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Book

Maier D, Megler VM, Baptista AM, Jaramillo A, Seaton C, Turner PJ. 2012. Navigating Oceans of Data. 7338:1-19.

Abdel-Jabbar N, Baptista AM, Karna T, Turner P, Sen G. 2013. US Experience Will Advance Gulf Ecosystem Research.

Journal Article

Anderson CR, Davis RE, Bandolin NS, Baptista AM, Tebo BM. 2011. Analysis of in situ manganese(II) oxidation in the Columbia River and offshore plume: linking Aurantimonas and the associated microbial community to an active biogeochemical cycle. Environmental Microbiology.

Roegner GC, Seaton C, Baptista AM. 2011. Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries and Coasts. 34(2):281-296.

Green V, Bueno Watts N, Wegner K, Thompson M, Johnson AF, Peterson TD, Baptista AM. 2013. Coastal Margin Science and Education in the Era of Collaboratories. Currents. 28(3)

Roegner GC, Needoba JA, Baptista AM. 2011. Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.

Priest GR, Goldfinger C, Wang K, Witter RC, Zhang Y, Baptista AM. 2009. Confidence levels for tsunami-inundation limits in northern Oregon inferred from a 10,000-year history of great earthquakes at the Cascadia subduction zone. Natural Hazards. 54(1):27-73.

Azevedo A., Oliveira A, Fortunato AB, Zhang Y, Baptista AM. 2014. A cross-scale numerical modeling system for management support of oil spill accidents. Marine Pollution Bulletin. 80(1-2):132-147.

Bräuer SL, Adams C, Kranzler K, Murphy D, Xu M, Zuber P, Simon HM, Baptista AM, Tebo BM. 2011. Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3)

Bräuer SL, Kranzler K, Goodson N, Murphy D, Simon HM, Baptista AM, Tebo BM. 2013. Dark Carbon Fixation in the Columbia River’s Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors. Estuaries and Coasts. 36:1073-1083.

Miller J, Teel D, Baptista AM, Morgan C. 2013. Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences.

Zhang Y, Baptista AM. 2008. An Efficient and Robust Tsunami Model on Unstructured Grids. Part I: Inundation Benchmarks. Pure and Applied Geophysics. 165(11-12):2229-2248.

Frolov S, Baptista AM, Zhang Y, Seaton C. 2009. Estimation of ecologically significant circulation features of the Columbia River estuary and plume using a reduced-dimension Kalman filter. Continental Shelf Research. 29(2):456-466.

Burke BJ, Anderson JJ, Baptista AM. 2014. Evidence for multiple navigational sensory capabilities by Chinook salmon. Aquatic Biology.

Bruland KW, Lohan MC, Aguilar-Islas AM, Smith GJ, Sohst B, Baptista AM. 2008. Factors influencing the chemistry of the near-field Columbia River plume: Nitrate, silicic acid, dissolved Fe, and dissolved Mn. Journal of Geophysical Research. 113

Frolov S, Baptista AM, Leen TK, Lu Z, van der Merwe R. 2009. Fast data assimilation using a nonlinear Kalman filter and a model surrogate: An application to the Columbia River estuary. Dynamics of Atmospheres and Oceans. 48(1-3):16-45.

van der Merwe R, Leen TK, Lu Z, Frolov S, Baptista AM. 2007. Fast neural network surrogates for very high dimensional physics-based models in computational oceanography. Neural Networks. 20(4):462-478.

Burla M, Baptista AM, Casillas E, Williams JG, Marsh DM. 2010. The influence of the Columbia River plume on the survival of steelhead (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha): a numerical exploration. Canadian Journal of Fisheries & Aquatic Sciences. 67(10):1671-1684.

Hugo RC, Smythe WF, McAllister SM, Young B, Maring B, Baptista AM. 2013. Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)

Herfort L, Peterson TD, McCue LA, Crump BC, Prahl FG, Baptista AM, Campbell V, Warnick R l, Selby M, Roegner GC et al.. 2011. Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquatic Microbial Ecology. 62

Gilbert M, Needoba JA, Koch C, Barnard A, Baptista AM. 2013. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Estuaries and Coasts. 36(4):708-727.

Frolov S, Baptista AM, Wilkin M. 2008. Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658.

Hickey BM, Kudela RM, Nash JD, Bruland KW, Peterson WT, MacCready P, Lessard EJ, Jay DA, Banas NS, Baptista AM et al.. 2010. River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17)

Baptista AM, Howe B, Freire J, Maier D, Silva CT. 2008. Scientific Exploration in the Era of Ocean Observatories. Computing in Science & Engineering. 10(3):53-58.

Burla M, Baptista AM, Zhang Y, Frolov S. 2010. Seasonal and interannual variability of the Columbia River plume: A perspective enabled by multiyear simulation databases. Journal of Geophysical Research. 115(C00B16)

Smith MW, Herfort L, Tyrol K, Suciu D, Campbell V, Crump BC, Peterson TD, Zuber P, Baptista AM, Simon HM. 2010. Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin. PLoS ONE . 5(10):e13312.

Chawla A, Jay DA, Baptista AM, Wilkin M, Seaton C. 2008. Seasonal Variability and Estuary-Shelf Interactions in Circulation Dynamics of a River-dominated Estuary. Estuaries and Coasts . 31

Zhang Y, Baptista AM. 2008. SELFE: A semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation. Ocean Modelling. 21(3-4):71-96.

Ghindilis A L., Smith MW, Schwarzkopf K R., Zhan C, Evans D R., Baptista AM, Simon HM. 2009. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. Electroanalysis. 21(13):1459-1468.

Fortunato CS, Herfort L, Zuber P, Baptista AM, Crump BC. 2012. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal. 6:554-563.

Rathmell K, Wilkin M, Welle P, Mattson T, Baptista AM. 2013. A Very Smart Kayak .... Currents. 28(3)

Peer-reviewed Conference Paper

Dang T, Bulusu N, Feng W, Frolov S, Baptista AM. 2010. CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors. INFOCOM, 2010 Proceedings IEEE . :1-5.

Howe B, Lawson P, Bellinger R, Anderson EW, Santos E, Freire J, Scheidegger C, Baptista AM, Silva CT. 2008. End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory. 2008 IEEE Fourth International Conference on eScience (eScience). :127-134.

Dang T, Frolov S, Bulusu N, Baptista AM. 2007. Near Optimal Sensor Selection in the COlumbia RIvEr (CORIE) Observation Network for Data Assimilation Using Genetic Algorithms. International Conference on Distributed Computing in Sensor Systems (DCOSS). 4549:253-266.

Thesis

Burla M. 2009. The Columbia River estuary and plume: natural variability, anthropogenic change and physical habitat for salmon. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation

Frolov S. 2007. Enabling Technologies for Data Assimilation in a Coastal-Margin Observatory. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation

Hyde N. 2007. Towards national estuarine modeling and characterization/classification systems: a pilot study for Coos Bay. Division of Environmental & Biomolecular Systems. Masters Thesis