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H

Hansen C, Johnson C, Pascucci V, Silva CT. 2011. Visualization for Data-Intensive Science. The Fourth Paradigm. :153-163.

Haynes V. 2013. Development of novel impedimetric assays for rapid detection of E. coli. Division of Environmental & Biomolecular Systems. Master of Science

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.

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, 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, 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, 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, Campbell V, Futrell S, Zuber P. 2011. Myrionecta rubra bloom initiation in the Columbia River estuary. Estuarine, Coastal and Shelf Science.

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)

Hosen JD, Febria CM, Crump BC, Palmer MA. 2017. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition. Front. Microbiol.. 8:1452.

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.

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, 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, Maier D, Bright L. 2007. Smoothing the ROI Curve for Scientific Data Management Applications. Third Biennial Conference on Innovative Data Systems Research (CIDR).

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)

Maier D, Megler VM, Baptista AM, Jaramillo A, Seaton C, Turner PJ. 2012. Navigating Oceans of Data. 7338:1-19.

J

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)

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)

K

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.

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

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.

Karna T, Baptista AM. 2016. Water age in the Columbia River estuary. Estuarine, Coastal and Shelf Science. 183(Part A):249-259.

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.

Kilgren R. 2006. Numerical simulations of large river plumes in the Pacific Northwest. Division of Environmental & Biomolecular Systems. Master of Science

Kirby RM, Silva CT. 2008. The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5):78-83.

Koop D, Scheidegger C, Freire J, Silva CT. 2010. The Provenance of Workflow Upgrades. 3rd International Provenance and Annotation Workshop (IPAW) 2010.

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

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)

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 .

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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

Lopez JE, Baptista AM. 2017. Benchmarking an unstructured grid sediment model in an energetic estuary. Ocean Modeling. 110:32-48.

Lopez JE. 2017. Sediment dynamics in an energetic estuary. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

M

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

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

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.

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

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.

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

Megler VM, Maier D. 2011. Finding Haystacks with Needles: Ranked Search for Data Using Geospatial and Temporal Characteristics. 23rd Scientific and Statistical Database Management Conference.

Megler VM, Maier D. 2013. Data Near Here: Bringing Relevant Data Closer to Scientists. Computing in Science and Engineering,. 15(3):44-53.

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)

Megler VM, Maier D. 2013. Taming the Metadata Mess. 29th IEEE International Conference on Data Engineering.

Megler VM, Maier D. 2015. Demonstrating "Data Near Here": Scientific Data Search. SIGMOD '15.

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.

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)

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

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.

N

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.

Needoba JA, Peterson TD, Johnson KS. 2012. Method for Quantification of Aquatic Primary Production and Net Ecosystem Metabolism using in situ Dissolved Oxygen Sensors. Molecular Biological Technologies for Ocean Sensing.

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.

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.

P

Palacios SL, Peterson TD, Kudela RM. 2009. Development of synthetic salinity from remote sensing for the Columbia River plume. 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)

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

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.

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)

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.

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.

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.

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.

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.

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