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Z

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

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

Zhang Y, Baptista AM. 2008. SELFE: A semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation. Ocean Modelling. 21(3-4):71-96.

Zhang Y, Baptista AM. 2008. An Efficient and Robust Tsunami Model on Unstructured Grids. Part I: Inundation Benchmarks. Pure and Applied Geophysics. 165(11-12):2229-2248.

Y

Youngblut ND, Wirth JS, Henriksen JR, Smith MW, Simon HM, Metcalf WW, Whitaker RJ. 2015. Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME J. 10 March 2015

Yamada S B, Kosro MP. 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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Xu M. 2013. Characterization of the metabolic properties and ecological functions of Thaumarchaeota in terrestrial environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

W

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)

Wilkin J, Rosenfeld L, Allen A, Baltes R, Baptista A, He R, Hogan P, Kurapov A, Mehra A, Quintrell J et al.. 2017. Advancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System. Journal of Operational Oceanography. :1-12.

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.

Watson S. 2017. Insights Into Microbial Phosphorus Cycling In The Columbia River Estuary. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

Wang S, Maier D, Ooi BChin. 2016. Fast and Adaptive Indexing of Multi-Dimensional Observational Data. Proceedings of the VLDB Endowment. 9(14):1683-1694.

Wang H, Scheidegger C, Silva CT. 2009. Bandwidth Selection and Reconstruction Quality in Point-Based Surfaces. IEEE Transactions on Visualization and Computer Graphics. 15(4):572-582.

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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.

Vo H, Callahan SP, Smith N, Silva CT, Martin W, Owen D, Weinstein D. 2007. iRun: Interactive Rendering of Large Unstructured Grids.. 7th Eurographics Symposium on Parallel Graphics and Visualization.

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.

van der Merwe R, Leen TK, Lu Z, Frolov S, Baptista AM. 2007. Fast neural network surrogates for very high dimensional physics-based models in computational oceanography. Neural Networks. 20(4):462-478.

T

Tuttle C, Nonato LG, Silva CT. 2010. PedVis: A Structured, Space-Efﬁcient Technique for Pedigree Visualization. EEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Information Visualization 2010). (6)

Tausz C. 2015. Phytoplankton dynamics in off-channel habitats of the lower Columbia River estuary. Division of Environmental & Biomolecular Systems. Master of Science

S

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

Smythe WF. 2017. Morphological Characterization of Bacteriogenic Manganese Oxides From Three Model Manganese (II/III) Oxidizing Bacterial Species. Journal of Postdoctoral Research. 5(3):7-13.

Smythe WF. 2015. Biomineralization in extreme iron and manganese depositing environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

Smythe WF, Hugo RC, McAllister SM. 2017. Incorporation Of Traditional Knowledge Into Geoscience Education: An Effective Method Of Native American Instruction. Journal of Sustainability Education. 14

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.

Smith MW, Herfort L, Fortunato CS, Crump BC, Simon HM. 2017. Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary. MicrobiologyOpen. (e00467)

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.

Smith MW, Davis RE, Youngblut ND, Karna T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM. 2015. Metagenomic evidence for reciprocal particle exchange between the mainstream estuary and lateral bay sediments of the lower Columbia River. Frontiers in Microbiology. 6:1074.

Smith MW, Ghindilis A.L., Seoudi I.A., Smith K., Billharz R., Simon HM. 2014. A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus. PLOS ONE. 9(5)

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 .

Simon HM, Smith MW, Herfort L. 2014. Focused review: Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Frontiers in Microbiology.

Silva CT, Freire J, Callahan SP. 2007. Provenance for Visualizations: Reproducibility and Beyond. Computing in Science & Engineering. 9(5):82-89.

Silva CT, Tohline JE. 2008. Guest Editorial: Special Issue on Computational Provenance. Computing in Science and Engineering.. 10(3)

Silva CT, Freire J. 2008. Software Infrastructure for exploratory visualization and data analysis: past, present, and future. Journal of Physics: Conference Series. 125:012100.

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

Shcherbina AY, McNeil CL, Baptista AM. 2016. Model-aided Lagrangian interpretation of non-synoptic estuarine observations. Limnology and Oceanography: Methods.

Schreiner JM. 2009. Uniform and Adaptive (Re) Meshing of Surfaces. Computer Science. Ph.D. Dissertation

Scheidegger C, Vo H, Koop D, Freire J, Silva CT. 2007. Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. 13(6):1560-1567.

Scheidegger C, Vo H, Koop D, Freire J, Silva CT. 2008. Querying and re-using workflows with VsTrails. ACM SIGMOD international Conference on Management of Data.

Scheidegger C, Koop D, Santos E, Vo H, Callahan SP, Freire J, Silva CT. 2008. Tackling the Provenance Challenge one layer at a time. Concurrency and Computation: Practice and Experience. 20(5):473-483.

Saraceno M, Strub PT, Kosro MP. 2008. Estimates of sea surface height and near-surface alongshore coastal currents from combinations of altimeters and tide gauges. Journal of Geophysical Research. 113(C11)

Santos E, Tierny J, Khan A, Grimm B, Lins L, Freire J, Pascucci V, Silva CT, Klasky S, Barreto R et al.. 2009. 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.

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

Santos E, Lins L, Ahrens J, Freire J, Silva CT. 2009. VisMashup: Streamlining the Creation of Custom Visualization Applications. IEEE Transactions on Visualization and Computer Graphics. 15(6):1539-1546.

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Rostaminia M. 2017. Change in variability in the Columbia River estuary: a habitat perspective. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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

Roland LA, McCarthy MD, Peterson TD, Walker BD. 2009. 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.

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

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.

Rodrigues M, Oliveira A, Queiroga H, Fortunato AB, Zhang Y. 2009. Three-dimensional modeling of the lower trophic levels in the Ria de Aveiro (Portugal). Ecological Modelling. 220(9-10):1274-1290.

Rodrigues M, Oliveira A, Costa M, Fortunato AB, Zhang Y. 2009. Sensitivity analysis of an ecological model applied to the Ria de Aveiro.. Journal of Coastal Research. (Special Issue 56):448-452.

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.

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

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Priest GR, Goldfinger C, Wang K, Witter RC, Zhang Y, Baptista AM. 2009. 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.

Plant JN, Johnson KS, Needoba JA, Coletti LJ. 2009. NH4-Digiscan: an in situ and laboratory ammonium analyzer for estuarine, coastal and shelf waters. Limnology and Oceanography.

Pfeiffer-Herbert AS, Prahl FG, Hales B, Lerczak JA, Pierce SD, Levine MD. 2015. 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.

Petes LE, Menge BA, Chan F, Webb MAH. 2008. Gonadal tissue color is not a reliable indicator of sex in rocky intertidal mussels. Aquatic Biology. 3:63-70.

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

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.

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)

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.

Palacios SL, Peterson TD, Kudela RM. 2009. Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114

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

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Nidzieko NJ, Needoba JA, Monismith SG, Johnson KS. 2014. Fortnightly Tidal Modulations Affect Net Community Production in a Mesotidal Estuary. Estuaries and Coasts. 37(1):91-110.

Nguyen H, Kang E Y, Freire J. 2008. Automatically Extracting Form Labels. Proceedings of the 2008 IEEE 24th International Conference on Data Engineering (ICDE 2008). :1498-1500.

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.

Nechad B., Ruddick K., Schroeder T., Oubelkhier K., Blondeau-Patisseri D., Cherukuru N., Brando V., Dekker A., Clementson L., Banks A.C. et al.. 2015. 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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Moran M.A., Kujawinski E.B., Stubbins A., Fatland R., Aluwihare L.I., Buchan A., Crump B.C., Dorrestein P.C., Dyhrman S.T., Hess N.J. et al.. 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.

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

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)

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.

Megler VM, Maier D, Bottomly D, White L, McWeeney S, Wilmot B. 2015. Data Like This: Ranked Search of Genomic Data. ExploreDB.

Megler VM. 2014. Ranked Similarity Search of Scientific Datasets: An Information Retrieval Approach. Computer Science. Doctor of Philosophy Dissertation

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.

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

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)

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