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M
Megler VM, Maier D, Bottomly D, White L, McWeeney S, Wilmot B.  2015.  Data Like This: Ranked Search of Genomic Data. ExploreDB.
Megler VM.  2014.  Ranked Similarity Search of Scientific Datasets: An Information Retrieval Approach. Computer Science. Doctor of Philosophy Dissertation
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.
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)
McKibben M.  2016.  Above and Below: Oregon Coastal Phytoplankton Bloom Dynamics from Sea and Space. Oceanography. Doctor of Philosophy
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.
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
Maier MA, Peterson TD.  2016.  Prevalence of chytrid parasitism among diatom populations in the lower Columbia River (2009–2013). Freshwater Biology.
Maier MA, Peterson TD.  2014.  Observations of a Diatom Chytrid Parasite in the Lower Columbia River. Northwest Science. 88(3):234-245.
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.
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.
Maier D, Megler VM, Tufte K.  2014.  Challenges for Dataset Search (keynote). International Conference on Database Systems for Advanced Applications. 8421
L
Lopez JE.  2017.  Sediment dynamics in an energetic estuary. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
Lopez JE, Baptista AM.  2017.  Benchmarking an unstructured grid sediment model in an energetic estuary. Ocean Modeling. 110:32-48.
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
K
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, Peterson TD.  2009.  Influence of a buoyant river plume on phytoplankton nutrient dynamics: What controls standing stocks and productivity? Journal of Geophysical Research. 114
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)
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, 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.  2012.  Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy
Koop D, Scheidegger C, Freire J, Silva CT.  2010.  The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.
Kirby RM, Silva CT.  2008.  The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5):78-83.
Kilgren R.  2006.  Numerical simulations of large river plumes in the Pacific Northwest. Division of Environmental & Biomolecular Systems. Master of Science
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.
Karna T, Baptista AM.  2016.  Water age in the Columbia River estuary. Estuarine, Coastal and Shelf Science. 183(Part A):249-259.
Karna T, Baptista AM.  2016.  Evaluation of a long-term hindcast simulation for the Columbia River estuary. Ocean Modelling. 99:1-14.
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.
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.
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.
Kahn P.  2014.  Ecology and diversity of heterotrophic protists in the Columbia River coastal margin. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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.
J
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)
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)
H
Maier D, Megler VM, Baptista AM, Jaramillo A, Seaton C, Turner PJ.  2012.  Navigating Oceans of Data. 7338:1-19.
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)
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.
Howe B, Maier D, Bright L.  2007.  Smoothing the ROI Curve for Scientific Data Management Applications. Third Biennial Conference on Innovative Data Systems Research (CIDR).
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, Green-Fishback H, Maier D.  2009.  Scientific Mashups: Runtime-Configurable Data Product Ensembles. Proceedings of the 21st International Conference, SSDBM 2009. 5566:19-36.
Hosen JD, Febria CM, Crump BC, Palmer MA.  2017.  Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition. Front. Microbiol.. 8:1452.
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)
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, Seaton C, Wilkin M, Roman B, Preston CM, Marin, III R, Seitz K, Smith MW, Haynes V, Scholin CA et al..  2016.  Use of continuous, real-time observations & model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler. Limnol. Oceanogr. Methods. 14(1):50-67.
Herfort L, Maxey K, Vorhees I, Simon HM, Grobler K, Peterson TD, Zuber P.  2017.  Use of Highly Specific Molecular Markers Reveals Positive Correlation between Abundances of Mesodinium cf. major and its Preferred Prey, Teleaulax amphioxeia, During Red Water Blooms in the Columbia River Estuary. J. Eukaryotic Microbiol..
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
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.
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.
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.
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.
Haynes V.  2013.  Development of novel impedimetric assays for rapid detection of E. coli. Division of Environmental & Biomolecular Systems. Master of Science
Hansen C, Johnson C, Pascucci V, Silva CT.  2011.  Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.
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.
G
Gregg T, Prahl FG, Simoneit BRT.  2015.  Suspended particulate matter transport of polycyclic aromatic hydrocarbons in the lower Columbia River and its estuary. Limnology and Oceanography.
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
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)
Goldman JH.  2011.  Applications of Fluorescence Spectroscopy for Monitoring Water Quality in an Urban Watershed. Division of Environmental & Biomolecular Systems. Masters
Goldman JH, Rounds SA, Needoba JA.  2012.  Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.
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.
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.
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.
Golda RL.  2017.  Assessing The Influence Of Environmental Ph On Algal Physiology Using A Novel Culture System. Division of Environmental & Biomolecular Systems. Doctor of Philosophy
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.
Gilbert M.  2011.  Nutrient Loading and Transformations in the Columbia River Estuary Determined by High Resolution In Situ Sensors. Division of Environmental & Biomolecular Systems. Masters
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, 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)
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., 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.
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.
F
Frolov S, Baptista AM, Wilkin M.  2008.  Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658.
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.
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.
Frolov S.  2007.  Enabling Technologies for Data Assimilation in a Coastal-Margin Observatory. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation
Freire J, Koop D, Santos E, Silva CT.  2008.  Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.
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.

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A calibration equation for oxygen optodes based on physical properties of the sensing foil
Authors: C. McNeil; E.A. D’Asaro
Journal Title: Limnology and Oceanography: Methods
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