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In Press

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.

2017

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.

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

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

Rostaminia M. 2017. Change in variability in the Columbia River estuary: a habitat perspective. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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.

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.

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

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.

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

Watson S. 2017. Insights Into Microbial Phosphorus Cycling In The Columbia River Estuary. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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)

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.

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.

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

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..

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

2016

McKibben M. 2016. Above and Below: Oregon Coastal Phytoplankton Bloom Dynamics from Sea and Space. Oceanography. Doctor of Philosophy

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.

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.

Karna T, Baptista AM. 2016. Evaluation of a long-term hindcast simulation for the Columbia River estuary. Ocean Modelling. 99:1-14.

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.

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.

Shcherbina AY, McNeil CL, Baptista AM. 2016. Model-aided Lagrangian interpretation of non-synoptic estuarine observations. Limnology and Oceanography: Methods.

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

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.

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

2015

Smythe WF. 2015. Biomineralization in extreme iron and manganese depositing environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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.

Megler VM, Maier D, Bottomly D, White L, McWeeney S, Wilmot B. 2015. Data Like This: Ranked Search of Genomic Data. ExploreDB.

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

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

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.

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.

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.

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.

Fortunato CS, Crump BC. 2015. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient. PLoS ONE. 10(11):e0140578.

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.

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.

Tausz C. 2015. Phytoplankton dynamics in off-channel habitats of the lower Columbia River estuary. Division of Environmental & Biomolecular Systems. Master of Science

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)

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.

2014

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)

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)

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.

Maier D, Megler VM, Tufte K. 2014. Challenges for Dataset Search (keynote). International Conference on Database Systems for Advanced Applications. 8421

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.

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

Burke BJ, Anderson JJ, Baptista AM. 2014. Evidence for multiple navigational sensory capabilities by Chinook salmon. Aquatic Biology.

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.

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.

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)

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

Megler VM. 2014. Ranked Similarity Search of Scientific Datasets: An Information Retrieval Approach. Computer Science. Doctor of Philosophy Dissertation

2013

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)

Xu M. 2013. Characterization of the metabolic properties and ecological functions of Thaumarchaeota in terrestrial environments. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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)

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.

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.

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

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.

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

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.

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

DeLorenzo S. 2013. Inorganic Carbon-Assimilating Microbial Communities in the Pacific Northwest Coastal Margin. Division of Environmental & Biomolecular Systems. Doctor of Philosophy

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)

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)

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.

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.

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

Abdel-Jabbar N, Baptista AM, Karna T, Turner P, Sen G. 2013. US Experience Will Advance Gulf Ecosystem Research.

Rathmell K, Wilkin M, Welle P, Mattson T, Baptista AM. 2013. A Very Smart Kayak .... Currents. 28(3)

2012

Goldman JH, Rounds SA, Needoba JA. 2012. Applications of Fluorescence Spectroscopy for Predicting Percent Wastewater in an Urban Stream. Environmental Science & Technology.

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

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