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Publications
Factors influencing the chemistry of the near-field Columbia River plume: Nitrate, silicic acid, dissolved Fe, and dissolved Mn. Journal of Geophysical Research. 113
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2008. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima. MicrobiologyOpen. e522
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2017. Evolution of the phytoplankton assemblage in a long-lived mesoscale eddy in the eastern Gulf of Alaska. Marine Ecology Progress Series. 424:53-73.
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2011. .
2014. Evaluation of Daphnid Grazing on Microscopic Zoosporic Fungi by Using Comparative Threshold Cycle Quantitative PCR. Applied and Environmental Microbiology. 82(13):3868-3874.
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2016. Evaluation of a long-term hindcast simulation for the Columbia River estuary. Ocean Modelling. 99:1-14.
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2016. Evaluation of a coastal ocean circulation model for the Columbia River plume in summer 2004. Journal of Geophysical Research. 114
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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.
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2009. Estimates of sea surface height and near-surface alongshore coastal currents from combinations of altimeters and tide gauges. Journal of Geophysical Research. 113(C11)
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2008. Enumeration of Parasitic Chytrid Zoospores in the Columbia River via Quantitative PCR. Applied and Environmental Microbiology. 82(13):3857-3867.
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2016. An Efficient and Robust Tsunami Model on Unstructured Grids. Part I: Inundation Benchmarks. Pure and Applied Geophysics. 165(11-12):2229-2248.
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2008. Ecosystem Engineers in the Pelagic Realm: Alteration of Habitat by Species Ranging from Microbes to Jellyfish. Integrative and Comparative Biology. 50(2):188-200.
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2010. Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary. J Plankton Res. :1-11.
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2017. Disinfection of Ballast Water with Iron Activated Persulfate. Environmental Science & Technology. 47(20)
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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.
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2013. Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element. MicrobiologyOpen. 3(5):764-776.
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2014. Direct Volume Rendering: A 3D Plotting Technique for Scientific Data. Computing in Science & Engineering. 10(1):88-92.
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2008. Diatom dynamics in a long-lived mesoscale eddy in the northeast subarctic Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers.
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2012. Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114
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2009. Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.
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2012. Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions. Journal of Microbiological Methods. 136:78-87.
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2017. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME Journal.
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2013. Determination of intracellular pH in phytoplankton using the fluorescent probe, SNARF, with detection by fluorescence spectroscopy. Journal of Microbiological Methods.
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In Press. Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences of the United States of America. 113(12):3143-3151.
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2016. Data Near Here: Bringing Relevant Data Closer to Scientists. Computing in Science and Engineering,. 15(3):44-53.
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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.
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2013. Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3)
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2011. A cross-scale numerical modeling system for management support of oil spill accidents. Marine Pollution Bulletin. 80(1-2):132-147.
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2014. Co-variation of crenarchaeol and branched GDGTs in globally-distributed marine and freshwater sedimentary archives. Global and Planetary Change. 92-93
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2012. Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem. Frontiers in Microbiology.
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2013. 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.
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2009. CoastColour Round Robin data sets: A database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters. Earth System Science Data. 7(2):319-348.
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2015. Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.
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2011. Coastal Margin Science and Education in the Era of Collaboratories. Currents. 28(3)
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2013. Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries and Coasts. 34(2):281-296.
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2011. Circumpolar synchrony in big river bacterioplankton. Proceedings of the National Academy of Sciences. 106(50):21208-21212.
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2009. A calibration equation for oxygen optodes based on physical properties of the sensing foil. Limnology and Oceanography: Methods.
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2014. Benchmarking an unstructured grid sediment model in an energetic estuary. Ocean Modeling. 110:32-48.
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2017. Bandwidth Selection and Reconstruction Quality in Point-Based Surfaces. IEEE Transactions on Visualization and Computer Graphics. 15(4):572-582.
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2009. Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974
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2011. Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2)
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2013. Assessing the relative importance of local and regional processes on the survival of a threatened salmon population. PLoS ONE. 9(6)
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2014. Are Datasets Like Documents?: Evaluating Similarity-Based Ranked Search Over Scientific Data IEEE Transactions on Knowledge and Data Engineering. (99)
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2014. Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.
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2012. Application of highly discriminating unique sequence elements of the 28S rRNA gene for determination of protest biogeography. In Preparation.
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0. 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.
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2011. Advancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System. Journal of Operational Oceanography. :1-12.
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2017. An adaptive framework for visualizing unstructured grids with time-varying scalar fields. Parallel Computing. 33(6):391-405.
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2007. Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.
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2011. Method for Quantification of Aquatic Primary Production and Net Ecosystem Metabolism using in situ Dissolved Oxygen Sensors. Molecular Biological Technologies for Ocean Sensing.
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2012. .
2013.
Navigating Oceans of Data. 7338:1-19.
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2012. Pages
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