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

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.

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.

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.

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.

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.

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

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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.

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)

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.

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

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

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.

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

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.

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 .

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.

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

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.

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

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

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)

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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.

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.

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.

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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.

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

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.

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.

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)

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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

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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.

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

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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.

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