach for establishing causality in field studies. Human and Ecological Risk Assessment 9:231-257. PDF
Rose, K.A. 2005. Lack of relationship between simulated fish population responses and their life history traits: inaccurate models, incorrect analysis, or site-specific factors. Canadian Journal of Fisheries and Aquatic Sciences 62:886-902. PDF
Richmond, C.E., D.L. Breitburg, K.A. Rose. 2005. The role of environmental generalist species in ecosystem function. Ecological Modelling 188:279-295. PDF

Crustaceans

Brouwer, M., P. Larkin, N. J. Brown-Peterson, C. King, S. Manning and N. Denslow. 2004. Effects of hypoxia on gene and protein expression in the blue crab, Callinectes sapidus. Marine Environmental Research 58:787-792. PDF
Brouwer, M., N.J. Brown-Peterson, P. Larkin, S. Manning, N. Denslow and K.A. Rose. 2005. Molecular and organismal indicators of chronic and intermittent hypoxia in marine crustacean. Estuarine Indicators, S. Bortone, Ed. CRC Press, Boca Raton, FL. pp:261-274. PDF
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. PDF

Biofilms

M. A. Lewis, R. A. Snyder, A. Nocker. J.E. Lepo.. 2004. Microbial Biofilms as Integrative Sensors of Environmental Quality. Peer-reviewed (Snyder also delivered oral presentation). Estuarine Indicators Symposium, Sanibel, Fla.; (CRC press, Steve Bortone, ed.)
Nocker A., J. E. Lepo, and R. A. Snyder. 2004. Influence of an oyster reef on development of the microbial heterotrophic Community of an estuarine biofilm. Appl. Environ. Microbiol. 70:6834-6845. PDF

Macrobenthos

Rakocinski, C.F., and G.A. Zapfe. 2005. Chapter 20. Macrobenthic process indicators of estuarine condition. S.A. Bortone (ed.). Estuarine Indicators. CRC Press. Boca Raton, Florida. PDF
Rakocinski, C.F. and J.A. McLelland (2005). Macroinfauna. CHAPTER TBA, 18 pp. In: Peterson, M.S., G.L. Waggy, and M. Woodrey (eds.) The Grand Bay National Estuarine Research Reserve Site Profile, Biloxi, Mississippi.

General Issues

Niemi, Gerald, Denice Wardrop, Robert Brooks, Susan Anderson, Valerie Brady, Hans Paerl, Chet Rakocinski, Marius Brouwer, Barbara Levinson, Michael McDonald. 2004. Rationale for a New Generation of Ecological Indicators for Coastal Waters. Env. Health Perspect. 112: 979-986. PDF
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