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Publications
Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.
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2011. Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling.
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2011. 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. 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. Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME J. 10 March 2015
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2015. 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. Characterization of the metabolic properties and ecological functions of Thaumarchaeota in terrestrial environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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2013. Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA.. Natural Hazards. 63(1)
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2012. 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. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.
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2012. Insights Into Microbial Phosphorus Cycling In The Columbia River Estuary. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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2017. Fast and Adaptive Indexing of Multi-Dimensional Observational Data. Proceedings of the VLDB Endowment. 9(14):1683-1694.
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2016. 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. iRun: Interactive Rendering of Large Unstructured Grids.. 7th Eurographics Symposium on Parallel Graphics and Visualization.
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2007. Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems. Computer Graphics Forum. 29(3):1073-1082.
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2010. When big data leads to lost data. Proceedings of the 5th Ph.D. workshop on Information and knowledge - PIKM '12. :1.
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2012. 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. PedVis: A Structured, Space-Efficient Technique for Pedigree Visualization. EEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Information Visualization 2010). (6)
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2010. Phytoplankton dynamics in off-channel habitats of the lower Columbia River estuary. Division of Environmental & Biomolecular Systems. Master of Science
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2015. Ecosystem Modeling of the Oregon Shelf: Everything but the Kitchen Sink. Interdisciplinary Studies on Environmental Chemistry. 5
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2011. Biomineralization in extreme iron and manganese depositing environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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2015. Incorporation Of Traditional Knowledge Into Geoscience Education: An Effective Method Of Native American Instruction. Journal of Sustainability Education. 14
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2017. 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. 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. Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem. Frontiers in Microbiology.
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2013. 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. 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. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .
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2012. 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. Focused review: Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Frontiers in Microbiology.
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2014. Software Infrastructure for exploratory visualization and data analysis: past, present, and future. Journal of Physics: Conference Series. 125:012100.
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2008. Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84.
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2011. Provenance for Visualizations: Reproducibility and Beyond. Computing in Science & Engineering. 9(5):82-89.
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2007. Guest Editorial: Special Issue on Computational Provenance. Computing in Science and Engineering.. 10(3)
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2008. Model-aided Lagrangian interpretation of non-synoptic estuarine observations. Limnology and Oceanography: Methods.
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2016. Uniform and Adaptive (Re) Meshing of Surfaces. Computer Science. Ph.D. Dissertation
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2009. Querying and re-using workflows with VsTrails. ACM SIGMOD international Conference on Management of Data.
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2008. Tackling the Provenance Challenge one layer at a time. Concurrency and Computation: Practice and Experience. 20(5):473-483.
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2008. Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. 13(6):1560-1567.
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2007. 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. Enabling Advanced Visualization Tools in a Web-Based Simulation Monitoring System. 2009 5th IEEE International Conference on e-Science (e-Science)2009 Fifth IEEE International Conference on e-Science. :358-365.
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2009. Simplifying the Creation and Deployment of Collaborative Data Analysis and Visualization Tools. School of Computing. Ph.D. Dissertation
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2010. VisMashup: Streamlining the Creation of Custom Visualization Applications. IEEE Transactions on Visualization and Computer Graphics. 15(6):1539-1546.
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2009. Change in variability in the Columbia River estuary: a habitat perspective. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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2017. A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.
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2012. 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. 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. Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.
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2011. 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. Three-dimensional modeling of the lower trophic levels in the Ria de Aveiro (Portugal). Ecological Modelling. 220(9-10):1274-1290.
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2009. 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. A Very Smart Kayak .... Currents. 28(3)
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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. NH4-Digiscan: an in situ and laboratory ammonium analyzer for estuarine, coastal and shelf waters. Limnology and Oceanography.
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2009. 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. Gonadal tissue color is not a reliable indicator of sex in rocky intertidal mussels. Aquatic Biology. 3:63-70.
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2008. 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. 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. Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2)
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2013. 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. Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114
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2009. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
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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. Automatically Extracting Form Labels. Proceedings of the 2008 IEEE 24th International Conference on Data Engineering (ICDE 2008). :1498-1500.
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2008. 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. 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. 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. Biogeochemical and Molecular Biological Characterization of Nitrogen Cycle Processes in the Columbia River and Estuary. Division of Environmental and Biomolecular Systems. Masters Thesis
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2011. 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. 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. Data Like This: Ranked Search of Genomic Data. ExploreDB.
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2015. Ranked Similarity Search of Scientific Datasets: An Information Retrieval Approach. Computer Science. Doctor of Philosophy Dissertation
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2014. Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference.
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2011. Data Near Here: Bringing Relevant Data Closer to Scientists. Computing in Science and Engineering,. 15(3):44-53.
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2013. Are Datasets Like Documents?: Evaluating Similarity-Based Ranked Search Over Scientific Data IEEE Transactions on Knowledge and Data Engineering. (99)
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