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A

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

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

Anderson EW, Potter KC, Matzen LE, Shepherd JF, Preston GA, Silva CT. 2011. A User Study of Visualization Effectiveness Using EEG and Cognitive Load. Computer Graphics Forum. 30(3):791-800.

Anderson EW. 2011. The Analysis and Visualization of Electroencephalography Data Using a Provenance-Enabled Environment and its Applications to Visualization. Doctor of Philosophy in Computer Science

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.

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

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.

B

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

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.

Baptista AM, Howe B, Freire J, Maier D, Silva CT. 2008. Scientific Exploration in the Era of Ocean Observatories. Computing in Science & Engineering. 10(3):53-58.

Hyde N. 2007. Towards national estuarine modeling and characterization/classification systems: a pilot study for Coos Bay. Division of Environmental & Biomolecular Systems. Masters Thesis

Bavoil L, Callahan SP, Silva CT. 2008. Robust Soft Shadow Mapping with Backprojection and Depth Peeling. Journal of Graphics, GPU and Game Tools. 13

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.

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

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.

Bernardon FF, Ha LK, Callahan SP, Comba J, Silva CT. 2008. Transfer-Function Specification for Rendering Disparate Volumes. Computing in Science & Engineering. 10(6):82-89.

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)

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.

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.

Bright L, Maier D, Howe B. 2006. Managing the Forecast Factory. 22nd International Conference on Data Engineering Workshops (ICDEW'06). :64-64.

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

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)

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

Burla M. 2009. The Columbia River estuary and plume: natural variability, anthropogenic change and physical habitat for salmon. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation

Burla M, Baptista AM, Zhang Y, Frolov S. 2010. Seasonal and interannual variability of the Columbia River plume: A perspective enabled by multiyear simulation databases. Journal of Geophysical Research. 115(C00B16)

Burla M, Baptista AM, Casillas E, Williams JG, Marsh DM. 2010. The influence of the Columbia River plume on the survival of steelhead (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha): a numerical exploration. Canadian Journal of Fisheries & Aquatic Sciences. 67(10):1671-1684.

C

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.

Chawla A, Jay DA, Baptista AM, Wilkin M, Seaton C. 2008. Seasonal Variability and Estuary-Shelf Interactions in Circulation Dynamics of a River-dominated Estuary. Estuaries and Coasts . 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.

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.

D

Dang T, Frolov S, Bulusu N, Baptista AM. 2007. Near Optimal Sensor Selection in the COlumbia RIvEr (CORIE) Observation Network for Data Assimilation Using Genetic Algorithms. International Conference on Distributed Computing in Sensor Systems (DCOSS). 4549:253-266.

Dang TX. 2011. Scalable and Efficient Tasking for Dynamic Sensor Networks. Doctor of Philosophy in Computer Science

Dang T, Bulusu N, Feng W, Frolov S, Baptista AM. 2010. CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors. INFOCOM, 2010 Proceedings IEEE . :1-5.

Dang T, Bulusu N, Feng W. 2007. RIDA: A Robust Information-Driven Compression Architecture for Irregular Wireless Sensor Networks.. European Conference on Sensor Networks (EWSN).

Daniels J, Lizier M, Siqueira M, Silva CT, Nonato LG. 2011. Template-based quadrilateral meshing. Shape Modeling International (SMI) Conference 2011 . (3):471-482.

Daniels J, Ochotta T, Ha LK, Silva CT. 2008. Spline-based feature curves from point-sampled geometry. The Visual Computer. 24(6):449-462.

Daniels J, Ha LK, Ochotta T, Silva CT. 2007. Robust Smooth Feature Extraction from Point Clouds. IEEE International Conference on Shape Modeling and Applications 2007 (SMI '07). :123-136.

Daniels J, Anderson EW, Nonato LG, Silva CT. 2010. Interactive Vector Field Feature Identification. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2010).

Daniels J, Silva CT, Cohen E. 2009. Localized Quadrilateral Coarsening. Computer Graphics Forum. 28(5):1437-1444.

Daniels J, Silva CT, Cohen E. 2009. Semi-regular Quadrilateral-only Remeshing from Simplified Base Domains. Computer Graphics Forum. 28(5):1427-1435.

Davidson S, Cohen-Boulakia S, Eyal A, Ludäscher B, McPhillips T, Bowers S, Anand M K, Freire J. 2007. Provenance in Scientific Workflow Systems. IEEE Data Engineering Bulletin.

DeLorenzo S, Bräuer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P. 2012. Ubiquitous dissolved inorganic carbon assimilation by marine heterotrophic bacteria in the Pacific Northwest coastal ocean as determined by DNA-based stable isotope probing. PLoS ONE.

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

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.

E

Etiene T, Scheidegger C, Nonato LG, Kirby RM, Silva CT. 2009. Verifiable Visualization for Isosurface Extraction. IEEE Transactions on Visualization and Computer Graphics. 15(6):1227-1234.

Evans W, Hales B, Strutton PG. 2012. pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.

Evans W, Hales B, Strutton PG. 2011. Seasonal cycle of surface ocean pCO2 on the Oregon shelf. Journal of Geophysical Research. 116(C5)

F

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

Fortunato CS, Herfort L, Zuber P, Baptista AM, Crump BC. 2012. Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME Journal. 6:554-563.

Fortunato CS. 2012. Spatial and temporal variability of bacterioplankton communities across river to ocean environmental gradients. University of Maryland.

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.

Fortunato CS, Crump BC. 2011. Bacterioplankton Community Variation Across River to Ocean Environmental Gradients. Microbial Ecology. 61 / 1974

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

Freire J, Koop D, Santos E, Silva CT. 2008. Provenance for Computational Tasks: A Survey. Computing in Science & Engineering. 10(3):11-21.

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

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.

G

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.

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.

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., 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.

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

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.

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

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.

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.

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)

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

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.

H

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.

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