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Publications
Ranked Similarity Search of Scientific Datasets: An Information Retrieval Approach. Computer Science. Doctor of Philosophy Dissertation
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2014. 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. Above and Below: Oregon Coastal Phytoplankton Bloom Dynamics from Sea and Space. Oceanography. Doctor of Philosophy
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2016. 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. 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. Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.
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2013. Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.
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2013. Smoothing the ROI Curve for Scientific Data Management Applications. Third Biennial Conference on Innovative Data Systems Research (CIDR).
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2007. Scientific Mashups: Runtime-Configurable Data Product Ensembles. Proceedings of the 21st International Conference, SSDBM 2009. 5566:19-36.
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2009. Quarrying dataspaces: Schemaless profiling of unfamiliar information sources. 2008 IEEE 24th International Conference on Data Engineeing workshop (ICDE Workshop 2008). :270-277.
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2008. Managing the Forecast Factory. 22nd International Conference on Data Engineering Workshops (ICDEW'06). :64-64.
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2006. iRun: Interactive Rendering of Large Unstructured Grids.. 7th Eurographics Symposium on Parallel Graphics and Visualization.
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2007. 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. Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference.
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2015. Data Like This: Ranked Search of Genomic Data. ExploreDB.
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2015. Data Like This: Ranked Search of Genomic Data. ExploreDB.
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2015. Data Like This: Ranked Search of Genomic Data. ExploreDB.
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2015. CrowdLabs: Social Analysis and Visualization for the Sciences. 23rd International Conference on Scientific and Statistical Database Management (SSDBM). 6809
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2011. Challenges for Dataset Search (keynote). International Conference on Database Systems for Advanced Applications. 8421
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2014. Challenges for Dataset Search (keynote). International Conference on Database Systems for Advanced Applications. 8421
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2014. A Very Smart Kayak .... Currents. 28(3)
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2013. A User Study of Visualization Effectiveness Using EEG and Cognitive Load. Computer Graphics Forum. 30(3):791-800.
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2011. Use of Highly Specific Molecular Markers Reveals Positive Correlation between Abundances of Mesodinium cf. major and its Preferred Prey, Teleaulax amphioxeia, During Red Water Blooms in the Columbia River Estuary. J. Eukaryotic Microbiol..
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2017. Use of continuous, real-time observations & model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler. Limnol. Oceanogr. Methods. 14(1):50-67.
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2016. Tidal and diel dynamics of M. major and its specific Teleaulax prey generate red water blooms in the Columbia River estuary. In Preparation.
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0. 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. River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17)
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2010. 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. Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions . 33(8)
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2010. 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. 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. Observations of a Diatom Chytrid Parasite in the Lower Columbia River. Northwest Science. 88(3):234-245.
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2014. Numerical modeling of circulation in high-energy estuaries: A Columbia River estuary benchmark. Ocean Modelling. 88:54-71.
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2015. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.
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2012. 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. Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophysical Research Letters .
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2010. 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. 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. Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)
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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. 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. 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. 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. 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. Incorporation Of Traditional Knowledge Into Geoscience Education: An Effective Method Of Native American Instruction. Journal of Sustainability Education. 14
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2017. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .
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2012. 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. Fast and Adaptive Indexing of Multi-Dimensional Observational Data. Proceedings of the VLDB Endowment. 9(14):1683-1694.
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2016. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima. MicrobiologyOpen. e522
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2017. 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 coastal ocean circulation model for the Columbia River plume in summer 2004. Journal of Geophysical Research. 114
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2009. 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. 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. 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. 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 real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.
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2012. 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. 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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