Journal of Geophysical Research, Special Section: Wind-Driven Circulation and Ecosystem Response Off the Oregon Coast: Results From the Coastal Ocean Advances in Shelf Transport (COAST) Program

Avicola, G., J. N. Moum, A. Perlin, and M. D. Levine (2007) Enhanced turbulence due to the superposition of internal gravity wave shear on the coastal upwelling jet. J. Geophys. Res., in press.

Bane, J. M., M. D. Levine, R. M. Samelson, S. M. Haines, M. F. Meaux, N. Perlin, P. M. Kosro, and T. Boyd (2005) Atmospheric forcing of the Oregon coastal ocean during the 2001 upwelling season, J. Geophys. Res., 110, C10S02, doi:10.1029/2004JC002653.

Bane, J. M., Y. H. Spitz, R. M. Letelier, and W. T. Peterson (2007) Intraseasonal oscillations in Oregon's coastal upwelling system: From the Jet Stream to zooplankton. Proc. Natl. Acad. Sci., USA, in press.

Barth, J. A., D. Hebert, A. C. Dale and D. S. Ullman (2004) Direct observations of along-isopycnal upwelling and diapycnal velocity at a shelfbreak front. J. Phys. Oceanogr., 34, 543-565.

Barth, J. A., S. D. Pierce and T. J. Cowles (2005) Mesoscale structure and its seasonal evolution in the northern California Current System. Deep-Sea Res. II, 52, 5-28.

Barth, J. A., and P. A. Wheeler (2005) Introduction to special section: Coastal Advances in Shelf Transport. J. Geophys. Res., doi:10.1029/2005JC003124.

Barth, J. A., S. D. Pierce, and R. M. Castelao (2005) Time-dependent, wind-driven flow over a shallow midshelf submarine bank. J. Geophys. Res., doi:10.1029/2004JC002761.

Barth, J. A., B. A. Menge, J. Lubchenco, F. Chan, J. M. Bane, A. R. Kirincich, M. A. McManus, K. J. Nielsen, S. D. Pierce and L. Washburn (2007) Delayed upwelling alters nearshore coastal ocean ecosystems in the Northern California Current. Proc. Natl. Acad. Sci., USA, 104, 3719-3724.

Castelao, R. M., J. A. Barth, and T. P. Mavor (2005) Flow-topography interactions in the northern California Current System observed from geostationary satellite data. Geophys. Res. Letters, 32, L24612, doi:10.1029/2005GL024401.

Castelao, R. M., and J. A. Barth (2005) Coastal ocean response to summer upwelling favorable winds in a region of alongshore bottom topography variations off Oregon. J. Geophys. Res., 110, C10S04, doi:10.1029/2004JC002409.

Castelao, R. M. and J. A. Barth (2006) The relative importance of wind strength and along-shelf bathymetric variations on the separation of a coastal upwelling jet. J. Phys. Oceangr., 36, 412-425.

Castelao, R. M. and J. A. Barth (2006) Upwelling around Cabo Frio, Brazil: the importance of wind stress curl. Geophys. Res. Letters, 33, L03602, doi:10.1029/2005GL025182.

Castelao, R. M., T. P. Mavor, J. A. Barth, and L. C. Breaker (2006) Sea surface temperature fronts in the California Current System from geostationary satellite observations. J. Geophys. Res., 111, C09026, doi:10.1029/2006JC003541.

Castelao, R. M. and J. A. Barth (2007) The role of wind stress curl in jet separation at a cape. J. Phys. Oceangr., 37, 2652-2671.

Chase, Z., P. G. Strutton, and B. Hales (2007) Iron links river runoff and shelf width to phytoplankton biomass along the U.S. West Coast. Geophys. Res. Lett., 34, L04607, doi:10.1029/2006GL028069.

Chase, Z., B. Hales, T. J. Cowles, R. Schwartz, and A. van Geen (2005) Distribution and variability of iron input to Oregon coastal waters during the upwelling season. J. Geophys. Res., 110, C10S12, doi:10.1029/2004JC002590.

Choboter, P. F., R. M. Samelson, and J. S. Allen (2005) A new solution of a nonlinear model of upwelling. J. Phys. Oceanogr., 35, 532-544.

de Szoeke, R. A., and R. M. Samelson (2002) The duality between the Boussinesq and non-Boussinesq hydrostatic equations of motion. J. Phys. Oceanogr., 32, 2194-2203.

Dewar, W. K., R. M. Samelson, and G. K. Vallis (2005) The ventilated pool: a model of subtropical mode water. J. Phys. Oceanogr., 35, 137-150.

Durski, S. M., and J. S. Allen (2005) Finite amplitude evolution of instabilities associated with the coastal upwelling front. J. Phys. Oceanogr., 35, 1606-1628.

Edwards, K. A., P. MacCready, J. N. Moum, G. Pawlak, J. M. Klymak and A. Perlin (2004) Form drag and mixing due to tidal flow past a sharp point. J. Phys. Oceanogr., 34, 1297-1312.

Eisner, L. B. (2003) Relationships of in situ spectral absorption, pigment ratios and environmental parameters for phytoplankton assemblages in coastal waters. Ph.D. Thesis, Oregon State University, 225 pp.

Eisner, L. B., and T. J. Cowles (2005) Spatial variations in phytoplankton pigment ratios, optical properties, and environmental gradients in Oregon coast surface waters. J. Geophys. Res., 110, C10S14, doi:10.1029/2004JC002614.

Erofeeva, S. Y., G. D. Egbert and P. M. Kosro (2003) Tidal currents on the central Oregon shelf: Models, data and assimilation. J. Geophys. Res., 108(C5), 3148, doi:10.1029/2002JC001615.

Gan, J., and J. S. Allen (2002a) A modeling study of shelf circulation off northern California in the region of the Coastal Ocean Dynamics Experiment. Response to relaxation of upwelling winds. J. Geophys. Res., 107(C9), 3123, doi: 10.1029/2000JC000768.

Gan, J., and J. S. Allen (2002b) A modeling study of shelf circulation off northern California in the region of the Coastal Ocean Dynamics Experiment, 2, Simulations and comparisons with observations. J. Geophys. Res., 107(C11), 3184, doi: 10.1029/2001JC001190.

Gan, J., and J. S. Allen (2005) Modeling upwelling circulation off the Oregon coast. J. Geophys. Res., 110, C10S07, doi:10.1029/2004JC002692.

Gan, J., and J. S. Allen (2005) On open boundary conditions for a limited-area coastal model off Oregon. Part 1: Response to idealized wind forcing. Ocean Modelling, 8(1-2), 115-133, doi: 10.1016/j.ocemod.2003.12.006.

Gan, J., J. S. Allen and R. M. Samelson (2005) On open boundary conditions for a limited-area coastal model off Oregon. Part 2: Response to wind forcing from a regional mesoscale atmospheric model. Ocean Modelling, 8(1-2), 155-173, doi: 10.1016/j.ocemod.2003.12.007.

Gómez-Gutiérrez, J., L. R. Feinberg, T. Shaw, and W. T. Peterson (2006) Variability of brood size and female length of Euphausia pacifica Hansen among three populations in the North Pacific. Mar. Ecol. Prog, Ser. 323:185-194.

Gómez-Gutiérrez, J., L. R. Feinberg, T. C. Shaw, and W.T. Peterson (2007) Interannual and geographical variability of the brood size of the euphausiids Euphausia pacifica and Thysanoessa spinifera along the Oregon coast (1999-2004). Deep-Sea Res. (in revision)

Grantham, B. A., F. Chan, K. J. Nielsen, D. S. Fox, J. A. Barth, A. Huyer, J. Lubchenco and B. A. Menge (2004) Upwelling-driven nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature, 429, 749-754.

Hales, B., L. Karp-Boss, A. Perlin, and P. A. Wheeler (2006) Oxygen production and carbon sequestration in an upwelling coastal margin. Global Biogeochemical Cycles, 20, GB3001, doi: 10.1029/2005GB002517.

Hales, B., T. Takahashi, and L. Bandstra (2004) Atmospheric CO2 uptake by a coastal upwelling system. Global Biogeochemical Cycles, 19, GB1009, doi: 10.1029/2004GB002295.

Hales, B., J. N. Moum, P. Covert, and A. Perlin (2005) Irreversible nitrate fluxes due to turbulent mixing in a coastal upwelling system. J. Geophys. Res., 110, C10S11, doi:10.1029/2004JC002685.

Huyer, A., J. H. Fleischbein, J. Keister, P. M. Kosro, N. Perlin, R. L. Smith, and P. A. Wheeler (2005) Two coastal upwelling domains in the northern California Current system. J. Marine Res., 63, 901-929.

Karp-Boss, L., P. A. Wheeler, B. Hales, and P. Covert (2004) Distributions and variability of particulate organic matter in a coastal upwelling system. J. Geophys. Res., 109, C09010, doi:10.1029/2003JC002184.

Kirincich, A. R., J. A. Barth, B. A. Grantham, B. A. Menge, and J. Lubchenco (2005) Wind-driven inner-shelf circulation off central Oregon during summer, J. Geophys. Res., 110, C10S03, doi:10.1029/2004JC002611.

Kirincich, A. R. and J. A. Barth (2007) Spatial and temporal variability of inner-shelf circulation along the central Oregon coast during summer. J. Phys. Oceanogr., submitted.

Klymak, J. M. and J. N. Moum (2003) Internal solitary waves of elevation advancing on a shoaling shelf. Geophys. Res. Lett., 30(20), 2045, doi:10.1029/2003GL017706.

Kosro, P. M. (2003) Enhanced southward flow over the Oregon shelf in 2002: A conduit for subarctic water. Geophys. Res. Lett., 30(15), 8023, doi:10.1029/2003GL017436.

Kosro, P. M. (2005) On the spatial structure of coastal circulation off Newport, Oregon, during spring and summer 2001 in a region of varying shelf width, J. Geophys. Res., 110, C10S06, doi:10.1029/2004JC002769.

Kudela, R. M., N. S. Banas, J. A. Barth, E. R. Frame, D. A. Jay, J. L. Largier, E. J. Lessard, T. D. Peterson, and A. J. Vander Woude (2008) New insights into the controls and mechanisms of plankton productivity in coastal upwelling waters of the northern California Current system, Oceanography, 21, 46-59.

Kuebel-Cervantes, B. T., J. S. Allen, and R. M. Samelson (2004) Lagrangian characteristics of continental shelf flows forced by periodic wind stress. Nonlinear Processes in Geophysics, 11(1), 3-16.

Kuebel-Cervantes, B. T., and J. S. Allen (2006) Numerical model solutions of continental shelf flows off Northern California Deep-Sea Res. II, 53, 2956-2984.

Kurapov, A. L., J. S. Allen, G. D. Egbert, R. N. Miller, P. M. Kosro, M. Levine, and T. Boyd (2005) Distant effect of assimilation of moored currents into a model of coastal wind-driven circulation off Oregon. J. Geophys. Res., 110, C02022, doi:10.1029/2003JC002195.

Kurapov, A. L., J. S. Allen, G. D. Egbert, R. N. Miller, P.M. Kosro, M. D. Levine, T. Boyd, and J. A. Barth (2005) Assimilation of moored velocity data in a model of coastal wind-driven circulation off Oregon: Multivariate capabilities, J. Geophys. Res., 110, C10S08, doi:10.1029/2004JC002493.

Kurapov, A. L., J. S, Allen, G. D. Egbert, and R. N. Miller (2005) Modeling bottom mixed layer variability on the mid-Oregon shelf during summer upwelling, J. Phys. Oceanogr., 35, 1629-1649.

Lamb, J., and W. Peterson (2005) Ecological zonation of zooplankton in the COAST study region off central Oregon in June and August 2001 with consideration of retention mechanisms, J. Geophys. Res., 110, C10S15, doi:10.1029/2004JC002520.

Landers, S. C., J. Gómez-Gutiérrez and W. T. Peterson (2006) Gymnodinioides pacifica, n. sp., an exuviotrophic ciliated protozoan (Ciliophora, Apostomatida) from euphausiids of the Northeastern Pacific, European J. Protistology, 42:97-106.

Liu, J. G., R. Samelson, and C. Wang (2006) Global weak solutions of planetary geostrophic equations with inviscid geostrophic balance, Applicable Analysis, 85, 593-605, doi: 10.1080/00036810500328299.

Lyman, J., D. Chelton, R. de Szoeke, and R. M. Samelson (2005) Tropical instability waves as a resonance between equatorial Rossby waves. J. Phys. Oceanogr., 35, 232-254.

Meaux, M. F. (2004) The marine atmospheric boundary layer over the Oregon coastal upwelling system during summer 2001, M.S. thesis, Dept. of Marine Sciences, University of North Carolina, Chapel Hill, 107pp.

Moum, J. N., and W. D. Smyth (2006) The pressure disturbance of a nonlinear internal wave train. J. Fluid Mech., 558, 153-177.

Moum, J. N., J. M. Klymak, J. D. Nash, A. Perlin, and W. D. Smyth (2007) Energy transport by nonlinear internal waves. J. Phys. Oceanogr., 37(7), 1968-1988.

Moum, J. N., A. Perlin, J. M. Klymak, M. D. Levine, T. Boyd, and P. M. Kosro (2004) Convectively-driven mixing in the bottom boundary layer. J. Phys. Oceanogr., 34, 2189-2202.

Moum, J. N., J. D. Nash, and J. M. Klymak (2008) Small-scale processes in the coastal ocean. Oceanography, 21, 22-33.

Newberger, P. A., J. S. Allen, and Y. H. Spitz (2003) Analysis and comparison of three ecosystem models. J. Geophys. Res., 108(C3), 3061, doi:10.1029/2001JC001182.

O'Keefe, S. (2005) Observing the Coastal Ocean with HF Radar, Master's Thesis, Oregon State University, 103 pp.

Ott, M. W., J. A. Barth and A. Y. Erofeev (2004) Microstructure measurements from a towed undulating platform. J. Atmos. Oceanic Tech., 21, 1621-1632.

Ott, M. W., J. A. Barth and A. Y. Erofeev (2005) Summertime downwelling off the Oregon coast, J. Geophys. Res., submitted.

Perlin, A., J. N. Moum, J. M. Klymak, M. D. Levine, T. Boyd and P. M. Kosro (2007) Organization of stratification, turbulence, and veering in bottom Ekman layers. J. Geophys. Res., 112, C05S90, doi:10.1029/2004JC002641.

Perlin, A., J. N. Moum, J. M. Klymak, M. D. Levine, T. Boyd, and P. M. Kosro (2005) A modified law-of-the-wall applied to oceanic bottom boundary layers, J. Geophys. Res., 110, C10S10, doi:10.1029/2004JC002310.

Perlin, A., J. N. Moum, and J. Klymak (2005) Response of the bottom boundary layer over a sloping shelf to variations in alongshore wind, J. Geophys. Res., 110, C10S09, doi:10.1029/2004JC002500.

Perlin, N., R. M. Samelson and D. B. Chelton (2004) Scatterometer and model wind and wind stress in the Oregon-California coastal zone. Monthly Weather Review, 132, 2110-2129.

Ruttenberg, K. C., and S. T. Dhyrman (2005) Temporal and spatial variability of dissolved organic and inorganic phosphorus, and metrics of phosphorus bioavailability in an upwelling-dominated coastal system, J. Geophys. Res., 110, C10S13, doi:10.1029/2004JC002837.

Samelson, R. M. (2004) Simple mechanistic models of mid-depth meridional overturning. J. of Phys. Oceanogr., 34, 2096-2103.

Samelson, R. M., R. Temam, C. Wang, and S. Wang (2003) Surface pressure Poisson equation formulation of the primitive equations: numerical schemes. SIAM J. of Numerical Analysis, 41, 1163-1194.

Samelson, R. M., E. D. Skyllingstad, D. B. Chelton, S. K. Esbensen, L. W. O'Neill, and N. Thum (2006) On the coupling of wind stress and sea surface temperature. J. of Climate, 19, 1557-1566.

Samelson, R. M., J. S. Allen, and P. MacCready (2008) Progress in coastal ocean modeling during CoOP. Oceanography, 21, 136-147.

Sotka, E. E., J. P. Wares, J. A. Barth, R. K. Grosberg, and S. R. Palumbi (2004) Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula, Molecular Ecology, 13, 2143-2156.

Spitz, Y. H., P. A. Newberger, and J. S. Allen (2003) Ecosystem response to upwelling off the Oregon coast: Behavior of three nitrogen-based models, J. Geophys. Res., 108(C3), 3062, doi:10.1029/2001JC001181.

Spitz, Y. H., J. S. Allen, and J. Gan (2005) Modeling of ecosystem processes on the Oregon shelf during the 2001 summer upwelling, J. Geophys. Res., 110, C10S17, doi:10.1029/2005JC002870.

Sutor, M., T. J. Cowles, W. T. Peterson, and J. Lamb (2005) Comparison of acoustic and net sampling systems to determine patterns in zooplankton distribution, J. Geophys. Res., 110, C10S16, doi:10.1029/2004JC002681.

Sutor, M. (2005) Vertical distribution patterns of plankton and their relationship to physical factors over the continental shelf off Oregon. Ph.D. Thesis, Oregon State University, 297 pp.

Wetz, M. S. (2003) Production and partitioning of organic matter during simulated phytoplankton blooms. Master's Thesis, Oregon State University, 92 pp.

Wetz, M. S. (2006) Dynamics of Organic Matter Production and Degradation during Coastal Diatom Blooms. Ph. D. Thesis, Oregon State University, 131 pp.

Wetz, M. S. and P. A. Wheeler (2003) Production and partitioning of organic matter during simulated phytoplankton blooms, 48(5), Limnol. Oceanogr., 1808-1817.

Wetz, M. S. and P. A. Wheeler (2004) Response of bacteria to simulated upwelling phytoplankton blooms, Marine Ecology Progress Series, 272, 49-57.

Wetz, M. S., P. A. Wheeler, and R. M. Letelier (2004) Light-induced growth of phytoplankton collected during the winter from the benthic boundary layer off Oregon, USA, Marine Ecology Progress Series, 280, 95-104.

Wetz, M. S., B. Hales, P. A. Wheeler, Z. Chase, and M. M. Whitney (2006) Riverine input of macronutrients, iron, and organic matter to the coastal ocean off Oregon, USA, during the winter, Limnol. Oceanogr., 51(5), 2221-2231.

Wetz, M. S. and P. A. Wheeler (2007) Release of dissolved organic matter by coastal diatoms, Limnol. Oceanogr., 52, 798-807.

Whitney, M. M. and J. S. Allen (2009) Coastal wind-driven circulation in the vicinity of a bank. Part I: modeling flow over idealized symmetric banks, J. Phys. Oceanogr., 39, 1273-1297.

Whitney, M. M. and J. S. Allen (2009) Coastal wind-driven circulation in the vicinity of a bank. Part II: modeling flow over the Heceta Bank complex on the Oregon coast, J. Phys. Oceanogr., 39, 1298-1316.