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Publications

Found 202 results
Author [ Type(Asc)] Year
Journal Article
Durkin CA, Bender SJ, Chan KYK, Gaessner K, Grunbaum D, Armburst EV.  2013.  Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography. :1707-1726.
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.
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.
Daniels J, Silva CT, Cohen E.  2009.  Semi-regular Quadrilateral-only Remeshing from Simplified Base Domains. Computer Graphics Forum. 28(5):1427-1435.
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.
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
Evans W, Hales B, Strutton PG.  2011.  Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5)
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.
Burla M, Baptista AM, 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)
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.
McKibben SM, Strutton PG, Foley DG, Peterson TD, White AE.  2012.  Satellite-based detection and monitoring of phytoplankton blooms along the Oregon Coast. Journal of Geophysical Research. 117(12)
Bavoil L, Callahan SP, Silva CT.  2008.  Robust Soft Shadow Mapping with Backprojection and Depth Peeling. Journal of Graphics, GPU and Game Tools. 13
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)
Ghindilis A L., Smith MW, Simon HM, Seoudi IA, Yazvenko NS, Murray IA, Fu X, Smith K, Jen-Jacobson L, Xu S-yong.  2015.  Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Scientific Reports. 5(7737)
Herfort L, Peterson TD, Prahl FG, McCue LA, Needoba JA, Crump BC, Roegner GC, Campbell V, Zuber P.  2012.  Red waters of Myrionecta rubra are biogeochemical hotspots for the Columbia River estuary with impacts on primary/secondary productions and nutrient cycles. Estuaries and Coasts.
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)
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)
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.
Crump BC, Fine LM, Fortunato CS, Herfort L, Needoba JA, Murdock S, Prahl FG.  2017.  Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary. Limnology and Oceanography.
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.
Davidson S, Cohen-Boulakia S, Eyal A, Ludäscher B, McPhillips T, Bowers S, Anand M K, Freire J.  2007.  Provenance in Scientific Workflow Systems. IEEE Data Engineering Bulletin.
Silva CT, Freire J, Callahan SP.  2007.  Provenance for Visualizations: Reproducibility and Beyond. Computing in Science & Engineering. 9(5):82-89.
Freire J, Koop D, Santos E, Silva CT.  2008.  Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.
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.
Maier MA, Peterson TD.  2016.  Prevalence of chytrid parasitism among diatom populations in the lower Columbia River (2009–2013). Freshwater Biology.
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
Evans W, Hales B, Strutton PG.  2012.  pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
Frolov S, Baptista AM, Wilkin M.  2008.  Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658.
Palacios SL, Peterson TD, Kudela RM.  2012.  Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
Maier MA, Peterson TD.  2014.  Observations of a Diatom Chytrid Parasite in the Lower Columbia River. Northwest Science. 88(3):234-245.
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.
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.
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.
Zhang Y, Witter RC, Priest GP.  2011.  Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.
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.
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.
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)
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.
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
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.
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 .
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.
S. McKibben M, Watkins-Brandt KS, A Wood M, Hunter M, Forster Z, Hopkins A, Du X, Eberhart B-T, Peterson WT, White AE.  2015.  Monitoring Oregon Coastal Harmful Algae: Observations and implications of a harmful algal bloom-monitoring project. Harmful Algae. 50:32-44.
Shcherbina AY, McNeil CL, Baptista AM.  2016.  Model-aided Lagrangian interpretation of non-synoptic estuarine observations. Limnology and Oceanography: Methods.
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
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)
Fortunato CS, Crump BC.  2015.  Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient. PLoS ONE. 10(11):e0140578.
Anthony S, Prahl FG, Peterson TD.  2012.  Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)
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.
Johnson KS, Needoba JA.  2008.  Mapping the spatial variability of plankton metabolism using nitrate and oxygen sensors on an autonomous underwater vehicle. Limnology and Oceanography. 53(5 PART 2)
Daniels J, Silva CT, Cohen E.  2009.  Localized Quadrilateral Coarsening. Computer Graphics Forum. 28(5):1437-1444.
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.
Hugo RC, Smythe WF, McAllister SM, Young B, Maring B, Baptista AM.  2013.  Lessons Learned from a Geoscience Education Program in an Alaska Native Community. Journal of Sustainability Education . 5(2151-7452)
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.
Jannasch HW, Coletti LJ, Johnson KS, Fitzwater SE, Needoba JA, Plant JN.  2008.  The land/ocean biogeochemical observatory: A robust networked mooring system for continuously monitoring complex biogeochemical cycles in estuaries. Limnology and Oceanography: Methods. 6(JUL, July 2008)
Bueno Watts N, Smythe WF.  2013.  It Takes a Community to Raise a Scientist: A Case for Community-Inspired Research and Science Education in an Alaska Native Community. Currents. 28(3)
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.
Burla M, Baptista AM, 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.
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
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
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.
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.
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 .
Silva CT, Tohline JE.  2008.  Guest Editorial: Special Issue on Computational Provenance. Computing in Science and Engineering.. 10(3)
Golda RL, Golda MD, Peterson TD, Needoba JA.  2017.  Graphical coding data and operational guidance for implementation or modification of a LabVIEW®-based pHstat system for the cultivation of microalgae. Data in Brief. 12(June 2017):463-470.
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.
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
Roland LA, Zhang Y, Wang HV, Maderich V, Brovchenko I.  2012.  A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.
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.
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.
Berger M, Gustavo Nonato L, Pascucci V, Silva CT.  2010.  Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.
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.
Frolov S, Baptista AM, 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.
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.

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