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Herfort L., Maxey K., Voohees I., Simon H.M., Grobler K., T.D. P, Zuber P.. 0. Tidal and diel dynamics of M. major and its specific Teleaulax prey generate red water blooms in the Columbia River estuary. In Preparation.

2007

Bernardon FF, Callahan SP, Comba J, Silva CT. 2007. An adaptive framework for visualizing unstructured grids with time-varying scalar fields. Parallel Computing. 33(6):391-405.

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.

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.

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

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. 2007. Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. 13(6):1560-1567.

Daniels J, Ha LK, Ochotta T, Silva CT. 2007. Robust Smooth Feature Extraction from Point Clouds. IEEE International Conference on Shape Modeling and Applications 2007 (SMI '07). :123-136.

2008

Callahan SP, Callahan JH, Scheidegger C, Silva CT. 2008. Direct Volume Rendering: A 3D Plotting Technique for Scientific Data. Computing in Science & Engineering. 10(1):88-92.

Callahan SP, Callahan JH, Scheidegger C, Silva CT. 2008. Direct Volume Rendering: A 3D Plotting Technique for Scientific Data. Computing in Science & Engineering. 10(1):88-92.

Howe B, Lawson P, Bellinger R, Anderson EW, Santos E, Freire J, Scheidegger C, Baptista AM, Silva CT. 2008. End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory. 2008 IEEE Fourth International Conference on eScience (eScience). :127-134.

Howe B, Lawson P, Bellinger R, Anderson EW, Santos E, Freire J, Scheidegger C, Baptista AM, Silva CT. 2008. End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory. 2008 IEEE Fourth International Conference on eScience (eScience). :127-134.

Howe B, Lawson P, Bellinger R, Anderson EW, Santos E, Freire J, Scheidegger C, Baptista AM, Silva CT. 2008. End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory. 2008 IEEE Fourth International Conference on eScience (eScience). :127-134.

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)

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)

Bruland KW, Lohan MC, Aguilar-Islas AM, Smith GJ, Sohst B, Baptista AM. 2008. Factors influencing the chemistry of the near-field Columbia River plume: Nitrate, silicic acid, dissolved Fe, and dissolved Mn. Journal of Geophysical Research. 113

Bruland KW, Lohan MC, Aguilar-Islas AM, Smith GJ, Sohst B, Baptista AM. 2008. Factors influencing the chemistry of the near-field Columbia River plume: Nitrate, silicic acid, dissolved Fe, and dissolved Mn. Journal of Geophysical Research. 113

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

Kirby RM, Silva CT. 2008. The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5):78-83.

Freire J, Koop D, Santos E, Silva CT. 2008. Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.

Freire J, Koop D, Santos E, Silva CT. 2008. Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.

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

Bavoil L, Callahan SP, Silva CT. 2008. Robust Soft Shadow Mapping with Backprojection and Depth Peeling. Journal of Graphics, GPU and Game Tools. 13

Baptista AM, Howe B, Freire J, Maier D, Silva CT. 2008. Scientific Exploration in the Era of Ocean Observatories. Computing in Science & Engineering. 10(3):53-58.

Chawla A, Jay DA, Baptista AM, Wilkin M, Seaton C. 2008. Seasonal Variability and Estuary-Shelf Interactions in Circulation Dynamics of a River-dominated Estuary. Estuaries and Coasts . 31

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

Daniels J, Ochotta T, Ha LK, Silva CT. 2008. Spline-based feature curves from point-sampled geometry. The Visual Computer. 24(6):449-462.

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.

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.

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.

Bernardon FF, Ha LK, Callahan SP, Comba J, Silva CT. 2008. Transfer-Function Specification for Rendering Disparate Volumes. Computing in Science & Engineering. 10(6):82-89.

Koop D, Scheidegger C, Callahan SP, Freire J, Silva CT. 2008. VisComplete: Automating Suggestions for Visualization Pipelines. IEEE Transactions on Visualization and Computer Graphics. 14(6):1691-1698.

Koop D, Scheidegger C, Callahan SP, Freire J, Silva CT. 2008. VisComplete: Automating Suggestions for Visualization Pipelines. IEEE Transactions on Visualization and Computer Graphics. 14(6):1691-1698.

2009

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.

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.

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, 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.

Frolov S, Baptista AM, Zhang Y, Seaton C. 2009. Estimation of ecologically significant circulation features of the Columbia River estuary and plume using a reduced-dimension Kalman filter. Continental Shelf Research. 29(2):456-466.

Daniels J, Silva CT, Cohen E. 2009. Localized Quadrilateral Coarsening. Computer Graphics Forum. 28(5):1437-1444.

Daniels J, Silva CT, Cohen E. 2009. Semi-regular Quadrilateral-only Remeshing from Simplified Base Domains. Computer Graphics Forum. 28(5):1427-1435.

Ghindilis A L., Smith MW, Schwarzkopf K R., Zhan C, Evans D R., Baptista AM, Simon HM. 2009. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. Electroanalysis. 21(13):1459-1468.

Ghindilis A L., Smith MW, Schwarzkopf K R., Zhan C, Evans D R., Baptista AM, Simon HM. 2009. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. Electroanalysis. 21(13):1459-1468.

Ghindilis A L., Smith MW, Schwarzkopf K R., Zhan C, Evans D R., Baptista AM, Simon HM. 2009. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. Electroanalysis. 21(13):1459-1468.

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

Etiene T, Scheidegger C, Nonato LG, Kirby RM, Silva CT. 2009. Verifiable Visualization for Isosurface Extraction. IEEE Transactions on Visualization and Computer Graphics. 15(6):1227-1234.

Etiene T, Scheidegger C, Nonato LG, Kirby RM, Silva CT. 2009. Verifiable Visualization for Isosurface Extraction. IEEE Transactions on Visualization and Computer Graphics. 15(6):1227-1234.

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.

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.

2010

Berger M, Gustavo Nonato L, Pascucci V, Silva CT. 2010. Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.

Daniels J, Anderson EW, Nonato LG, Silva CT. 2010. Interactive Vector Field Feature Identification. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2010).

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)

Koop D, Scheidegger C, Freire J, Silva CT. 2010. The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.

Koop D, Scheidegger C, Freire J, Silva CT. 2010. The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 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)

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)

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)

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)

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)

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, 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, 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.

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

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.

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

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

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

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.

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.

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.

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.

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