Dissolved organic carbon interferes with the fluorometric ammonium assay via the inner filter effect. Limnology and Oceanography Methods.. Submitted.
Population dynamics of cryptophytes and molecular detection of Teleaulax amphioxeia nuclei and chloroplasts during a Mesodinium rubrum bloom. Aquatic Microbial Ecology.. Submitted.
Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME Journal.. In Press.
Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography.. In Press.
Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.. In Press.
Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2). 2013.
Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem. Frontiers in Microbiology.. 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.. 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.. 2013.
Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.. 2012.
Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.. 2012.
Diatom dynamics in a long-lived mesoscale eddy in the northeast subarctic Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers.. 2012.
A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.. 2012.
High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .. 2012.
Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy. 2012.
Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5). 2012.
Method for Quantification of Aquatic Primary Production and Net Ecosystem Metabolism using in situ Dissolved Oxygen Sensors. Molecular Biological Technologies for Ocean Sensing.. 2012.
Navigating Oceans of Data. 7338:1-19.. 2012.
Navigating Oceans of Data. 7338:1-19.. 2012.
Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.. 2012.
Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11). 2012.
pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.. 2012.
Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA.. Natural Hazards. 63(1). 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.. 2012.
Satellite-based detection and monitoring of phytoplankton blooms along the Oregon Coast. Journal of Geophysical Research. 117(12). 2012.
Solvent-Extractable Polycyclic Aromatic Hydrocarbons in Biochar: Influence of Pyrolysis Temperature and Feedstock. Environmental Science & Technology. 46(17):9333-9341.. 2012.
Spatial and temporal variability of bacterioplankton communities across river to ocean environmental gradients. University of Maryland.. 2012.
Ubiquitous dissolved inorganic carbon assimilation by marine heterotrophic bacteria in the Pacific Northwest coastal ocean as determined by DNA-based stable isotope probing. PLoS ONE.. 2012.
When big data leads to lost data. Proceedings of the 5th Ph.D. workshop on Information and knowledge - PIKM '12. :1.. 2012.
The Analysis and Visualization of Electroencephalography Data Using a Provenance-Enabled Environment and its Applications to Visualization. Doctor of Philosophy in Computer Science. 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.. 2011.
Applications of Fluorescence Spectroscopy for Monitoring Water Quality in an Urban Watershed. Division of Environmental & Biomolecular Systems. Masters. 2011.
Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974. 2011.
Biogeochemical and Molecular Biological Characterization of Nitrogen Cycle Processes in the Columbia River and Estuary. Division of Environmental and Biomolecular Systems. Masters Thesis. 2011.
Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries and Coasts. 34(2):281-296.. 2011.
Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.. 2011.
CrowdLabs: Social Analysis and Visualization for the Sciences. 23rd International Conference on Scientific and Statistical Database Management (SSDBM). 6809. 2011.
Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3). 2011.
Ecosystem Modeling of the Oregon Shelf: Everything but the Kitchen Sink. Interdisciplinary Studies on Environmental Chemistry. 5. 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.. 2011.
Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference.. 2011.
Mixing and biological production at eddy margins in the eastern Gulf of Alaska. Deep Sea Research Part I: Oceanographic Research Papers. 58. 2011.
Myrionecta rubra bloom initiation in the Columbia River estuary. Estuarine, Coastal and Shelf Science.. 2011.
Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquatic Microbial Ecology. 62. 2011.
Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.. 2011.
A Numerical Modeling Study of the Upwelling Source Waters along the Oregon Coast during 2005. Journal of Physical Oceanography. 41(1):88-112.. 2011.
Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Division of Environmental & Biomolecular Systems. Masters. 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.. 2011.
A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers. Procedia Computer Science. 4:648-657.. 2011.
Scalable and Efficient Tasking for Dynamic Sensor Networks. Doctor of Philosophy in Computer Science. 2011.
Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5). 2011.
Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal.. 2011.
Template-based quadrilateral meshing. Shape Modeling International (SMI) Conference 2011 . (3):471-482.. 2011.
Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling.. 2011.
A User Study of Visualization Effectiveness Using EEG and Cognitive Load. Computer Graphics Forum. 30(3):791-800.. 2011.
Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84.. 2011.
Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.. 2011.
CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors. INFOCOM, 2010 Proceedings IEEE . :1-5.. 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.. 2010.
Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.. 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.. 2010.
Interactive Vector Field Feature Identification. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2010).. 2010.
Linking ocean conditions to year class strength of the invasive European green crab, Carcinus maenas. Biological Invasions. 12(6):1791-1804.. 2010.
Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophysical Research Letters .. 2010.
PedVis: A Structured, Space-Efﬁcient Technique for Pedigree Visualization. EEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Information Visualization 2010). (6). 2010.
The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.. 2010.
Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions . 33(8). 2010.
River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17). 2010.
Seasonal and interannual variability of the Columbia River plume: A perspective enabled by multiyear simulation databases. Journal of Geophysical Research. 115(C00B16). 2010.
Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin. PLoS ONE . 5(10):e13312.. 2010.
Simplifying the Creation and Deployment of Collaborative Data Analysis and Visualization Tools. School of Computing. Ph.D. Dissertation. 2010.
Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems. Computer Graphics Forum. 29(3):1073-1082.. 2010.
Bandwidth Selection and Reconstruction Quality in Point-Based Surfaces. IEEE Transactions on Visualization and Computer Graphics. 15(4):572-582.. 2009.
- Knowledge Transfer
Estuaries and CoastsCMOP Seminar Series
Scientific talks about coastal-margin science, observatories and enabling technologies. Upcoming Seminars
Thesis Defense Webcasts
Probing Oceanic River Plumes by Gene Expression Analysis
John Paul, University of South Florida
CMOP researcher Tawnya Peterson discusses harmful algal blooms.
The OHSU Effect