Publications
| 2006 | 2007 | 2008 | 2009 | 2010 |
Ghindilis, A.L., K.R Schwarzkopf, D.S. Messing, I. Sezan, C. Zhan, M.W. Smith, Simon, HM, D.R. Evans (accepted 2010) Real-Time Biosensor Platform: Fully Integrated Device for Impedimetric Assays, ECS Transactions, Volume 33, Chemical Sensors 9: Chemical and Biological Sensors and Analytical Systems
CMOP contribution: 10-006
Rivas, D., R.M. Samelson (2010) A numerical modeling study of the upwelling source waters along the Oregon coast during 2005, Journal of Physical Oceanography
CMOP contribution: 10-005
Thanh D., N. Bulusu, W. Feng, S. Frolov, A. Baptista (2010) CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Sensors, INFOCOM, 2010 Proceedings IEEE , pp.1-5, 14-19 March 2010 doi: 10.1109/INFCOM.2010.5462234
CMOP contribution: 10-004
Burla, M., A.M. Baptista, E. Casillas, J.G. Williams and D.M. Marsh (in press 2010). The influence of the Columbia River plume on the survival of steelhead (Oncorhynchus mykiss) and Chinook salmon (O. tshawytscha): a numerical exploration. Canadian Journal of Fisheries & Aquatic Sciences
CMOP contribution: 10-003
Burla, M., A.M. Baptista, Y. Zhang and S. Frolov (2010). Seasonal and inter-annual variability of the Columbia River plume: A perspective enabled by multi-year simulation databases. Journal of Geophysical Research, doi:10.1029/2008JC004964 (2010).
CMOP contribution: 10-002
Hickey, B. M., R. M. Kudela, J. D. Nash, K. W. Bruland, W. T. Peterson, P. MacCready, E. J. Lessard, D. A. Jay, N. S. Banas, A. M. Baptista, E. P. Dever, P. M. Kosro, L. K. Kilcher, A. R. Horner-Devine, E. D. Zaron, R. M. McCabe, J. O. Peterson, P. M. Orton, J. Pan and M. C. Lohan (2010) River Influences on Shelf Ecosystems: Introduction and synthesis. Journal of Geophysical Research - Oceans. Vol. 115, C00B17, 26pp.
CMOP contribution: 10-001
Banas, N. S., E. J. Lessard, R. M. Kudela, P. MacCready, T. D. Peterson, B. M. Hickey and E. Frame (2009). Planktonic growth and grazing in the Columbia River plume region: A biophysical model study. Journal of Geophysical Research. 114(10): 1029.
CMOP contribution: 09-018
Crump, B. C., B. J. Peterson, P. A. Raymond, R.M. W. Amond, A. Rinehart, J. W. McClelland and R. M. Holmes (2009). Circumpolar synchrony in big river bacterioplankton. PNAS. vol. 106 no. 50 21208-21212.
CMOP contribution: 09-017
Dang T, N. Bulusu, W.Feng, S. Frolov, and A, Baptista (2009). CoTrack: A Framework for Tracking Dynamic Features with Static and Mobile Underwater Sensors. ACM
CMOP contribution: 09-016
Dietrich, C., J. Comba, L. Nedel, C. Scheidegger, J. Schreiner and C. Silva (2009). Improving Mesh Quality of Marching Cubes Using Edge Transformations. IEEE Transactions on Visualization and Computer Graphics. 15(1): 150-159.
CMOP contribution: 09-015
Dietrich, C. A., C. E. Scheidegger, J. L. D. Comba, L. P. Nedel and C. T. Silva (2009). Marching Cubes without Skinny Triangles. Computing in Science and Engineering. 11(2): 82-87.
CMOP contribution: 09-014
Dietrich, C. A., C. E. Scheidegger, J. M. Schreiner, J. L. D. Comba, L. P. Nedel and C. T. Silva (2009). Edge Transformations for Improving Mesh Quality of Marching Cubes. IEEE Transactions on Visualization and Computer Graphics. 15(1): 150-159.
CMOP contribution: 09-013
Frolov, S; Baptista, A; 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.
CMOP contribution: 09-012
Frolov, S., Z. Lu, R. van der Merwe, T.K. Leen, and A.M. Baptista, (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. 2008.10.004.
CMOP contribution: 09-011
Garcia-Mendoza, E., D. Rivas, A. Olivos-Ortiz, A. Almazan-Becerril, C. Castaneda-Vega and J. L. Pena-Manjarrez (2009). A toxic Pseudo-nitzschia bloom in Todos Santos Bay, northwestern Baja California, Mexico. Harmful Algae. 8(3): 493-503.
CMOP contribution: 09-010
Ghindilis, A. L., M. W. Smith, K. R. Schwarzkopf, C. Zhan, D. R. Evans, A. M. Baptista and H. M. Simon (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.
CMOP contribution: 09-009
Howe, B; Green-Fishback, H; Maier, D (2009). Scientific Mashups: Runtime-Configurable Data Product Ensembles. Scientific and Statistical Database Management Conference. 19-36.
CMOP& contribution: 09-008
Kudela, R. M. and T. D. Peterson (2009). Influence of a buoyant river plume on phytoplankton nutrient dynamics: What controls standing stocks and productivity? Journal of Geophysical Research. Res. 114.
CMOP contribution: 09-007
Liu, Y., P. MacCready, B. M. Hickey, E. P. Dever, P. M. Kosro and N. S. Banas (2009). Evaluation of a coastal ocean circulation model for the Columbia River plume in summer 2004. Journal of Geophysical Research. 114.
CMOP contribution: 09-006
Plant, J. N., K. S. Johnson, J. A. Needoba and L. J. Coletti (2009). NH4-Digiscan: An in situ and laboratory ammonium analyzer for estuarine, coastal, and shelf waters. Limnology and Oceanography: Methods. 7 (FEB): 144-156.
CMOP contribution: 09-005
Priest, G.R., C. Goldfinger, K. Wang, R. C. Witter, Y. Zhang and A. Baptista, (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. doi 10.1007/s11069-009-9453-5.
CMOP contribution: 09-004
Rodrigues, M., A. Oliveira, M. Costa, A. B. Fortunado and Y. Zhang (2009). Sensitivity analysis of an ecological model applied to the Ria de Aveiro. Journal of Coastal Research. (Special Issue 56).
CMOP contribution: 09-003
Rodrigues, M., A. Oliveira, H. Queiroga, A. B. Fortunado and Y. Zhang (2009). Three-Dimensional Modeling of the Lower Trophic Levels in the Ria de Aveiro (Portugal). Ecological Modeling. 220(9-10): 1274.
CMOP contribution: 09-002
Wang, H., C. E. Scheidegger and C. T. Silva (2009). Bandwidth Selection and Reconstruction Quality in Point-Based Surfaces. IEEE Transactions on Visualization and Computer Graphics. 15(4): 572-582.
CMOP contribution: 09-001
Baptista, A; Howe, B; Freire, J; Maier, D; Silva, C (2008). Scientific Exploration in the Era of Ocean Observatories. IEEE Computing in Science & Engineering. 10(3): 53-58.
CMOP contribution: 08-021
Bruland, K.W., Lohan, M.C., Aguilar-Islas, A.M., Smith, G.J., Sohst, B., Baptista, A. (2008). Factors influencing the chemistry of the near-field Columbia River plume: nitrate, silicic acid, dissolved Fe, and dissolved Mn. Journal of Geophysical Research - Oceans. 113, C00B02 (23 pp.).
CMOP contribution: 08-020
Bavoil, L., Callahan, S. and Silva, C. (2008). Robust Soft Shadow Mapping with Backprojection and Depth Peeling. Journal of Graphics, GPU and Game Tools. 13(1): 19-30.
CMOP contribution: 08-019
Bernardon, F; Ha, L; Callahan, S; Comba, J; Silva, C (2008). Interactive Transfer Function Specification for Direct Volume Rendering of Disparate Volumes. Computing in Science and Engineering.
CMOP contribution: 08-018
Callahan, S. P., J. H. Callahan, Scheidegger, C. E. and Silva, C. (2008). Direct Volume Rendering: A 3D Plotting Technique for Scientific Data. Computing in Science and Engineering. 10(1): 88-92.
CMOP contribution: 08-017
Chawla, A., Jay, D.A., Baptista, A.M., Wilkin, M., Seaton, C. (2008). Seasonal variability and estuary-shelf interactions in circulation dynamics of a river- dominated estuary. Estuaries and Coasts. 31(2): 269-288.
CMOP contribution: 08-016
Daniels II, J., Ochotta, T., Ha, L. K., and Silva, C. T. (2008). Spline-based feature curves from point-sampled geometry. The Visual Computer: International Journal of Computer Graphics. 24, 6 (May. 2008), 449-462.
CMOP contribution: 08-015
Freire, J; Koop, D; Santos, E; Silva, C (2008). Provenance for Computational Tasks: A Survey. Computing in Science and Engineering. 10(3): 11-21.
CMOP contribution: 08-014
Frolov, S., Baptista, A., Zhang, Y. and Seaton, C. (2008). Estimation of Ecologically Significant Circulation Features of the Columbia River Estuary and Plume Using a Reduced-Dimension Kalman Filter. Ocean Dynamics. 29(2) 456-466.
CMOP contribution: 08-013
Frolov, S; Baptista, A; Wilkin, M. (2008). Optimizing Placement of Fixed Observational Sensors in a Coastal Observatory. Continental Shelf Research. 28(19): 2644-2658.
CMOP contribution: 08-012
Jannasch, H W; Coletti, L J; Johnson, K S; Fitzwater, S E; Needoba, J A; Plant, J N (2008). Robust mooring systems for continuously monitoring of complex biogeochemical cycles in estuaries: Design, construction and internal results from Elkhorn Slough, CA. Limnology and Oceanography: Methods. 6: 263-276.
CMOP contribution: 08-011
Johnson, K S; Needoba, J A (2008). Mapping the spatial variability of plankton metabolism using nitrate and oxygen sensors on an autonomous underwater vehicle. Limnology and Oceanography: Methods. 53 (5 part 2): 2237-2250.
CMOP contribution: 08-010
Kirby, R M; Silva, C (2008). The Need for Verifiable Visualization. IEEE Computer Graphics and Applications. 28(5): 78-83.
CMOP contribution: 08-009
Koop, D; Scheidegger, C E; Callahan, S P; Vo, H T; Freire, J; Silva, C (2008). VisComplete: Automating Suggestions for Visualization Pipeline. IEEE Transactions on Visualization and Computer Graphics. 14(6): 1691-1698.
CMOP contribution: 08-008
Kudela, R.M., Banas, N.S., Barth, J. A., Frame, E. R., Jay, D. A., Largier, J. L., Lessard, E. J., Peterson, T. D., and Vander Woude, A. J. (2008). New Insights into the Controls and Mechanisms of Plankton Productivity on the US West Coast. Oceanography. 21(4): 46-59.
Saraceno, M; Strub, P; Kosro, P (2008). "Estimates of sea surface height and near-surface alongshore coastal currents from combinations of altimeters and tide gauges." Journal of Geophysical Research. 113(C11): 20.
CMOP contribution: 08-007
Scheidegger, C; Koop, D; Santos, E; Vo, H; Callahan, S; Freire, J; Silva, C (2008). Tackling the Provenance Challenge One Layer at a Time. Concurrency And Computation: Practice And Experience. (20(5)): 473-483.
CMOP contribution: 08-006
Scheidegger, C. E., Vo, H. T., Koop, D., Freire, J., and Silva, C. T. (2008). Querying and re-using workflows with VsTrails. ACM SIGMOD international Conference on Management of Data. (Vancouver, Canada, June 09 - 12, 2008).
CMOP contribution: 08-005
Silva, C; Freire, J (2008). Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present, and Future. Journal of Physics: Conference Series. 125.
CMOP contribution: 08-004
Silva, C. T., and Tohline, J. E. (2008). Guest Editorial: Special Issue on Computational Provenance. Computing in Science and Engineering. 10(3):9-10.
CMOP contribution: 08-003
Zhang, Y; Baptista, A (2008). Benchmarking a new finite-element tsunami model on unstructured grids. Pure and Applied Geophysics. 165: 2229-2248.
CMOP contribution: 08-002
Zhang, Y; Baptista, A (2008). SELFE: A semi-implicit Eulerian Lagrangian Finite-element model for cross-scale ocean circulation. Ocean Modelling. 21: 3-4, 71-96.
CMOP contribution: 08-001
Bavoil, L., Callahan, S. P., Lefohn, A., Comba, J. L., and Silva, C. T.
Bernardon, F; Callahan S.; Comba, J; Silva C (2007). An Adaptive Framework for Visualizing Unstructured Grids with Time-Varying Scalar Fields. Parallel Computing. 33(6): 391-405.
CMOP contribution: 07-015
Dang, T., Bulusu, N., and Feng, W. (2007). Rida: A robust information-driven data compression architecture for irregular wireless sensor networks. European Workshop on Sensor Networks (EWSN). Delft, The Netherlands. IEEE.
CMOP contribution: 07-014
Dang, T., Frolov, S., Bulusu, N., Feng, W, and Baptista, A., Near Optimal Sensor Selection in The CORIE Observation Network for Data Assimilation Using Genetic Algorithms. International Conference on Distributed Computing in Sensor Systems (DCOSS 2007). Santa Fe, New Mexico, June 2007.
CMOP contribution: 07-013
Daniels, J., Ha, L., Ochotta, T. and Silva, C.T. (2007). Robust Smooth Feature Extraction from Point Clouds. Shape Modeling International. 2007.
CMOP contribution: 07-012
Davidson, S., S. Cohen-Boulakia, et al. (2007). Provenance in Scientific Workflow Systems. IEEE Data Engineering Bulletin. (32(4)): 44-50.
CMOP contribution: 07-011
Dang, T., S. Frolov, N. Bulusu, W. Feng, and A. Baptista. (2007) Near Optimal Sensor Selection in The CORIE Observation Network for Data Assimilation Using Genetic Algorithms. International Conference on Distributed Computing in Sensor Systems (DCOSS). Santa Fe, New Mexico, June 2007.
CMOP contribution: 07-010
Dang, T., N. Bulusu, W. Feng. (2007) RIDA: A Robust Information-Driven Compression Architecture for Irregular Wireless Sensor Networks. European Conference on Sensor Networks (EWSN). Delft, Netherlands, Jan. 2007.
CMOP contribution: 07-009
Howe, B., D. Maier, L. Bright. (2007) Smoothing the ROI Curve for Scientific Data Management Applications Third Biennial Conference on Innovative Data Systems Research (CIDR).
CMOP contribution: 07-008
Howe, B., N. Hagerty, E. Van Matre, D. Maier, A. M. Baptista, C. Seaton, P. Turner, The Ocean Appliance: Complete Platform Provisioning for Low-Cost Data Sharing. IEEE/MTS Oceans. 2007, Vancouver, BC, October 2007.
CMOP contribution: 07-007
Myers, E., A. Zhang, F. Aikman, Y. Zhang, A. Baptista, P. Turner and C. Seaton. Evaluation and Transition of a Columbia River Nowcast/Forecast Circulation Model to NOAA’s National Ocean Service, extended abstract, Coastal Zone ‘07, Portland, OR, July 2007.
CMOP contribution: 07-006
Scheidegger, C. E., Vo, H. T., Koop, D. and Freire, J. (2007). Querying and Creating Visualizations by Analogy. IEEE Transactions on Visualization and Computer Graphics. (Proceedings of IEEE Visualization) 13(6): 1560-1567.
CMOP contribution: 07-005
Silva, C., Freire, J., Callahan, S. P. (2007). Provenance for Visualization: Reproducibility and Beyond. Computing in Science and Engineering. 9(5): 82-89.
CMOP contribution: 07-004
van der Merwe, R., Leen, T. K., Lu, Z, Frolov, S. and Batista, A. (2007). Fast Neural Network Surrogates for Very High Dimensional Physics-Based Models in Computational Oceanography. Neural Networks. (20): 462-478.
CMOP contribution: 07-003
Vo, H. T., Callahan, S. P., Smith, N., Silva, C. T., Martin, W., Owen, D., and Weinstein, D. (2007). iRun: Interactive Rendering of Large Unstructured Grids. 7th Eurographics Symposium on Parallel Graphics and Visualization, Lugano, Switzerland.
CMOP contribution: 07-002
Zhang, Y., A. Baptista, K. Wang, C. Goldfinger, R. Witter, G. Priest, C. Peterson, K. Cruikshank. Hydrodynamic simulations of historic tsunamis from the Cascadia Subduction Zone. extended abstract, Coastal Zone ’07, Portland, OR, July 2007.
CMOP contribution: 07-001
Baptista, A., CORIE: the first decade of a coastal-margin collaborative observatory, Oceans'06. MTS/ IEEE, Boston, MA, 2006.
CMOP contribution: 06-002
Bright, L., D. Maier, B. Howe. Managing the Forecast Factory. Proc. ICDE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow), 2006.
CMOP contribution: 06-001
Other Dissemination Activities
DIVR White Paper 2006 (.pdf)
This activity is a white paper written by Eda Davis-Butts and addresses STEM Diversity. The paper was prepared to inform the conversation and the work of a statewide initiative in Oregon. The paper reflects the research framework of The SMILE Program.
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