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Publications

Found 202 results
Author [ Type(Asc)] Year
Journal Article
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
Herfort L, Crump BC, Fortunato CS, McCue LAnn, Campbell V, Simon HM, Baptista A, Zuber P.  2017.  Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima. MicrobiologyOpen. e522
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.
Burke BJ, Anderson JJ, Baptista AM.  2014.  Evidence for multiple navigational sensory capabilities by Chinook salmon. Aquatic Biology.
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
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.
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)
Maier MA, Peterson T.D..  2016.  Enumeration of Parasitic Chytrid Zoospores in the Columbia River via Quantitative PCR. Applied and Environmental Microbiology. 82(13):3857-3867.
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.
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.
Hamilton M, Hennon GMM, Morales R, Needoba JA, Peterson TD, Schatz M, Swalwell J, E. Armbrust V, Ribalet F.  2017.  Dynamics of Teleaulax-like cryptophytes during the decline of a red water bloom in the Columbia River Estuary. J Plankton Res. :1-11.
Ahn S, Peterson TD, Righter J, Miles DM, Tratnyek PG.  2013.  Disinfection of Ballast Water with Iron Activated Persulfate. Environmental Science & Technology. 47(20)
Miller J, Teel D, Baptista AM, Morgan C.  2013.  Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon. Canadian Journal of Fisheries and Aquatic Sciences.
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.
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.
Peterson TD, Harrison PJ.  2012.  Diatom dynamics in a long-lived mesoscale eddy in the northeast subarctic Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers.
Palacios SL, Peterson TD, Kudela RM.  2009.  Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114
Ghindilis A L., Smith MW, Messing DS, Haynes VN, Middleton GB, Schwarzkopf K R., Campbell CE, Zhan C, Ulrich B, Frasier MJ et al..  2012.  Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets. Biosensors and Bioelectronics.
Golda RL, Golda MD, Hayes JA, Peterson TD, Needoba JA.  2017.  Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions. Journal of Microbiological Methods. 136:78-87.
Fortunato CS, Eiler A., Herfort L, Needoba JA, Peterson TD, Crump BC.  2013.  Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin. ISME Journal.
Golda-VanEeckhoutte RL, Roof LT, Needoba JA, Peterson TD.  In Press.  Determination of intracellular pH in phytoplankton using the fluorescent probe, SNARF, with detection by fluorescence spectroscopy. Journal of Microbiological Methods.
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.
Megler VM, Maier D.  2013.  Data Near Here: Bringing Relevant Data Closer to Scientists. Computing in Science and Engineering,. 15(3):44-53.
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)
Azevedo A., Oliveira A, Fortunato AB, Zhang Y, Baptista AM.  2014.  A cross-scale numerical modeling system for management support of oil spill accidents. Marine Pollution Bulletin. 80(1-2):132-147.
Fietz S., Huguet C., Bendle J., Escala M., Gallacher C., Herfort L, Jamieson R., Martínez-Garcia A., McClymont E.L., Peck V.L. et al..  2012.  Co-variation of crenarchaeol and branched GDGTs in globally-distributed marine and freshwater sedimentary archives. Global and Planetary Change. 92-93
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.
Priest GR, Goldfinger C, Wang K, Witter RC, Zhang Y, Baptista AM.  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.
Nechad B., Ruddick K., Schroeder T., Oubelkhier K., Blondeau-Patisseri D., Cherukuru N., Brando V., Dekker A., Clementson L., Banks A.C. et al..  2015.  CoastColour Round Robin data sets: A database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters. Earth System Science Data. 7(2):319-348.
Roegner GC, Needoba JA, Baptista AM.  2011.  Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary. PLoS ONE. 6(4):e18672.
Green V, Bueno Watts N, Wegner K, Thompson M, Johnson AF, Peterson TD, Baptista AM.  2013.  Coastal Margin Science and Education in the Era of Collaboratories. Currents. 28(3)
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.
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.
McNeil C, D’Asaro E.A.  2014.  A calibration equation for oxygen optodes based on physical properties of the sensing foil. Limnology and Oceanography: Methods.
Lopez JE, Baptista AM.  2017.  Benchmarking an unstructured grid sediment model in an energetic estuary. Ocean Modeling. 110:32-48.
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.
Fortunato CS, Crump BC.  2011.  Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974
Peterson TD, Golda RL, Garcia ML, Li B, Maier MA, Needoba JA, Zuber P.  2013.  Associations between Mesodinium rubrum and cryptophyte algae in the Columbia River estuary. Aquatic Microbial Ecology. 68(2)
Miller J.A., Teel D.J., Peterson W.T., Baptista AM.  2014.  Assessing the relative importance of local and regional processes on the survival of a threatened salmon population. PLoS ONE. 9(6)
Megler VM, Maier D.  2014.  Are Datasets Like Documents?: Evaluating Similarity-Based Ranked Search Over Scientific Data IEEE Transactions on Knowledge and Data Engineering. (99)
Goldman JH, Rounds SA, Needoba JA.  2012.  Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.
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.
Anderson CR, Davis RE, Bandolin NS, Baptista AM, 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.
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.
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.

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