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Publications

Found 49 results
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Thesis
Kilgren R.  2006.  Numerical simulations of large river plumes in the Pacific Northwest. Division of Environmental & Biomolecular Systems. Master of Science
Koop D.  2012.  Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy
Kahn P.  2014.  Ecology and diversity of heterotrophic protists in the Columbia River coastal margin. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
Peer-reviewed Conference Paper
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.
Koop D, Scheidegger C, Freire J, Silva CT.  2010.  The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.
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.
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.
Journal Article
Karna T, Baptista AM.  2016.  Water age in the Columbia River estuary. Estuarine, Coastal and Shelf Science. 183(Part A):249-259.
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.
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.
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.
Kahn P., Herfort L., Crump B.C., Zuber P., Peterson T.D..  0.  Spatiotemporal distribution of heterotrophic protists in the Columbia River coastal margin, USA. Rejected at AEM, 2014. Undergoinging revision.
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.
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.
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)
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)
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)
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.
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.
Freire J, Koop D, Santos E, Silva CT.  2008.  Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.
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
Palacios SL, Peterson TD, Kudela RM.  2012.  Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
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.
Karna T, Baptista AM, Lopez JE, Turner PJ, McNeil C, Sanford TB.  2015.  Numerical modeling of circulation in high-energy estuaries: A Columbia River estuary benchmark. Ocean Modelling. 88:54-71.
Kudela RM, Banas NS, Barth JA, Frame E, Jay DA, Largier JL, Lessard EJ, Peterson TD, Vander Woude AJ.  2008.  New Insights into the Controls and Mechanisms of Plankton Productivity on the US West Coast.. Oceanography. 21(4)
Kirby RM, Silva CT.  2008.  The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5):78-83.
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 .
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 .
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.
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.
Baptista AM, Seaton C, Wilkin M, Riseman S, Needoba JA, Maier D, Turner PJ, Karna T, Lopez JE, Herfort L et al..  2015.  Infrastructure for collaborative science and societal applications in the Columbia River estuary. Frontiers of Earth Science. 9(4):659-682.
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
Bellmore R.A., Harrison J.A., Needoba J.A., Brooks E., Keller C.K..  2015.  Hydrologic control of dissolved organic carbon and nitrogen and dissolved organic matter quality in a semi-arid artificially drained agricultural catchment. Water Resources Research. 51(10):8146–8164.
Maier MA, Uchii K., Peterson T.D., Kagami M..  2016.  Evaluation of Daphnid Grazing on Microscopic Zoosporic Fungi by Using Comparative Threshold Cycle Quantitative PCR. Applied and Environmental Microbiology. 82(13):3868-3874.
Karna T, Baptista AM.  2016.  Evaluation of a long-term hindcast simulation for the Columbia River estuary. Ocean Modelling. 99:1-14.
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
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)
Kahn P, Herfort L, Peterson TD, Zuber P.  2014.  Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element. MicrobiologyOpen. 3(5):764-776.
Palacios SL, Peterson TD, Kudela RM.  2009.  Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114
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.
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.
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)
Kahn P., Voorhees I., McAteer D., Herfort L., Peterson T.D., Crump B.C., Zuber P..  0.  Application of highly discriminating unique sequence elements of the 28S rRNA gene for determination of protest biogeography. In Preparation.
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.