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2010

Ghindilis A L., Schwarzkopf K R., Messing DS, Sezan I, Schuele P, Zhan C, Smith MW, Simon HM, Evans D R.. 2010. Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays. ECS Transactions . 33(8)

Hickey BM, Kudela RM, Nash JD, Bruland KW, Peterson WT, MacCready P, Lessard EJ, Jay DA, Banas NS, Baptista AM et al.. 2010. River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17)

Burla M, Baptista AM, Zhang Y, Frolov S. 2010. Seasonal and interannual variability of the Columbia River plume: A perspective enabled by multiyear simulation databases. Journal of Geophysical Research. 115(C00B16)

Smith MW, Herfort L, Tyrol K, Suciu D, Campbell V, Crump BC, Peterson TD, Zuber P, Baptista AM, Simon HM. 2010. Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin. PLoS ONE . 5(10):e13312.

Santos E. 2010. Simplifying the Creation and Deployment of Collaborative Data Analysis and Visualization Tools. School of Computing. Ph.D. Dissertation

Vo H, Osmari DK, Summa B, Comba J, Pascucci V, Silva CT. 2010. Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems. Computer Graphics Forum. 29(3):1073-1082.

2011

Anderson EW. 2011. The Analysis and Visualization of Electroencephalography Data Using a Provenance-Enabled Environment and its Applications to Visualization. Doctor of Philosophy in Computer Science

Anderson CR, Davis RE, Bandolin NS, Baptista AM, Tebo BM. 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.

Goldman JH. 2011. Applications of Fluorescence Spectroscopy for Monitoring Water Quality in an Urban Watershed. Division of Environmental & Biomolecular Systems. Masters

Fortunato CS, Crump BC. 2011. Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974

Moeller F. 2011. Biogeochemical and Molecular Biological Characterization of Nitrogen Cycle Processes in the Columbia River and Estuary. Division of Environmental and Biomolecular Systems. Masters Thesis

Roegner GC, Seaton C, Baptista AM. 2011. Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries and Coasts. 34(2):281-296.

Roegner GC, Needoba JA, Baptista AM. 2011. Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.

Mates P, Santos E, Freire J, Silva CT. 2011. CrowdLabs: Social Analysis and Visualization for the Sciences. 23rd International Conference on Scientific and Statistical Database Management (SSDBM). 6809

Bräuer SL, Adams C, Kranzler K, Murphy D, Xu M, Zuber P, Simon HM, Baptista AM, Tebo BM. 2011. Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3)

Spitz YH. 2011. Ecosystem Modeling of the Oregon Shelf: Everything but the Kitchen Sink. Interdisciplinary Studies on Environmental Chemistry. 5

Peterson TD, Crawford DW, Harrison PJ. 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.

Megler VM, Maier D. 2011. Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference.

Peterson TD, Crawford DW, Harrison PJ. 2011. Mixing and biological production at eddy margins in the eastern Gulf of Alaska. Deep Sea Research Part I: Oceanographic Research Papers. 58

Herfort L, Peterson TD, Campbell V, Futrell S, Zuber P. 2011. Myrionecta rubra bloom initiation in the Columbia River estuary. Estuarine, Coastal and Shelf Science.

Herfort L, Peterson TD, McCue LA, Crump BC, Prahl FG, Baptista AM, Campbell V, Warnick R l, Selby M, Roegner GC et al.. 2011. Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquatic Microbial Ecology. 62

Zhang Y, Witter RC, Priest GP. 2011. Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.

Rivas D, Samelson RM. 2011. A Numerical Modeling Study of the Upwelling Source Waters along the Oregon Coast during 2005. Journal of Physical Oceanography. 41(1):88-112.

Gilbert M. 2011. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Division of Environmental & Biomolecular Systems. Masters

Herfort L, Peterson TD, McCue LA, Zuber P. 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.

Koop D, Santos E, Mates P, Vo H, Bonnet P, Bauer B, Surer B, Troyer M, Williams DN, Tohline JE et al.. 2011. A Provenance-Based Infrastructure to Support the Life Cycle of Executable Papers. Procedia Computer Science. 4:648-657.

Dang TX. 2011. Scalable and Efficient Tasking for Dynamic Sensor Networks. Doctor of Philosophy in Computer Science

Evans W, Hales B, Strutton PG. 2011. Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5)

Daniels J, Lizier M, Siqueira M, Silva CT, Nonato LG. 2011. Template-based quadrilateral meshing. Shape Modeling International (SMI) Conference 2011 . (3):471-482.

Zhang Y, Witter RC, Priest GR. 2011. Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling.

Anderson EW, Potter KC, Matzen LE, Shepherd JF, Preston GA, Silva CT. 2011. A User Study of Visualization Effectiveness Using EEG and Cognitive Load. Computer Graphics Forum. 30(3):791-800.

Silva CT, Anderson EW, Santos E, Freire J. 2011. Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84.

Hansen C, Johnson C, Pascucci V, Silva CT. 2011. Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.

2012

Goldman JH, Rounds SA, Needoba JA. 2012. Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.

Fietz S., Huguet C., Bendle J., Escala M., Gallacher C., Herfort L, Jamieson R., Martínez-Garcia A., McClymont E.L., Peck V.L. et al.. 2012. Co-variation of crenarchaeol and branched GDGTs in globally-distributed marine and freshwater sedimentary archives. Global and Planetary Change. 92-93

Ghindilis A L., Smith MW, Messing DS, Haynes VN, Middleton GB, Schwarzkopf K R., Campbell CE, Zhan C, Ulrich B, Frasier MJ et al.. 2012. Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.

Peterson TD, Harrison PJ. 2012. Diatom dynamics in a long-lived mesoscale eddy in the northeast subarctic Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers.

Roland LA, Zhang Y, Wang HV, Maderich V, Brovchenko I. 2012. A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.

Smith MW, Maier MA, Suciu D, Peterson TD, Bradstreet T, Nakayama J, Simon HM. 2012. High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field. Harmful Algae .

Koop D. 2012. Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy

Anthony S, Prahl FG, Peterson TD. 2012. Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)

Needoba JA, Peterson TD, Johnson KS. 2012. Method for Quantification of Aquatic Primary Production and Net Ecosystem Metabolism using in situ Dissolved Oxygen Sensors. Molecular Biological Technologies for Ocean Sensing.

Maier D, Megler VM, Baptista AM, Jaramillo A, Seaton C, Turner PJ. 2012. Navigating Oceans of Data. 7338:1-19.

White AE, Foster RA, Benitez-Nelson CR, Masqué P, Verdeny E, Popp BN, Arthur KE, Prahl FG. 2012. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Progress in Oceanography.

Palacios SL, Peterson TD, Kudela RM. 2012. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)

Evans W, Hales B, Strutton PG. 2012. pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.

Witter RC, Jaffe B, Zhang Y, Priest GR. 2012. Reconstructing hydrodynamic flow parameters of the 1700 tsunami at Cannon Beach, Oregon, USA.. Natural Hazards. 63(1)

Herfort L, Peterson TD, Prahl FG, McCue LA, Needoba JA, Crump BC, Roegner GC, Campbell V, Zuber P. 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.

McKibben SM, Strutton PG, Foley DG, Peterson TD, White AE. 2012. Satellite-based detection and monitoring of phytoplankton blooms along the Oregon Coast. Journal of Geophysical Research. 117(12)

Keiluweit M, Kleber M, Sparrow MA, Simoneit BRT, Prahl FG. 2012. Solvent-Extractable Polycyclic Aromatic Hydrocarbons in Biochar: Influence of Pyrolysis Temperature and Feedstock. Environmental Science & Technology. 46(17):9333-9341.

Fortunato CS. 2012. Spatial and temporal variability of bacterioplankton communities across river to ocean environmental gradients. University of Maryland.

Fortunato CS, Herfort L, Zuber P, Baptista AM, Crump BC. 2012. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal. 6:554-563.

DeLorenzo S, Bräuer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P. 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.

Megler VM, Maier D. 2012. When big data leads to lost data. Proceedings of the 5th Ph.D. workshop on Information and knowledge - PIKM '12. :1.

2013

Peterson TD, Golda RL, Garcia ML, Li B, Maier MA, Needoba JA, Zuber P. 2013. Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2)

Xu M. 2013. Characterization of the metabolic properties and ecological functions of Thaumarchaeota in terrestrial environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

Green V, Bueno Watts N, Wegner K, Thompson M, Johnson AF, Peterson TD, Baptista AM. 2013. Coastal Margin Science and Education in the Era of Collaboratories. Currents. 28(3)

Smith MW, Zeigler_Allen L, Allen A, Herfort L, Simon HM. 2013. Contrasting Genomic Properties of Free-living and Particle-attached Microbial Assemblages within a Coastal Ecosystem. Frontiers in Microbiology.

Bräuer SL, Kranzler K, Goodson N, Murphy D, Simon HM, Baptista AM, Tebo BM. 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.

Megler VM, Maier D. 2013. Data Near Here: Bringing Relevant Data Closer to Scientists. Computing in Science and Engineering,. 15(3):44-53.

Fortunato CS, Eiler A., Herfort L, Needoba JA, Peterson TD, Crump BC. 2013. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME Journal.

Haynes V. 2013. Development of novel impedimetric assays for rapid detection of E. coli. Division of Environmental & Biomolecular Systems. Master of Science

Miller J, Teel D, Baptista AM, Morgan C. 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.

Ahn S, Peterson TD, Righter J, Miles DM, Tratnyek PG. 2013. Disinfection of Ballast Water with Iron Activated Persulfate. Environmental Science & Technology. 47(20)

DeLorenzo S. 2013. Inorganic Carbon-Assimilating Microbial Communities in the Pacific Northwest Coastal Margin. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

Bueno Watts N, Smythe WF. 2013. It Takes a Community to Raise a Scientist: A Case for Community-Inspired Research and Science Education in an Alaska Native Community. Currents. 28(3)

Hugo RC, Smythe WF, McAllister SM, Young B, Maring B, Baptista AM. 2013. Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)

Gilbert M, Needoba JA, Koch C, Barnard A, Baptista AM. 2013. Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Estuaries and Coasts. 36(4):708-727.

Durkin CA, Bender SJ, Chan KYK, Gaessner K, Grunbaum D, Armburst EV. 2013. Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography. :1707-1726.

Megler VM, Maier D. 2013. Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.

Abdel-Jabbar N, Baptista AM, Karna T, Turner P, Sen G. 2013. US Experience Will Advance Gulf Ecosystem Research.

Rathmell K, Wilkin M, Welle P, Mattson T, Baptista AM. 2013. A Very Smart Kayak .... Currents. 28(3)

2014

Megler VM, Maier D. 2014. Are Datasets Like Documents?: Evaluating Similarity-Based Ranked Search Over Scientific Data IEEE Transactions on Knowledge and Data Engineering. (99)

Miller J.A., Teel D.J., Peterson W.T., Baptista AM. 2014. Assessing the relative importance of local and regional processes on the survival of a threatened salmon population. PLoS ONE. 9(6)

McNeil C, D’Asaro E.A. 2014. A calibration equation for oxygen optodes based on physical properties of the sensing foil. Limnology and Oceanography: Methods.

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