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2007

Frolov S. 2007. Enabling Technologies for Data Assimilation in a Coastal-Margin Observatory. Division of Environmental & Biomolecular Systems. Ph.D. Dissertation

van der Merwe R, Leen TK, Lu Z, Frolov S, Baptista AM. 2007. Fast neural network surrogates for very high dimensional physics-based models in computational oceanography. Neural Networks. 20(4):462-478.

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.

Silva CT, Freire J, Callahan SP. 2007. Provenance for Visualizations: Reproducibility and Beyond. Computing in Science & Engineering. 9(5):82-89.

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.

Scheidegger C, Vo H, Koop D, Freire J, Silva CT. 2007. Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. 13(6):1560-1567.

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).

2008

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.

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.

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)

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)

Frolov S, Baptista AM, Wilkin M. 2008. Optimizing fixed observational assets in a coastal observatory. Continental Shelf Research. 28(19):2644-2658.

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

Scheidegger C, Vo H, Koop D, Freire J, Silva CT. 2008. Querying and re-using workflows with VsTrails. ACM SIGMOD international Conference on Management of Data.

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.

Silva CT, Freire J. 2008. Software Infrastructure for exploratory visualization and data analysis: past, present, and future. Journal of Physics: Conference Series. 125:012100.

Scheidegger C, Koop D, Santos E, Vo H, Callahan SP, Freire J, Silva CT. 2008. Tackling the Provenance Challenge one layer at a time. Concurrency and Computation: Practice and Experience. 20(5):473-483.

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.

2009

Santos E, Tierny J, Khan A, Grimm B, Lins L, Freire J, Pascucci V, Silva CT, Klasky S, Barreto R et al.. 2009. Enabling Advanced Visualization Tools in a Web-Based Simulation Monitoring System. 2009 5th IEEE International Conference on e-Science (e-Science)2009 Fifth IEEE International Conference on e-Science. :358-365.

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, 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.

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

Rodrigues M, Oliveira A, Costa M, Fortunato AB, Zhang Y. 2009. Sensitivity analysis of an ecological model applied to the Ria de Aveiro.. Journal of Coastal Research. (Special Issue 56):448-452.

Rodrigues M, Oliveira A, Queiroga H, Fortunato AB, Zhang Y. 2009. Three-dimensional modeling of the lower trophic levels in the Ria de Aveiro (Portugal). Ecological Modelling. 220(9-10):1274-1290.

Santos E, Lins L, Ahrens J, Freire J, Silva CT. 2009. VisMashup: Streamlining the Creation of Custom Visualization Applications. IEEE Transactions on Visualization and Computer Graphics. 15(6):1539-1546.

2010

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

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 .

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

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)

2011

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

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

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.

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.

Silva CT, Anderson EW, Santos E, Freire J. 2011. Using VisTrails and Provenance for Teaching Scientific Visualization. Computer Graphics Forum. 30(1):75-84.

2012

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.

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.

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)

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.

2013

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.

2014

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.

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.

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.

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)

2016

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.

2017

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

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)

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, 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.

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