Publications

Found 103 results

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Submitted
Anthony S, Prahl FG, Peterson TD.  Submitted.  Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. Abstract
Kahn P, Herfort L, Peterson TD, McCue L, Zuber P.  Submitted.  Seasonal variation of the protist assemblage in the Columbia River coastal margin assessed using 18S rRNA gene sequences. Microbial Ecology. Abstract
In Press
Herfort L, Peterson TD, Prahl FG, McCue LA, Needoba JA, Crump BC, Roegner GC, Campbell V, Zuber P.  In Press.  Red waters of Myrionecta rubra are biogeochemical hotspots for the Columbia River estuary with impacts on primary/secondary productions and nutrient cycles. Estuaries and Coast.. Abstract
2011
Silva CT, Anderson EW, Santos E, Freire J.  2011.  Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84. Abstract
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. Abstract
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. Abstract
Roegner GC, Needoba JA, Baptista A.  2011.  Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672. Abstract
Zhang Y, Witter RC, Priest GR.  2011.  Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling. Abstract
Koop D, Santos E, Mates P, Vo HT, 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. Abstract
Megler, V.M., Maier D.  2011.  Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference. Abstract
Daniels J, Lizier M, Siqueira M, Silva CT, Nonato LG.  2011.  Template-based quadrilateral meshing. Shape Modeling International (SMI) Conference 2011 . (3):471-482. Abstract
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. Abstract
Anderson CR, Davis RE, Bandolin NS, Baptista A, 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. Abstract
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 Abstract
Fortunato CS, Crump BC.  2011.  Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974 Abstract
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 A.  2011.  Climatic and tidal forcing of hydrography and chlorophyll concentrations in the Columbia River estuary. Estuaries and Coasts. 34(2):281-296. Abstract
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 Abstract
Bräuer SL, Adams C, Kranzler K, Murphy D, Xu M, Zuber P, Simon HM, Baptista A, Tebo BM.  2011.  Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. Environmental Microbiology . 13(3) Abstract
Spitz YH.  2011.  Ecosystem Modeling of the Oregon Shelf: Everything but the Kitchen Sink. Interdisciplinary Studies on Environmental Chemistry. 5 Abstract
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. Abstract
Herfort L, Peterson TD, McCue L, Crump BC, Prahl FG, Baptista A, 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 Abstract
Zhang Y, Witter RW, Priest GP.  2011.  Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling. Abstract
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. Abstract
Fortunato CS, Herfort L, Zuber P, Baptista A, Crump BC.  2011.  Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal. Abstract
Hansen C, Johnson C, Pascucci V, Silva CT.  2011.  Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.
2010
Yamada SB, Kosro MP.  2010.  Linking ocean conditions to year class strength of the invasive European green crab, Carcinus maenas. Biological Invasions. 12(6):1791-1804. Abstract
Hickey BM, Kudela RM, Nash JD, Bruland KW, Peterson WT, MacCready P, Lessard EJ, Jay DA, Banas NS, Baptista A et al..  2010.  River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research. 115(C00B17) Abstract
Burla M, Baptista A, 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) Abstract
Dang T, Bulusu N, Feng W, Frolov S, Baptista A.  2010.  CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors. INFOCOM, 2010 Proceedings IEEE . :1-5. Abstract
Breitburg DL, Crump BC, Dabiri JO, Gallegos CL.  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. Abstract
Berger M, Gustavo Nonato L, Pascucci V, Silva CT.  2010.  Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281. Abstract
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. Abstract
Burla M, Baptista A, Casillas E, Williams JG, Marsh DM.  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. Abstract
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).
Kudela RM, Horner-Devine AR, Banas NS, Hickey BM, Peterson TD, McCabe RM, Lessard EJ, Frame E, Bruland KW, Jay DA et al..  2010.  Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophysical Research Letters . Abstract
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) Abstract
Koop D, Scheidegger C, Freire J, Silva CT.  2010.  The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010. Abstract
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) Abstract
Smith MW, Herfort L, Tyrol K, Suciu D, Campbell V, Crump BC, Peterson TD, Zuber P, Baptista A, 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. Abstract
Santos E.  2010.  Simplifying the Creation and Deployment of Collaborative Data Analysis and Visualization Tools. School of Computing. Ph.D. Dissertation
2009
Howe B, Green-Fishback H, Maier D.  2009.  Scientific Mashups: Runtime-Configurable Data Product Ensembles. Proceedings of the 21st International Conference, SSDBM 2009. 5566:19-36. Abstract
Palacios SL, Peterson TD, Kudela RM.  2009.  Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114 Abstract
Liu Y, MacCready P, Hickey BM, Dever EP, Kosro MP, Banas NS.  2009.  Evaluation of a coastal ocean circulation model for the Columbia River plume in summer 2004. Journal of Geophysical Research. 114 Abstract
Kudela RM, Peterson TD.  2009.  Influence of a buoyant river plume on phytoplankton nutrient dynamics: What controls standing stocks and productivity? Journal of Geophysical Research. 114 Abstract
Banas NS, Lessard EJ, Kudela RM, MacCready P, Peterson TD, Hickey BM, Frame E.  2009.  Planktonic growth and grazing in the Columbia River plume region: A biophysical model study. Journal of Geophysical Research. 114 Abstract
Crump BC, Peterson BJ, Raymond PA, Amon RMW, Rinehart A, McClelland JW, Holmes RM.  2009.  Circumpolar synchrony in big river bacterioplankton. Proceedings of the National Academy of Sciences. 106(50):21208-21212. Abstract
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. Abstract
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. Abstract
Frolov S, Baptista A, Leen TK, Lu Z, van der Merwe R.  2009.  Fast data assimilation using a nonlinear Kalman filter and a model surrogate: An application to the Columbia River estuary. Dynamics of Atmospheres and Oceans. 48(1-3):16-45. Abstract
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. Abstract
Daniels J, Silva CT, Cohen E.  2009.  Localized Quadrilateral Coarsening. Computer Graphics Forum. 28(5):1437-1444. Abstract
Daniels J, Silva CT, Cohen E.  2009.  Semi-regular Quadrilateral-only Remeshing from Simplified Base Domains. Computer Graphics Forum. 28(5):1427-1435. Abstract
Ghindilis A L, Smith MW, Schwarzkopf K R, Zhan C, Evans D R, Baptista A, 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. Abstract
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. Abstract
Frolov S, Baptista A, 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. Abstract
Garcia-Mendoza E, Rivas D, Olivosortiz A, Almazanbecerril A, Castanedavega C, Penamanjarrez J.  2009.  A toxic Pseudo-nitzschia bloom in Todos Santos Bay, northwestern Baja California, Mexico. Harmful Algae. 8(3):493-503. Abstract
Burla M.  2009.  The Columbia River estuary and plume: natural variability, anthropogenic change and physical habitat for salmon. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation
Priest GR, Goldfinger C, Wang K, Witter RC, Zhang Y, Baptista A.  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. Abstract
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. Abstract
Gregg T.  2009.  Investigation of Polycyclic Aromatic Hydrocarbons (PAHs) transport by Suspended Particulate Matter (SPM) in the lower Columbia River and its Estuary. College of Oceanic and Atmospheric Sciences. Masters Thesis
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. Abstract
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. Abstract
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.
Schreiner JM.  2009.  Uniform and Adaptive (Re) Meshing of Surfaces. Computer Science. Ph.D. Dissertation
2008
Howe B, Lawson P, Bellinger R, Anderson EW, Santos E, Freire J, Scheidegger C, Baptista A, 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. Abstract
Nguyen H, Kang EY, Freire J.  2008.  Automatically Extracting Form Labels. Proceedings of the 2008 IEEE 24th International Conference on Data Engineering (ICDE 2008). :1498-1500. Abstract
Howe B, Maier D, Rayner N, Rucker J.  2008.  Quarrying dataspaces: Schemaless profiling of unfamiliar information sources. 2008 IEEE 24th International Conference on Data Engineeing workshop (ICDE Workshop 2008). :270-277. Abstract
Daniels J, Ochotta T, Ha LK, Silva CT.  2008.  Spline-based feature curves from point-sampled geometry. The Visual Computer. 24(6):449-462. Abstract
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) Abstract
Bruland KW, Lohan MC, Aguilar-Islas AM, Smith GJ, Sohst B, Baptista A.  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 Abstract
Zhang Y, Baptista A.  2008.  SELFE: A semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation. Ocean Modelling. 21(3-4):71-96. Abstract
Zhang Y, Baptista A.  2008.  An Efficient and Robust Tsunami Model on Unstructured Grids. Part I: Inundation Benchmarks. Pure and Applied Geophysics. 165(11-12):2229-2248. Abstract
Frolov S, Baptista A, Wilkin M.  2008.  Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658. Abstract
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. Abstract