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Book

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

Book Chapter

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.

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

Journal Article

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.

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)

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)

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.

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)

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.

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.

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.

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

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

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.

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 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.

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. 2009. Development of synthetic salinity from remote sensing for the Columbia River plume. Journal of Geophysical Research. 114

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.

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.

Ahn S, Peterson TD, Righter J, Miles DM, Tratnyek PG. 2013. Disinfection of Ballast Water with Iron Activated Persulfate. Environmental Science & Technology. 47(20)

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.

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 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.

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.

Berger M, Gustavo Nonato L, Pascucci V, Silva CT. 2010. Fiedler trees for multiscale surface analysis. Computers & Graphics. 34(3):272-281.

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.

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.

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 .

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.

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.

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.

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

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.

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)

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.

Anthony S, Prahl FG, Peterson TD. 2012. Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)

Anthony S, Prahl FG, Peterson TD. 2012. Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)

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

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.

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 .

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 .

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, 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, 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

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)

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.

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.

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.

Zhang Y, Witter RC, Priest GP. 2011. Nonlinear Tsunami-Tide Interaction in 1964 Prince William Sound. Ocean Modeling.

Maier MA, Peterson TD. 2014. Observations of a Diatom Chytrid Parasite in the Lower Columbia River. Northwest Science. 88(3):234-245.

Palacios SL, Peterson TD, Kudela RM. 2012. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)

Palacios SL, Peterson TD, Kudela RM. 2012. Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)

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

Maier MA, Peterson TD. 2016. Prevalence of chytrid parasitism among diatom populations in the lower Columbia River (2009–2013). Freshwater Biology.

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.

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.

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)

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, 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.

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)

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)

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.

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.

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.

Vo H, Osmari DK, Summa B, Comba J, Pascucci V, Silva CT. 2010. Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems. Computer Graphics Forum. 29(3):1073-1082.

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.

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.

Zhang Y, Witter RC, Priest GR. 2011. Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Modelling.

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..

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