Zamudio, L., P. J. Hogan, and E. J. Metzger: Summer generation of the Southern Gulf of California eddy train. J. Geophys. Res., 113, C06020, doi:10.1029/2007JC004467.

B. Backeberg, J. A. Johannessen, L. Bertino, C. J. Reason, 2008: The greater Agulhas Current system: An integrated study of its mesoscale variability. Journal of Operational Oceanography, 1, (1), 29-44.

Kara, A.B., A. A. Wallcraft, and M. A. Bourassa, 2008: Air-sea stability effects on the 10 m winds over the global ocean: Evaluations of air-sea flux algorithms. J. Geophys. Res., 113, C04009, doi:10.1029/2007JC004324.

Hofmann, E. E., J.-N. Druon, K. Fennel, M. Friedrichs, D. Haidvogel, C. Lee, A. Mannino, C. McClain, R. Najjar, J. Siewert, J. O’Reilly, D. Pollard, M. Previdi, S. Seitzinger, S. Signorini, J. Wilkin, 2008: Eastern U.S. Continental Shelf Carbon Budget: Integrating Models, Data Assimilation, and Analysis. Oceanography, 21, 86-104.

Thacker, W. W., 2008: Estimating Salinity between 25° and 45°S in the Atlantic Ocean Using Local Regression. Journal of Atmospheric and Oceanic Technology, 25, 114-130, doi: 10.1175/2007JTECHO530.1

Chang, Y., T. M. Ozgokmen, H. Peters, X. Xu, 2008: Numerical Simulation of the Red Sea Outflow Using HYCOM and Comparison with REDSOX Observations. JPO, 38, 337-358, doi: 10.1175/2007JPO3697.1

Zamudio, L., P. J. Hogan, 2008: Nesting the Gulf of Mexico in Atlantic HYCOM: Oceanographic processes generated by Hurricane Ivan. Ocean Modelling, 21, 106-125.

Kara, A.B., A.J. Wallcraft, P.J. Martin, and E.P. Chassignet, 2008: Performance of mixed layer models in simulating SST in the Equatorial Pacific Ocean. J. Geophys. Res., 113, C02020, doi:10.1029/2007JC004250.

K.A. Lisaeter, G. Evensen and S. Laxon, 2007: Assimilating synthetic CryoSat sea ice thickness in a coupled ice-ocean model. J. Geophys. Res., 112, C07023, doi:10.1029/2006JC003786.

Kelly, K., L. Thompson, W. Cheng and E.J. Metzger, 2007: Evaluation of HYCOM in the Kuroshio Extension region using new metrics. J. Geophys. Res. , 112, C01004, doi:10.1029/2006JC003614.

Lee, S.-K., D.B. Enfield, and C. Wang, 2007: What drives seasonal onset and decay of the Western Hemisphere Warm Pool?. Journal of Climate, 20 2133-2146.

Thacker, W. W., 2007: Data assimilation with inequality constraints. Ocean Modelling, 16, 264–276, doi:10.1016/j.ocemod.2006.11.001

Chassignet, E.P., H.E. Hurlburt, O.M. Smedstad, G.R. Halliwell, P.J. Hogan, A.J. Wallcraft, R. Baraille, and R. Bleck, 2007: The HYCOM (HYbrid Coordinate Ocean Model) data assimilative system. J. Mar. Sys., 65, 60-83.

Aretxabaleta, A., B.O. Blanton, H.E. Seim, F.E. Werner, J.R. Nelson, and E.P. Chassignet, 2007: Cold event in the South Atlantic Bight during summer of 2003: Model simulations and implications. J. Geophys. Res., 112, C05022, doi:10.1029/2006JC003903.

Xu, X., E.P. Chassignet, J.F. Price, T.M. Özgökmen, and H. Peters, 2007: A regional modeling study of the entraining Mediterranean outflow. J. Geophys. Res., 112, C12005, doi:10.1029/2007JC004145.

Halkides, D. J., W. Han, T. Lee, and Y. Masumoto, 2007: Effects of sub-seasonal variability on seasonal-to-interannual Indian Ocean meridional heat transport. Geophys. Res. Lett., 34, L12605, doi:10.1029/2007GL030150.

Kara, A. B., A. J. Wallcraft, E. J. Metzger, H. E. Hurlburt, and C. W. Fairall, 2007: Wind stress drag coefficient over the global ocean. J. Climate, 20, 5856-5864.

Winther, N. G., Morel, Y., Evensen, G., 2007: Efficiency of high order numerical schemes for momentum advection. J. Marine Systems., 67, 31-46, doi:10.1016/j.jmarsys.2006.08.004.

Chen, W., M. J. McPhaden, D. Zhang, E. J. Metzger, 2007: Recent Changes in the Pacific Subtropical Cells Inferred from an Eddy-Resolving Ocean Circulation Model. J. Phys. Oceanogr., 37, 1340-1356.

Kara, A. B., and C. N. Barron, 2007: Fine-resolution satellite--based daily sea surface temperatures over the global ocean. J. Geophys. Res., 112, C05041, doi:10.1029/2006JC004021.

Kara, A. B., H. E. Hurlburt, and W.-Y. Loh, 2007: Which near-surface atmospheric variable drives air-sea temperature differences over the global ocean? J. Geophys. Res., 112, C05020, doi:10.1029/2006JC003833.

Han, W., D. Yuan, W. T. Liu, D. J. Halkides, 2007: Intraseasonal variability of Indian Ocean sea surface temperature during boreal winter: Madden-Julian Oscillation versus submonthly forcing and processes. J. Geophys. Res., 112(C4), C04001, doi:10.1029/2006JC003791.

Kara, A. B., E. J. Metzger, and M. A. Bourassa, 2007: Ocean current and wave effects on wind stress drag coefficient over the global ocean. Geophys. Res. Lett., 34, L01604, doi:10.1029/2006GL027849.

Kara, A.B., A.J. Wallcraft, and H.E. Hurlburt, 2007: A correction for land contamination of atmospheric variables near land-sea boundaries. J. Phys. Oceanogr., 37, 803-818.

Hogan, P. J., and H. E. Hurlburt, 2006: Why do IntraThermocline Eddies Form in the Japan/East Sea? A modeling perspective Oceanography, 19(3), 134-143.

Thacker, W.C., 2006: Estimating salinity to complement observed temperature: 1. Gulf of Mexico. Journal of Marine Systems, 65, 224-248, doi:10.1016/j.jmarsys.2005.06.008

Thacker, W.C., and L. Sindlinger, 2006: Estimating salinity to complement observed temperature: 2. Northwestern Atlantic. Journal of Marine Systems, 65, 249-267, doi:10.1016/j.jmarsys.2005.06.007

Klinger, B. A., C. Cruz, and P. Schopf, 2006: Targeted Shapiro filter in an ocean model. Ocean Modelling, 13, 148-155.

Winther, N. G., Johannessen, J. A., 2006: North sea circulation: Atlantic inflow and its destination. J. Geophys. Res., 111, C12018, doi:10.1029/2005JC003310.

Kara, A. B, and H. E. Hurlburt, 2006: Daily inter--annual simulations of SST and MLD using atmospherically--forced OGCMs: Model evaluation in comparison to buoy time series. J. Mar. Sys., 62, 95--119.

C. N. Barron and A. B. Kara, 2006: Satellite-based daily SSTs over the global ocean Geophys. Res. Lett., 33, L15603, doi:10.1029/2006GL026356.

Winther, N. G. and Evensen, G., 2006: A hybrid coordinate ocean model for shelf sea simulation. Ocean Modelling, 13(3-4), 221-237, doi:10.1016/j.ocemod.2006.01.004.

Olascoaga, M. J., I. I. Rypina, M. G. Brown, F. J. Beron-Vera, H. Koçak, L. E. Brand, G. R. Halliwell, and L. K Shay, 2006: Persistent Transport Barrier on the West Florida Shelf. Geophys. Res. Lett., 33, L22603, doi:10.1029/2006GL027800.

Hogan, P.J., O.M. Smedstad, S. Reidlinger, A.J. Wallcraft, G.A. Jacobs, W. Teague and H.E. Hurlburt, 2006: Model-data comparisons and numerical modeling and prediction efforts at the Naval Research Laboratory. Proceedings of the CREAMS/PICES International Workshop on Model/Data Intercomparison for the Japan/East Sea, 21-22 August 2006, Busan, Korea, pp. 69-73.

Hogan, P.J. and H.E. Hurlburt, 2006: Why do intra thermocline eddies form in the Japan/East Sea? A modeling perspective. Oceanography, 19(3), 134-143.

Chassignet, E.P., and J. Verron (Eds.), 2006: Ocean Weather Forecasting: An Integrated View of Oceanography. Springer, 577 pp.

Rothstein, L.M., J.J. Cullen, M. Abott, E.P. Chassignet, K. Denman, S. Doney, H. Ducklow, K. Fennel, M. Follows, D. Haidvogel, E. Hoffman, D. Karl, J. Kindle, I. Lima, M. Maltrud, C. McClain, D. McGillicuddy, J. Olascoaga, Y. Spitz, J. Wiggert, and J. Yoder, 2006: Modeling ocean ecosystems - the PARADIGM program. Oceanography, 19, 16-45.

Xu, X., Y.S. Chang, H. Peters, T.M. Özgökmen,, and E.P. Chassignet, 2006: Parameterization of gravity current entrainment for ocean circulation models using a high-order 3D nonhydrostatic spectral element model. Ocean Modelling, 14, 19-44.

Yuan, D., and W. Han, 2006: Roles of Equatorial Waves and Western Boundary Refelection in the Seasonal Circulation of the Equatorial Indian Ocean. JPO, 36, 930-944.

Han, W., W. T. Liu, and J Lin, 2006: Impact of atmospheric submonthly oscillations on sea surface temperature of the tropical Indian Ocean. Geophysical Research Letters, 33, doi:10.1029/2005GL025082.

Han, W., T. Shinoda, L.-L. Fu, and J. P. McCreary, 2006: Impact of Atmospheric Intraseasonal Oscillations on the Indian Ocean Dipole during the 1990s. JPO, 36, 670-690.

Chassignet, E.P., H.E. Hurlburt, O.M. Smedstad, G.R. Halliwell, A.J. Wallcraft, E.J. Metzger, B.O. Blanton, C. Lozano, D.B. Rao, P.J. Hogan, and A. Srinivasan, 2006: Generalized vertical coordinates for eddy-resolving global and coastal ocean forecasts. Oceanography, 19, 20-31.

Bleck, R., 2006: On the use of hybrid vertical coordinates in ocean circulation modeling. In: Ocean Weather Forecasting: An Integrated View of Oceanography, Chassignet, E.P., and J. Verron (Eds.), Springer, 109-126.

Chassignet, E.P., H.E. Hurlburt, O.M. Smedstad, G.R. Halliwell, P.J. Hogan, A.J. Wallcraft, and R. Bleck, 2006: Ocean prediction with the Hybrid Coordinate Ocean Model (HYCOM). In: Ocean Weather Forecasting: An Integrated View of Oceanography, Chassignet, E.P., and J. Verron (Eds.), Springer, 413-426.

Sun, W., M. Cetin, W. C. Thacker, T. M. Chin, and A. S. Willsky, 2006: Variational approaches on discontinuity localization and field estimation in sea surface temperature and soil moisture. IEEE Transactions on Geoscience and Remote Sensing, 44, 336-350.

Kara, A. B., H. E. Hurlburt, A. J. Wallcraft, and M. A. Bourassa, 2006: CORRIGENDUM for Black Sea mixed layer sensitivity to various wind and thermal forcing products on climatological time scales. J. Climate, 19, 494-495.

Lopez, M., L. Zamudio, and F Padilla, 2005: Effects of the 1997– 1998 El Nino on the exchange of the northern Gulf of California. J. Geophys. Res., 110, C11005, doi:10.1029/2004JC002700.

Cummings, J.A., 2005: Operational multivariate ocean data assimilation. Quart. J. Royal Met. Soc., Part C, 131(613), 3583-3604.

Chassignet, E.P., H.E. Hurlburt, O.M. Smedstad, C.N. Barron, D.S. Ko, R.C. Rhodes, J.F. Shriver, A.J. Wallcraft, and R.A. Arnone, 2005: Assessment of ocean prediction systems in the Gulf of Mexico using ocean color. In "Circulation in the Gulf of Mexico: Observations and models", W. Sturges and A. Lugo-Fernadez, Eds., AGU Monograph Series, 161, 87-100.

Kara, A. B., H. E. Hurlburt, A. J. Wallcraft, and M. A. Bourassa, 2005: Black Sea mixed layer sensitivity to various wind and thermal forcing products on climatological time scales. J. Climate, 18(24), 5266--5293.

Chang, Y., X. Xu, T.M. Özgökmen, E.P. Chassignet, H. Peters, and P.F. Fisher, 2005: Comparison of gravity current mixing parameterizations and calibration using a high-resolution 3D nonhydrostatic spectral element model. Ocean Modelling, 10, 342-368, doi:10.1016/j.ocemod.2004.11.002

Han, W., 2005: Origins and dynamics of the 90-day and 30-60 day variations in the equatorial Indian Ocean. J. Phys. Oceanogr., 35, 708-728.

Lee, S.-K., D. B. Enfield, and C. Wang, 2005: Ocean general circulation model sensitivity experiments on the annual cycle of Western Hemisphere Warm Pool. J. Geophys. Res., 110, C09004, doi:10.1029/2004JC002640.

Kara, A. B., H. E. Hurlburt, and A. J. Wallcraft, 2005: Stability-dependent exchange coefficients for air-sea fluxes. J. Atmos. Oceanic. Technol., 22, 1080-1094.
[see also http://www7320.nrlssc.navy.mil/nasec/nasec.html]

Birol F., J.-M. Brankart, J.M. Lemoine, P. Brasseur, and J. Verron, 2005: Assimilation of satellite altimetry referenced to the new GRACE geoid estimate. Geophys. Res. Letters, 32, L06601, doi :10.1029/2004GL02329.

Kara, A. B., A. J. Wallcraft, and H. E. Hurlburt, 2005: How does solar attenuation depth affect the ocean mixed layer? Water turbidity and atmospheric forcing impacts on the simulation of seasonal mixed layer variability in the turbid Black Sea. J. Climate, 18, 389-409.

Kara, A. B., A. J. Wallcraft, and H. E. Hurlburt, 2005: A new solar radiation penetration scheme for use in ocean mixed layer studies: an application to the Black Sea using a fine-resolution Hybrid Coordinate Ocean Model (HYCOM)*. J. Phys. Oceanogr., 35, 13-32.

Kara, A. B., A. J. Wallcraft, and H. E. Hurlburt, 2005: Sea surface temperature sensitivity to water turbidity from simulations of the turbid Black Sea using HYCOM*. J. Phys. Oceanogr., 35, 33-54.

Shaji, C., C. Wang, G.R. Halliwell, Jr., and A.J. Wallcraft, 2005: Simulation of tropical Pacific and Atlantic Oceans using a hybrid coordinate ocean model. Ocean Modelling, 9, 253-282.

Birol F., J.-M. Brankart, F. Castruccio, P. Brasseur, and J. Verron, 2004: Impact of the Ocean Mean Dynamic Topography on Satellite Data Assimilation. Mar. Geodesy, 27, 59-78.

Han, W., P.J. Webster, R. Lukas, P. Hacker, and A. Hu, 2004: Impact of atmospheric intraseasonal variability in the Indian Ocean: low-frequency rectification in equatorial surface current and transport. J. Phys. Oceanogr., 34, 1350-1372.

Halliwell, G.R., 2004: Evaluation of vertical coordinate and vertical mixing algorithms in the HYbrid Coordinate Ocean Model (HYCOM). Ocean Modelling, 7, 285-322.

Thacker, W.C., S.-K. Lee, and G.R. Halliwell, Jr., 2004: Assimilating 20 years of Atlantic XBT data into HYCOM: a first look. Ocean Modeling, 7, 183-210.

Bleck, R., and S. Sun, 2004: Diagnostics of the oceanic thermohaline circulation in a coupled climate model. Global and Planetary Change, 40, 233-248.

Thacker, W.C., 2003: Data-model-error compatibility. Ocean Modeling, 5, 233-247.

Halliwell, Jr., G.R., R.H. Weisberg, and D.A. Mayer, 2003: A synthetic float analysis of upper-limb meridional overturning circulation interior ocean pathways in the tropical/subtropical atlantic. Interhemispheric Water Exchange in the Atlantic Ocean, P. Malanotte-Rizzoli and G. Goni, eds., Elsevier, 93-136.

Chassignet, E.P., L.T. Smith, G.R. Halliwell, and R. Bleck, 2003: North Atlantic simulation with the HYbrid Coordinate Ocean Model (HYCOM): Impact of the vertical coordinate choice, reference density, and thermobaricity. J. Phys. Oceanogr., 33, 2504-2526.

Sun, S., and J. Hansen, 2003: Climate simulations for 1951-2050 with a coupled atmoshere-ocean model. J. Climate, 16, 2807-2826.

Bleck, R., 2002: An oceanic general circulation model framed in hybrid isopycnic-cartesian coordinates. Ocean Modelling, 4, 55-88.

Thacker, W. C., and O. E. Esenkov, 2002: Assimilating {XBT} data into HYCOM. Journal of Atmospheric and Oceanic Technology, 19, 709-724.