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Publications
Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography. :1707-1726.
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2013. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. Electroanalysis. 21(13):1459-1468.
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2009. Sensitivity analysis of an ecological model applied to the Ria de Aveiro.. Journal of Coastal Research. (Special Issue 56):448-452.
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2009. Semi-regular Quadrilateral-only Remeshing from Simplified Base Domains. Computer Graphics Forum. 28(5):1427-1435.
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2009. SELFE: A semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation. Ocean Modelling. 21(3-4):71-96.
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2008. Seasonal Variability and Estuary-Shelf Interactions in Circulation Dynamics of a River-dominated Estuary. Estuaries and Coasts . 31
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2008. Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5)
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2011. Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin. PLoS ONE . 5(10):e13312.
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2010. Seasonal and interannual variability of the Columbia River plume: A perspective enabled by multiyear simulation databases. Journal of Geophysical Research. 115(C00B16)
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2010. Scientific Exploration in the Era of Ocean Observatories. Computing in Science & Engineering. 10(3):53-58.
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2008. Satellite-based detection and monitoring of phytoplankton blooms along the Oregon Coast. Journal of Geophysical Research. 117(12)
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2012. Robust Soft Shadow Mapping with Backprojection and Depth Peeling. Journal of Graphics, GPU and Game Tools. 13
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2008. River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17)
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2010. Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Scientific Reports. 5(7737)
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2015. Red waters of Myrionecta rubra are biogeochemical hotspots for the Columbia River estuary with impacts on primary/secondary productions and nutrient cycles. Estuaries and Coasts.
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2012. Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA.. Natural Hazards. 63(1)
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2012. Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions . 33(8)
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2010. Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. 13(6):1560-1567.
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2007. Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary. Limnology and Oceanography.
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2017. A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers. Procedia Computer Science. 4:648-657.
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2011. Provenance in Scientific Workflow Systems. IEEE Data Engineering Bulletin.
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2007. Provenance for Visualizations: Reproducibility and Beyond. Computing in Science & Engineering. 9(5):82-89.
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2007. Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.
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2008. Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter to turbidity maxima of the Columbia River estuary. Marine Ecology Progress Series. 438:19-31.
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2011. Prevalence of chytrid parasitism among diatom populations in the lower Columbia River (2009–2013). Freshwater Biology.
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2016. Planktonic growth and grazing in the Columbia River plume region: A biophysical model study. Journal of Geophysical Research. 114
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2009. pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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2012. Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658.
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2008. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
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2012. Observations of a Diatom Chytrid Parasite in the Lower Columbia River. Northwest Science. 88(3):234-245.
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2014. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Estuaries and Coasts. 36(4):708-727.
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2013. A Numerical Modeling Study of the Upwelling Source Waters along the Oregon Coast during 2005. Journal of Physical Oceanography. 41(1):88-112.
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2011. Numerical modeling of circulation in high-energy estuaries: A Columbia River estuary benchmark. Ocean Modelling. 88:54-71.
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2015. Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.
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2011. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.
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2012. NH4-Digiscan: an in situ and laboratory ammonium analyzer for estuarine, coastal and shelf waters. Limnology and Oceanography.
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2009. A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus. PLOS ONE. 9(5)
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2014. New Insights into the Controls and Mechanisms of Plankton Productivity on the US West Coast.. Oceanography. 21(4)
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2008. The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5):78-83.
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2008. Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquatic Microbial Ecology. 62
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2011. Myrionecta rubra bloom initiation in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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2011. Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophysical Research Letters .
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2010. Morphological Characterization of Bacteriogenic Manganese Oxides From Three Model Manganese (II/III) Oxidizing Bacterial Species. Journal of Postdoctoral Research. 5(3):7-13.
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2017. Monitoring Oregon Coastal Harmful Algae: Observations and implications of a harmful algal bloom-monitoring project. Harmful Algae. 50:32-44.
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2015. Model-aided Lagrangian interpretation of non-synoptic estuarine observations. Limnology and Oceanography: Methods.
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2016. Mixing and biological production at eddy margins in the eastern Gulf of Alaska. Deep Sea Research Part I: Oceanographic Research Papers. 58
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2011. Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary. MicrobiologyOpen. (e00467)
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2017. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient. PLoS ONE. 10(11):e0140578.
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2015. Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)
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2012. Metagenomic evidence for reciprocal particle exchange between the mainstream estuary and lateral bay sediments of the lower Columbia River. Frontiers in Microbiology. 6:1074.
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2015. Mapping the spatial variability of plankton metabolism using nitrate and oxygen sensors on an autonomous underwater vehicle. Limnology and Oceanography. 53(5 PART 2)
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2008. Localized Quadrilateral Coarsening. Computer Graphics Forum. 28(5):1437-1444.
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2009. Linking ocean conditions to year class strength of the invasive European green crab, Carcinus maenas. Biological Invasions. 12(6):1791-1804.
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2010. Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)
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2013. A large-volume micro-filtration system for isolating suspended particulate organic matter from seawater: fabrication and assessment of recovery and composition vs. GFF filters from central N. Pacific. Limnology and Oceanography Methods. 7:64-80.
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2009. The land/ocean biogeochemical observatory: A robust networked mooring system for continuously monitoring complex biogeochemical cycles in estuaries. Limnology and Oceanography: Methods. 6(JUL, July 2008)
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2008. It Takes a Community to Raise a Scientist: A Case for Community-Inspired Research and Science Education in an Alaska Native Community. Currents. 28(3)
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2013. Infrastructure for collaborative science and societal applications in the Columbia River estuary. Frontiers of Earth Science. 9(4):659-682.
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2015. 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.
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2010. Influence of a buoyant river plume on phytoplankton nutrient dynamics: What controls standing stocks and productivity? Journal of Geophysical Research. 114
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2009. Incorporation Of Traditional Knowledge Into Geoscience Education: An Effective Method Of Native American Instruction. Journal of Sustainability Education. 14
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2017. Hydrologic control of dissolved organic carbon and nitrogen and dissolved organic matter quality in a semi-arid artificially drained agricultural catchment. Water Resources Research. 51(10):8146–8164.
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2015. High resolution sampling of methane transport in the Columbia River near-field plume: implications for sources and sinks in a river-dominated estuary. Limnology & Oceanography.
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2015. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .
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2012. Guest Editorial: Special Issue on Computational Provenance. Computing in Science and Engineering.. 10(3)
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2008. Graphical coding data and operational guidance for implementation or modification of a LabVIEW®-based pHstat system for the cultivation of microalgae. Data in Brief. 12(June 2017):463-470.
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2017. Gonadal tissue color is not a reliable indicator of sex in rocky intertidal mussels. Aquatic Biology. 3:63-70.
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2008. Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME J. 10 March 2015
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2015. A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.
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2012. Fortnightly Tidal Modulations Affect Net Community Production in a Mesotidal Estuary. Estuaries and Coasts. 37(1):91-110.
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2014. Focused review: Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Frontiers in Microbiology.
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2014. Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.
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2010. Fast neural network surrogates for very high dimensional physics-based models in computational oceanography. Neural Networks. 20(4):462-478.
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2007. 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.
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2009. Fast and Adaptive Indexing of Multi-Dimensional Observational Data. Proceedings of the VLDB Endowment. 9(14):1683-1694.
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2016.