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Publications

Found 180 results
Author Type [ Year(Asc)]
In Press
Lopez JE, Baptista AM.  In Press.  Benchmarking an unstructured grid sediment model in an energetic estuary. Ocean Modeling.
Karna T, Baptista AM.  In Press.  Water age in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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.
2015
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.
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.
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. Ph.D.
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)
Green V, Bueno Watts N, Wegner K, Thompson M, Johnson A, 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.
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)
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
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.
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.
Roland LA, Zhang Y, Wang HV, Maderich V, Brovchenko I.  2012.  A fully coupled wave-current model on unstructured grids. Journal of Geophysical Research.
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 .
Koop D.  2012.  Managing Provenance for Knowledge Discovery and Reuse. School of Computing. Doctor of Philosophy
Anthony S, Prahl FG, Peterson TD.  2012.  Methane dynamics in the Willamette River, Oregon, U.S.A.. Limnology and Oceanography. 57(5)
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.
Maier D, Megler VM, Baptista AM, Jaramillo A, Seaton C, Turner PJ.  2012.  Navigating Oceans of Data. 7338:1-19.
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.
Palacios SL, Peterson TD, Kudela RM.  2012.  Optical characterization of water masses within the Columbia River Plume. Journal of Geophysical Research. 117(11)
Evans W, Hales B, Strutton PG.  2012.  pCO2 distributions and air-water CO2 fluxes in the Columbia River estuary. Estuarine, Coastal and Shelf Science.
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.
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)
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.
Fortunato CS.  2012.  Spatial and temporal variability of bacterioplankton communities across river to ocean environmental gradients. University of Maryland.
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.
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.
Megler VM, Maier D.  2012.  When big data leads to lost data. Proceedings of the 5th Ph.D. workshop on Information and knowledge - PIKM '12. :1.

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