Publications
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Submitted. Coastal Margin Science and Education in the Era of Collaboratories. Currents.
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Submitted. Dissolved organic carbon interferes with the fluorometric ammonium assay via the inner filter effect. Limnology and Oceanography Methods.
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Submitted. It Takes a Community to Raise a Scientist: A Case for Community-Inspired Research and Science Education in an Alaska Native Community. Currents.
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Submitted. Population dynamics of cryptophytes and molecular detection of Teleaulax amphioxeia nuclei and chloroplasts during a Mesodinium rubrum bloom. Aquatic Microbial Ecology.
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Submitted. Seasonal variation of the protist assemblage in the Columbia River coastal margin assessed using 18S rRNA gene sequences. Microbial Ecology.
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In Press. Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography.
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In Press. Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.
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2013. Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2)
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2013. Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem. Frontiers in Microbiology.
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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.
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2013. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME Journal.
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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. Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)
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2013. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Estuaries and Coasts.
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2012. Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.
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2012. Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.
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2012. 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. A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.
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2012. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .
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2012. Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy
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2012. Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)
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2012. 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. Navigating Oceans of Data. 7338:1-19.
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2012. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.
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2012. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
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2012. pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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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. 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. Satellite-based detection and monitoring of phytoplankton blooms along the Oregon Coast. Journal of Geophysical Research. 117(12)
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2012. Solvent-Extractable Polycyclic Aromatic Hydrocarbons in Biochar: Influence of Pyrolysis Temperature and Feedstock. Environmental Science & Technology. 46(17):9333-9341.
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2012. Spatial and temporal variability of bacterioplankton communities across river to ocean environmental gradients. University of Maryland.
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2012. 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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2011. The Analysis and Visualization of Electroencephalography Data Using a Provenance-Enabled Environment and its Applications to Visualization. Doctor of Philosophy in Computer Science
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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.
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2011. Applications of Fluorescence Spectroscopy for Monitoring Water Quality in an Urban Watershed. Division of Environmental & Biomolecular Systems. Masters
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2011. Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974
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2011. 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. 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. CrowdLabs: Social Analysis and Visualization for the Sciences. 23rd International Conference on Scientific and Statistical Database Management (SSDBM). 6809
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2011. Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3)
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2011. Ecosystem Modeling of the Oregon Shelf: Everything but the Kitchen Sink. Interdisciplinary Studies on Environmental Chemistry. 5
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2011. 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. 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. 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. Myrionecta rubra bloom initiation in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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2011. 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. Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.
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2011. 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. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Division of Environmental & Biomolecular Systems. Masters
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2011. 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. A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers. Procedia Computer Science. 4:648-657.
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2011. Scalable and Efficient Tasking for Dynamic Sensor Networks. Doctor of Philosophy in Computer Science
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2011. Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5)
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2011. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal.
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2011. Template-based quadrilateral meshing. Shape Modeling International (SMI) Conference 2011 . (3):471-482.
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2011. Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling.
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2011. A User Study of Visualization Effectiveness Using EEG and Cognitive Load. Computer Graphics Forum. 30(3):791-800.
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2011. Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84.
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2011. Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.
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2010. CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors. INFOCOM, 2010 Proceedings IEEE . :1-5.
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2010. 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. Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.
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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.
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2010. Interactive Vector Field Feature Identification. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2010).
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2010. 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. Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophysical Research Letters .
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2010. 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. The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.
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2010. Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions . 33(8)
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2010. River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17)
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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. 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. Simplifying the Creation and Deployment of Collaborative Data Analysis and Visualization Tools. School of Computing. Ph.D. Dissertation
