Publications

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BOOK

This book is based on a hands-on modeling course taught in the MIT/WHOI Joint Program:
Glover, D.M., W.J. Jenkins, and S.C. Doney, 2011: Modeling Methods for Marine Science, Cambridge University Press book website (ISBN-13: 9780521867832).





Discussion Papers (in review)

Gehlen, M., R. Séférian, D.O.B. Jones, T. Roy, R. Roth, J. Barry, L. Bopp, S.C. Doney, J.P. Dunne, C. Heinze, F. Joos, J.C. Orr, L. Resplandy, J. Segschneider, and J. Tjiputra, 2014: Projected pH reductions by 2100 might put deep North Atlantic biodiversity a risk, Biogeosciences Discuss., 11, 8607-8634, doi:10.5194/bgd-11-8607-2014, http://www.biogeosciences-discuss.net/11/8607/2014/bgd-11-8607-2014.html

Jonsson, B.F., S. Doney, J. Dunne, and M.L. Bender, 2014: Evaluating Southern Ocean biological production in two ocean biogeochemical models on daily to seasonal time-Scales using satellite chlorophyll and O2/Ar observations, Biogeosciences Discuss., 11, 9629-9665, doi:10.5194/bgd-11-9629-2014, http://www.biogeosciences-discuss.net/11/9629/2014/bgd-11-9629-2014.html

Sitch, S., P. Friedlingstein, N. Gruber, S. Jones, G. Murray-Tortarolo, A. Ahlström, S.C. Doney, H. Graven, C. Heinze, C. Huntingford, S. Levis, P.E. Levy, M. Lomas, B. Poulter, N. Viovy, S. Zaehle, N. Zeng, A. Arneth, G. Bonan, L. Bopp, J.G. Canadell, F. Chevallier, P. Ciais, R. Ellis, M. Gloor, P. Peylin, S. Piao, C. Le Quéré, B. Smith, Z. Zhu, R. Myneni, 2013: Trends and drivers of regional sources and sinks of carbon dioxide over the past two decades, Biogeosciences Discuss., 10, 20113-20177, doi:10.5194/bgd-10-20113-2013, http://www.biogeosciences-discuss.net/10/20113/2013/bgd-10-20113-2013.html

Vogt, M., T. Hashioka, M. Payne, E.T. Buitenhuis, C. Le Quéré, S. Alvain, M.N. Aita, L. Bopp, S.C. Doney, T. Hirata, I. Lima, S. Sailley, and Y. Yamanaka, 2013: The distribution, dominance patterns and ecological niches of plankton functional types in Dynamic Green Ocean Models and satellite estimates, Biogeosciences Discuss., 10, 17193-17247, doi:10.5194/bgd-10-17193-2013, http://www.biogeosciences-discuss.net/10/17193/2013/bgd-10-17193-2013.html

Publications in Refereed Journals


2014

Benway, H.M., and S.C. Doney (2014). Scientific outcomes and future challenges of the Ocean Carbon and Biogeochemistry Program, Oceanography, 27(1), 106-107, doi:10.5670/oceanog.2014.13.

Doney, S.C., L. Bopp, and M.C. Long (2014). Historical and future trends in ocean climate and biogeochemistry, Oceanography, 27(1), 108-119, doi:10.5670/oceanog.2014.14.

Doney, S., A.A. Rosenberg, M. Alexander, F. Chavez, C.D. Harvell, G. Hofmann, M. Orbach, and M. Ruckelshaus, 2014: Ch. 24: Oceans and Marine Resources, in Climate Change Impacts in the United States: The Third National Climate Assessment, J.M. Melillo, Terese (T.C.) Richmond, and G.W. Yohe, Eds., U.S. Global Change Research Program, 557-578, doi:10.7930/J0RF5RZW, http://nca2014.globalchange.gov/report/regions/oceans

Halpern, B., C. Longo, C. Scarborough, D. Hardy, B.D. Best, S.C. Doney, S.K. Katona, K.L. McLeod, A.A. Rosenberg, and J.F. Samhouri, 2014: Assessing the health of the U.S. West Coast with a regional-scale application of the Ocean Health Index, PLoS One, 9(6), e98995. doi:10.1371/journal.pone.0098995

Ishii, M., R.A. Feely, K.B. Rodgers, G.-H. Park, R. Wanninkhof, D. Sasano, H. Sugimoto, C.E. Cosca, S. Nakaoka, M. Telszewski, Y. Nojiri, S.E. Mikaloff Fletcher, Y. Niwa, P.K. Patra, V. Valsala, H. Nakano, I. Lima, S.C. Doney, E.T. Buitenhuis, O. Aumont, J.P. Dunne, A. Lenton, and T. Takahashi, (2014). Air-sea CO2 flux in the Pacific Ocean for the period 1990-2009, Biogeosciences, 11, 709-734, doi:10.5194/bg-11-709-2014.

Le Quéré, C., G.P. Peters, R.J. Andres, R.M. Andrew, T.A. Boden, P. Ciais, P. Friedlingstein, R.A. Houghton, G. Marland, R. Moriarty, S. Sitch, P. Tans, A. Arneth, A. Arvanitis, D.C.E. Bakker, L. Bopp, J.G. Canadell, L.P. Chini, S.C. Doney, A. Harper, I. Harris, J.I. House, A.K. Jain, S.D. Jones, E. Kato, R.F. Keeling, K. Klein Goldewijk, A. Körtzinger, C. Koven, N. Lefèvre, F. Maignan, A. Omar, T. Ono, G.-H. Park, B. Pfeil, B. Poulter, M.R. Raupach, P. Regnier, C. Rödenbeck, S. Saito, J. Schwinger, J. Segschneider, B.D. Stocker, T. Takahashi, B. Tilbrook, S. van Heuven, N. Viovy, R. Wanninkhof, A. Wiltshire, and S. Zaehle, 2014: Global Carbon Budget 2013, Earth System Science Data, 6, 235-263, www.earth-syst-sci-data.net/6/235/2014/, doi:10.5194/essd-6-235-2014

Lima, I.D., P.J. Lam, and S.C. Doney (2014). Dynamics of particulate organic carbon flux in a global ocean model, Biogeosciences, 11, 1177-1198, doi:10.5194/bg-11-1177-2014.

Luo, Y.W., I.D. Lima, D.M. Karl, C.A. Deutsch, and S.C. Doney (2014). Data-based assessment of environmental controls on global marine nitrogen fixation, Biogeosciences, 11, 691-708, doi:10.5194/bg-11-691-2014.

Misumi, K., K. Lindsay, J.K. Moore, S.C. Doney, F.O. Bryan, D. Tsumune, and Y. Yoshida (2014). The iron budget in ocean surface waters in the 20th and 21st centuries: projections by the Community Earth System Model version 1, Biogeosciences, 11, 33-55, doi:10.5194/bg-11-33-2014.

Muller-Karger, F.E., M.T. Kavanaugh, E. Montes, W.M. Balch, M. Breitbart, F.P. Chavez, S.C. Doney, E.M. Johns, R.M. Letelier, M.W. Lomas, H.M. Sosik, and A.E. White, 2014: A framework for a marine biodiversity observing network within changing continental shelf seascapes, Oceanography, 27(2), 18-23, http://dx.doi.org/10.5670/oceanog.2014.56.

Nicholson, D., R.H.R. Stanley, and S. Doney, 2014: The triple oxygen isotope tracer of primary productivity in a dynamic ocean model, Global Biogeochem. Cycles, 28, 538-552, doi:10.1002/2013GB004704.

Saba, G.K., W.R. Fraser, V.S. Saba, R.A. Iannuzzi, K. Coleman, S.C. Doney, H.W. Ducklow, D.G. Martinson, T.N. Miles, D.L. Patterson-Fraser, S.E. Stammerjohn, D.K. Steinberg, and O.M. Schofield, 2014: Winter and spring controls on the summer food web of the coastal West Antarctic Peninsula, Nature Communications, 5, 4318, doi: 10.1038/ncomms5318
http://www.nature.com/ncomms/2014/140707/ncomms5318/full/ncomms5318.html

Siegel, D.A., K.O. Buesseler, S.C. Doney, S. Sailley, M.J. Behrenfeld, and P.W. Boyd, Global assessment of ocean carbon export using food-web models and satellite observations, Global Biogeochem. Cycles, 28, 181-196, doi:10.1002/2013GB004743

Walsh, J., D. Wuebbles, K. Hayhoe, J. Kossin, K. Kunkel, G. Stephens, P. Thorne, R. Vose, M. Wehner, J. Willis, D. Anderson, S. Doney, R. Feely, P. Hennon, V. Kharin, T. Knutson, F. Landerer, T. Lenton, J. Kennedy, and R. Somerville, 2014: Ch. 2: Our Changing Climate, in Climate Change Impacts in the United States: The Third National Climate Assessment, J.M. Melillo, Terese (T.C.) Richmond, and G.W. Yohe, Eds., U.S. Global Change Research Program, 19-67. doi:10.7930/J0KW5CXT, http://nca2014.globalchange.gov/report/our-changing-climate/introduction


2013

Andersson, A.J., L.A. Krug, N.R. Bates, and S.C. Doney (2013). Sea-air CO2 flux in the North Atlantic subtropical gyre: Role and influence of Sub-Tropical Mode Water formation, Deep-Sea Res. II, 91, 57-70, doi: 10.1016/j.dsr2.2013.02.022

Beaulieu, C., S.A. Henson, J.L. Sarmiento, J.P. Dunne, S.C. Doney, R.R. Rykaczewski, and L. Bopp (2013). Factors challenging our ability to detect long-term trends in ocean chlorophyll, Biogeosciences, 10, 2711-2724, doi:10.5194/bg-10-2711-2013.

Behrenfeld, M.J., S.C. Doney, I. Lima, E.S. Boss, and D.A. Siegel (2013) Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom, Global Biogeochem. Cycles, 27, 526-540, doi:10.1002/gbc.20050.

Behrenfeld, M.J., S.C. Doney, I. Lima, E.S. Boss, and D.A. Siegel (2013) Reply to a comment by Stephen M. Chiswell on: "Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom" by M. J. Behrenfeld et al. (2013), Global Biogeochem. Cycles, 27, 1294-1296, doi:10.1002/2013GB004720.

Bopp, L., L. Resplandy, J.C. Orr, S.C. Doney, J.P. Dunne, M. Gehlen, P. Halloran, C. Heinze, T. Ilyina, R. Séférian, J. Tjiputra, and M. Vichi (2013). Multiple stressors of ocean ecosystems in the 21st century: projections with CMIP5 models, Biogeosciences, 10, 6225-6245, doi:10.5194/bg-10-6225-2013.

Buitenhuis, E.T., M. Vogt, R. Moriarty, N. Bednaršek, S.C. Doney, K. Leblanc, C. Le Quéré, Y.-W. Luo, C. O'Brien, T. O'Brien, J. Peloquin, R. Schiebel, and C. Swan (2013). MAREDAT: Towards a world ocean atlas of MARine Ecosystem DATa, Earth System Science Data, 5, 227-239, doi:10.5194/essd-5-227-2013.

Doney, S.C. (2013). "Marine ecosystems, biogeochemistry, and climate." Chapter 31 in Ocean Circulation and Climate, 2nd Ed. A 21st century perspective, Eds. G. Siedler, S.M. Griffies, J. Gould, and J.A. Church, Academic Press, International Geophysics Series, Vol. 103, pp. 817-842, ISBN: 978-0-12-391851-2, ISSN: 0074-6142.

Doney, S.C., and D.K. Steinberg (2013). Marine biogeochemistry: The ups and downs of ocean oxygen, Nature Geosci., 6, 515-516, doi:10.1038/ngeo1872.

Doney, S.C. and S.F. Sailley (2013). When an ecological regime shift is really just stochastic noise, Proc. Nat. Acad. Sci. USA, 110(7), 2438-2439, doi:10.1073/pnas.1222736110.

Ducklow, H.W., and S.C. Doney (2013). What is the metabolic state of the oligotrophic ocean? A debate, Annu. Rev. Mar. Sci., 5, 525-533, doi:10.1146/annurev-marine-121211-172331.

Ducklow, H.W., W.R. Fraser, M.P. Meredith, S.E. Stammerjohn, S.C. Doney, D.G. Martinson, S.F. Sailley, O.M. Schofield, D.K. Steinberg, H.J. Venables, and C.D. Amsler (2013). West Antarctic Peninsula: An ice-dependent coastal marine ecosystem in transition, Oceanography, 26(3), 190-203, doi:10.5670/oceanog.2013.62.

Hashioka, T., M. Vogt, Y. Yamanaka, C. Le Quéré, E.T. Buitenhuis, M.N. Aita, S. Alvain, L. Bopp, T. Hirata, I. Lima, S. Sailley, and S.C. Doney (2013). Phytoplankton competition during the spring bloom in four plankton functional type models, Biogeosciences, 10, 6833-6850, doi:10.5194/bg-10-6833-2013.

Hauri, C., N. Gruber, M. Vogt, S.C. Doney, R.A. Feely, Z. Lachkar, A. Leinweber, A.M.P. McDonnell, M. Munnich, and G.-K. Plattner (2013). Spatiotemporal variability and long-term trends of ocean acidification in the California Current System, Biogeosciences, 10, 193-216, doi:10.5194/bg-10-193-2013 .

Jonsson, B.F., S.C. Doney, J. Dunne, and M. Bender (2013). Evaluation of the Southern Ocean O2/Ar-based NCP measurements in a model framework, J. Geophys. Res. Biogeosci., 118, doi:10.1002/jgrg.20032 .

Keppel-Aleks, G., J.T. Randerson, K. Lindsay, B.B. Stephens, J.K. Moore, S.C. Doney, P.E. Thornton, N.M. Mahowald, F.M. Hoffman, C. Sweeney, P.P. Tans, P.O. Wennberg, and S.C. Wofsy (2013). Atmospheric carbon dioxide variability in the Community Earth System Model: evaluation and transient dynamics during the twentieth and twenty-first centuries, J. Climate, 26, 4447-4475; doi:10.1175/JCLI-D-12-00589.1.

Khatiwala, S., T. Tanhua, S. Mikaloff Fletcher, M. Gerber, S.C. Doney, H.D. Graven, N. Gruber, G.A. McKinley, A. Murata, A.F. Rios, and C.L. Sabine (2013). Global ocean storage of anthropogenic carbon, Biogeosciences, 10, 2169-2191, doi:10.5194/bg-10-2169-2013.

Lenton, A., B. Tilbrook, R.M. Law, D. Bakker, S.C. Doney, N. Gruber, M. Ishii, M. Hoppema, N.S. Lovenduski, R.J. Matear, B.I. McNeil, N. Metzl, S.E. Mikaloff Fletcher, P.M.S. Monteiro, C. Rödenbeck, C. Sweeney, and T. Takahashi (2013). Sea-air CO2 fluxes in the Southern Ocean for the period 1990-2009, Biogeosciences, 10, 4037-4054, doi:10.5194/bg-10-4037-2013.

Le Quéré, C., R. J. Andres, T. Boden, T. Conway, R. A. Houghton, J. I. House, G. Marland, G. P. Peters, G.R. van der Werf, A. Ahlström, R.M. Andrew, L. Bopp, J.G. Canadell, P. Ciais, S.C. Doney, C. Enright, P. Friedlingstein, C. Huntingford, A.K. Jain, J. Jourdain, E. Kato, R.F. Keeling, K. Klein Goldewijk, S. Levis, P. Levy, M. Lomas, B. Poulter, M.R. Raupach, J. Schwinger, S. Sitch, B.D. Stocker, N. Viovy, S. Zaehle, and N. Zeng (2013). The global carbon budget 1959-2011, Earth System Science Data, 5, 165-185, doi:10.5194/essd-5-165-2013.

Long, M.C., K. Lindsay, S. Peacock, J.K. Moore, and S.C. Doney (2013). Twentieth-century ocean carbon uptake and storage in CESM1(BGC), J. Climate, 26(18), 6775-6800, doi: 10.1175/JCLI-D-12-00184.1.

Marinov, I., S.C. Doney, I.D. Lima, K. Lindsay, J.K. Moore, and N. Mahowald (2013). North-south asymmetry in the modeled phytoplankton response to climate change over the 21st century, Global Biogeochem. Cycles, 27, 1274-1290, doi:10.1002/2013GB004599.

Misumi, K., K. Lindsay, J.K. Moore, S.C. Doney, D. Tsumune, and Y. Yoshida (2013). Humic substances may control dissolved iron distributions in the global ocean: Implications from numerical simulations, Global Biogeochem. Cycles, 27, 450?462, doi:10.1002/gbc.20039.

Moore, J.K., K. Lindsay, S.C. Doney, M.C. Long, and K. Misumi, 2013: Marine ecosystem dynamics and biogeochemical cycling in the Community Earth System Model CESM1(BGC), J. Climate, 26(23), 9291-9321, doi: 10.1175/JCLI-D-12-00566.1.

Ruckelshaus, M., S.C. Doney, H.M. Galindo, J.P. Barry, F. Chan, J.E. Duffy, C.A. English, S.D. Gaines, J.M. Grebmeier, A.B. Hollowed, N. Knowlton, J. Polovina, N.N. Rabalais, W.J. Sydeman, and L.D. Talley (2013). Securing ocean benefits for society in the face of climate change, Marine Policy, 40, 154-159.

Sailley, S.F., H.W. Ducklow, H.V. Moeller, W.R. Fraser, O.M. Schofield, D.K. Steinberg, L.M. Garzio, and S.C. Doney (2013). Carbon fluxes and pelagic ecosystem dynamic near two western Antarctic Peninsula Adélie penguin colonies: an inverse model approach, Marine Ecology Progress Series, 492, 253-272, doi: 10.3354/meps10534.

Sailley, S., M. Vogt, S.C. Doney, M.N. Aita, L. Bopp, E.T. Buitenhuis, T. Hashioka, I. Lima, C. Le Quéré, and Y. Yamanaka (2013). Comparing food web structures and dynamics across a suite of global marine ecosystem models, Ecological Modeling, 261-262, 43-57, doi:10.1016/j.ecolmodel.2013.04.006

Sarma, V.V.S.S., A. Lenton, R.M. Law, N. Metzl, P.K. Patra, S. Doney, I.D. Lima, E. Dlugokencky, M. Ramonet, and V. Valsala (2013). Sea-air CO2 fluxes in the Indian Ocean between 1990 and 2009, Biogeosciences, 10, 7035-7052, doi:10.5194/bg-10-7035-2013.

Schofield, O., H. Ducklow, K. Bernard, S. Doney, D. Patterson-Fraser, K. Gorman, D. Martinson, M. Meredith, G. Saba, S. Stammerjohn, D. Steinberg, and W. Fraser (2013). Penguin biogeography along the West Antarctic Peninsula: Testing the canyon hypothesis with Palmer LTER observations, Oceanography, 26(3), 204-206, doi:10.5670/oceanog.2013.63.

Schuster, U., G.A. McKinley, N. Bates, F. Chevallier, S.C. Doney, A.R. Fay, M. González-Dávila, N. Gruber, S. Jones, J. Krijnen, P. Landschützer, N. Lefèvre, M. Manizza, J. Mathis, N. Metzl, A. Olsen, A.F. Rios, C. Rödenbeck, J.M. Santana-Casiano, T. Takahashi, R. Wanninkhof, and A.J. Watson (2013). An assessment of Atlantic and Arctic sea-air CO2 fluxes, 1990-2009, Biogeosciences, 10, 607-627, doi:10.5194/bg-10-607-2013.

Siegel, D.A., M.J. Behrenfeld, S. Maritorena, C.R. McClain, D. Antoine, S.W. Bailey, P.S. Bontempi, E.S. Boss, H.M. Dierssen, S.C. Doney, R.E. Eplee Jr., R.H. Evans, G.C. Feldman, E. Fields, B.A. Franz, N.A. Kuring, C. Mengelt, N.B. Nelson, F.S. Patt, W.D. Robinson, J.L. Sarmiento, C.M. Swan, P.J. Werdell, T.K. Westberry, J.G. Wilding, and J.A. Yoder (2013). Regional to global assessments of phytoplankton dynamics from the SeaWiFS mission, Remote Sensing Environ., 135, 77-91, doi:10.1016/j.rse.2013.03.025.

Wanninkhof, R., G.-H. Park, T. Takahashi, R.A. Feely, J.L. Bullister, and S.C. Doney (2013). Changes in deep-water CO2 concentrations over the last several decades determined from discrete pCO2 measurements, Deep-Sea Res. I, 74, 48-63, doi:10.1016/j.dsr.2012.12.005.

Wanninkhof, R., G.-H. Park, T. Takahashi, C. Sweeney, R. Feely, Y. Nojiri, N. Gruber, S.C. Doney, G.A. McKinley, A. Lenton, C. Le Quéré, C. Heinze, J. Schwinger, H. Graven, S. Khatiwala (2013). Global ocean carbon uptake: magnitude, variability and trends, Biogeosciences, 10, 1983-2000; doi:10.5194/bg-10-1983-2013.

Westberry, T.K., M.J. Behrenfeld, A.J. Milligan, and S.C. Doney (2013). Retrospective satellite ocean color analysis of purposeful and natural ocean iron fertilization, Deep-Sea Res. I, 73, 1-16;http://dx.doi.org/10.1016/j.dsr.2012.11.010.


2012

Cooley SR, Lucey N, Kite-Powell H, Doney SC (2012). Nutrition and income from molluscs today imply vulnerability to ocean acidification tomorrow. Fish and Fisheries 13: 182-215, DOI: 10.1111/j.1467-2979.2011.00424.x.

Cooley, S
., and S. Doney (2012). "Ocean acidification", in Encyclopedia of Environmetrics Second Edition, A.-H. El-Shaarawi and W. Piegorsch (eds)., John Wiley & Sons Ltd, Chichester, UK, pp. 1828-1834, doi:10.1002/9780470057339.vnn124.

Doney SC
, Ruckelshaus M, Emmett Duffy J, Barry JP, Chan F, English CA, Galindo HM, Grebmeier JM, Hollowed AB, Knowlton N, Polovina J, Rabalais NN, Sydeman WJ, Talley LD (2012). Climate Change Impacts on Marine Ecosystems. Annual Review of Marine Science 4: 11-37, DOI: 10.1146/annurev-marine-041911-111611. THE ARTICLE CAN BE ACCESSED VIA THE FOLLOWING E-PRINT URL:
http://arjournals.annualreviews.org/eprint/fzUZd7Z748TeHmB7p8cn/full/10.1146/annurev-marine-041911-111611

Ducklow, H., A. Clarke, R. Dickhut, S.C. Doney, H. Geisz, K. Huang, D.G. Martinson, M.P. Meredith, H.V. Moeller, M. Montes-Hugo, O. Schofield, S.E. Stammerjohn, D. Steinberg, and W. Fraser (2012). "Marine pelagic ecosystems: the West Antarctic Peninsula", in Antarctic Ecosystems: An Extreme Environment in a Changing World, eds. A.D. Rogers, N.M. Johnston, E.J. Murphy, A. Clarke, Wiley-Blackwell, ISBN: 978-1405198400.

Goodkin, N.F.,
E.R.M. Druffel, K.A. Hughen, and S.C. Doney (2012).  Two centuries of limited variability in subtropical North Atlantic thermocline ventilation, Nat. Commun., 3: 803, doi:10.1038/ncomms1811.

Guidi, L., Calil, P.H.R., Duhamel, S., Björkman, K.M., Doney, S.C., Jackson, G.A., Li, B., Church, M.J., Tozzi, S., Kolber, Z.S., Richards, K.J., Fong, A.A., Letelier, R.M., Gorsky, G., Stemmann, L., Karl, D.M. (2012). Does eddy-eddy interaction control surface phytoplankton distribution and carbon export in the North Pacific Subtropical Gyre?. Journal of Geophysical Research, 17, p. G02024, doi:10.1029/2012JG001984.

Halpern, B.S., C. Longo, D. Hardy, K.L. McLeod, J.F. Samhouri, S.K. Katona, K. Kleisner, S.E. Lester, J.O. Leary, M. Ranelletti, A.A. Rosenberg, C. Scarborough, E.R. Selig, B.D. Best, D.R. Brumbaugh, F.S. Chapin, L.B. Crowder, K.L. Daly, S.C. Doney, C. Elfes, M.J. Fogarty, S.D. Gaines, K.I. Jacobsen, L.B. Karrer, H.M. Leslie, E. Neeley, D. Pauly, S. Polasky, B. Ris, K. St. Martin, G.S. Stone, U.R. Sumaila, and D. Zeller (2012). An index to assess the health and benefits of the global ocean, Nature, 488, 615-620, doi: 10.1038/nature11397.

Hynes AM, Webb EA, Doney SC, Waterbury JB (2012). Comparison of cultured Trichodesmium (Cyanophyceae) with species characterized from the field. Journal of Phycology 48: 196-210, DOI: 10.1111/j.1529-8817.2011.01096.x.

Levine NM, Varaljay VA, Toole DA, Dacey JWH, Doney SC, Moran MA (2012). Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea. Environmental Microbiology 14: 1210-1223, doi:10.1111/j.1462-2920.2012.02700.x.

Luo, Y.-W., S.C. Doney, L.A. Anderson, M. Benavides, I. Berman-Frank, A. Bode, S. Bonnet, K.H. Boström, D. Böttjer, D.G. Capone, E.J. Carpenter, Y.L. Chen, M.J. Church, J.E. Dore, L.I. Falcón, A. Fernández, R.A. Foster, K. Furuya, F. Gómez, K. Gundersen, A.M. Hynes, D.M. Karl, S. Kitajima, R.J. Langlois, J. LaRoche, R.M. Letelier, E. Marañón, D.J. McGillicuddy Jr., P.H. Moisander, C.M. Moore, B. Mouriño-Carballido, M.R. Mulholland, J.A. Needoba, K.M. Orcutt, A.J. Poulton, E. Rahav, P. Raimbault, A.P. Rees, L. Riemann, T. Shiozaki, A. Subramaniam, T. Tyrrell, K.A. Turk-Kubo, M. Varela, T.A. Villareal, E.A. Webb, A.E. White, J. Wu, and J.P. Zehr (2012). Database for diazotrophs in global ocean: abundances, biomass and nitrogen fixation rates, Earth Syst. Sci. Data, 4, 47-73, doi:10.5194/essd-4-47-2012.

Luo, Y.-W., H.W. Ducklow, M.A.M. Friedrichs, M.J. Church, D.M. Karl, and S.C. Doney (2012). Interannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre. J. Geophys. Res. Biogeosci., 117, G03019, doi:10.1029/2011JG001830.

Mouw, C.B., Yoder, J.A., Doney, S.C. (2012). Impact of phytoplankton community size on a linked global ocean optical and ecosystem model. J. Mar. Systems 89:61-75, http://dx.doi.org/10.1016/j.jmarsys.2011.08.002.

Murphy, E.J., Cavanagh,,R.D., Hofmann, E.E., Hill, S.L., Constable, A.J., Costa, D.P., Pinkerton, M.H.,  Johnston, N.M., Trathan, P.N., Klinck, J.M., Wolf-Gladrow, D.A., Daly, K.L., Maury, O., Doney, S.C. (2012). Developing integrated models of Southern Ocean food webs: Including ecological complexity, accounting for uncertainty and the importance of scale. Progress in Oceanography, 102, 74–92, http://dx.doi.org/10.1016/j.pocean.2012.03.006

Nicholson, D.P., Stanley, R.H.R., Barkan, E., Karl, D.M., Luz, B., Quay, P.D., and Doney, S.C.  (2012). Evaluating triple oxygen isotope estimates of gross primary production at the Hawaii Ocean Time-series and Bermuda Atlantic Time-series Study sites, J. Geophys. Res., 117, C05012, doi:10.1029/2010JC006856.

Rothenberg, D., N. Mahowald, K. Lindsay, S.C. Doney, J.K. Moore, and P. Thornton (2012). Volcano impacts on climate and biogeochemistry in a coupled carbon-climate model, Earth Syst. Dynam., 3, 121-136, doi:10.5194/esd-3-121-2012.

Stanley, R.H.R., Doney, S.C., Jenkins, W.J., and Lott, III, D.E. (2012). Apparent oxygen utilization rates calculated from tritium and helium-3 profiles at the Bermuda Atlantic Time-series Study site, Biogeosciences, 9, 1969-1983, doi:10.5194/bg-9-1969-2012.


2011

Anderson LA, McGillicuddy Jr DJ, Maltrud ME, Lima ID, Doney SC (2011). Impact of eddy–wind interaction on eddy demographics and phytoplankton community structure in a model of the North Atlantic Ocean. Dynamics of Atmospheres and Oceans 52: 80-94, dx.doi.org/10.1016/j.dynatmoce.2011.01.003.

Aufdenkampe, A.K., E. Mayorga, P.A. Raymond, J.M. Melack, S.C. Doney, S.R. Alin, R.E. Aalto, and K. Yoo, 2011, Riverine coupling of biogeochemical cycles between land, oceans and atmosphere, Frontiers Ecology Environ., 9(1), 53-60, doi:10.1890/100014.

Boyd, P.W., C.S. Law, and S.C. Doney. 2011. Commentary: A climate change atlas for the ocean. Oceanography 24(2):13–16, http://dx.doi.org/10.5670/oceanog.2011.42.

Calil PHR, Doney SC
, Yumimoto K, Eguchi K, Takemura T (2011). Episodic upwelling and dust deposition as bloom triggers in low-nutrient, low-chlorophyll regions. Journal of Geophysical Research 116: C06030; doi:10.1029/2010JC006704.

Finzi, A.C., J.J. Cole, S.C. Doney, E.A. Holland, and R.B. Jackson, 2011: Research frontiers in the analysis of coupled biogeochemical cycles, Frontiers Ecology Environ., 9(1), 74-80, doi:10.1890/100137.

Goodkin NF, Levine NM, Doney SC, Wanninkhof R (2011). Impacts of temporal CO2 and climate trends on the detection of ocean anthropogenic CO2 accumulation. Global Biogeochem Cycles 25: GB3023, doi:10.1029/2010GB004009.

Howarth, R., F. Chan, D.J. Conley, J. Garnier, S.C. Doney, R. Marino, and G. Billen, 2011: Coupled biogeochemical cycles:  eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems, Frontiers Ecology Environ., 9(1), 18-26, doi:10.1890/100008.

Joint, I., S.C. Doney, and D.M. Karl, 2011: Will ocean acidification affect marine microbes? Int. Soc. Microbial Ecology J., 5, 1-7.

Lam PJ, Doney SC, Bishop JKB (2011). The dynamic ocean biological pump: Insights from a global compilation of particulate organic carbon, CaCO3, and opal concentration profiles from the mesopelagic. Global Biogeochem Cycles 25: GB3009, doi:10.1029/2010GB003868.

Levine NM, Doney SC, Lima I
, Wanninkhof R, Bates NR, Feely RA (2011). The impact of the North Atlantic Oscillation on the uptake and accumulation of anthropogenic CO2 by North Atlantic Ocean mode waters. Global Biogeochem Cycles 25: GB3022, doi:10.1029/2010GB003892.

Mahowald, N., K. Lindsay, D. Rothenberg, S.C. Doney, J.K. Moore, P. Thornton, J.T. Randerson, and Chris D. Jones, 2011: Desert dust and anthropogenic aerosol interactions in the Community Climate System Model coupled-carbon-climate model, Biogeosciences, 8, 387-414, doi:10.5194/bg-8-387-2011, www.biogeosciences.net/8/387/2011/

Misumi K, Tsumune D, Yoshida Y, Uchimoto K, Nakamura T, Nishioka J, Mitsudera H, Bryan FO, Lindsay K, Moore JK, Doney SC (2011). Mechanisms controlling dissolved iron distribution in the North Pacific: A model study. Journal of Geophysical Research 116: G03005, doi:10.1029/2010JG001541.

National Research Council, 2011: Climate Stabilization Targets: Emissions, Concentrations and Impacts over Decades to Millennia, National Academies Press, Washington DC, ISBN 0-309-15176-7, 298pp.

Parazoo, N. C., A. S. Denning, J. A. Berry, A. Wolf, D. A. Randall, S. R. Kawa, O. Pauluis, and S. C. Doney (2011), Moist synoptic transport of CO2 along the mid-latitude storm track, Geophys. Res. Lett., 38, L09804, doi:10.1029/2011GL047238.


2010

Baker, D.F., H. Bösch, S.C. Doney, D. O’Brien, and D.S. Schimel, 2010: Carbon source/sink information provided by column CO2 measurements from the Orbiting Carbon Observatory, Atmosp. Chem. Physics, 10, 4145-4165, doi:10.5194/acp-10-4145-2010.

Doney, S.C., 2010: The growing human footprint on coastal and open-ocean biogeochemistry, Science, 328, 1512-1516.

Feely, R.A., V.J. Fabry, A.G. Dickson, J.-P. Gattuso, J. Bijma, U. Riebesell, S. Doney, C. Turley, T. Saino, K. Lee, K. Anthony, and J. Kleypas, 2010: An international observational network for ocean acidification, In Proceedings of OceanObs'09: Sustained Ocean Observations and Information for Society (Vol. 2), Venice, Italy, 21–25 September 2009, ed. J. Hall, D.E. Harrison, and D. Stammer, ESA Publication WPP-306, doi:10.5270/OceanObs09.cwp.29, http://www.oceanobs09.net/

Gruber, N., A. Körtzinger, A. Borges, H. Claustre, S.C. Doney, R.A. Feely, M. Hood, M. Ishii, A. Kozyr, P. Monteiro, Y. Nojiri, C.L. Sabine, U. Schuster, D.W.R. Wallace, and R. Wanninkhof, 2010: Toward an integrated observing system for ocean carbon and biogeochemistry at a time of change. In Proceedings of OceanObs'09: Sustained Ocean Observations and Information for Society (Vol. 1), Venice, Italy, 21–25 September 2009, ed. J. Hall, D.E. Harrison, and D. Stammer, ESA Publication WPP-306, doi:10.5270/OceanObs09.pp.18, http://www.oceanobs09.net/

Gruber, N., S.C. Doney, S.R. Emerson, D. Gilbert, T. Kobayashi, A. Körtzinger, G.C. Johnson, K.S. Johnson, S.C. Riser, and O. Ulloa, 2010: Adding oxygen to Argo: Developing a global in-situ observatory for ocean deoxygenation and biogeochemistry, In Proceedings of the OceanObs'09: Sustained Ocean Observations and Information for Society (Vol. 2), Venice, Italy, 21–25 September 2009, ed. J. Hall, D.E. Harrison, and D. Stammer, ESA Publication WPP-306, doi:10.5270/OceanObs09.cwp.39, http://www.oceanobs09.net/

Henson, S.A., J.L. Sarmiento, J.P. Dunne, L. Bopp, I. Lima, S.C. Doney, J. John, and C. Beaulieu, 2010: Detection of anthropogenic climate change in satellite records of ocean chlorophyll and productivity, Biogeosciences, 7, 621-640, www.biogeosciences.net/7/621/2010/

Iglesias-Rodriguez, M.D., V.J. Fabry, A. Dickson, J.-P. Gattuso, J. Bijma, U. Riebesell, S. Doney, C. Turley, T. Saino, K. Lee, K. Anthony, and J. Kleypas, 2010: Developing a global ocean acidification observation network, In Proceedings of the OceanObs'09: Sustained Ocean Observations and Information for Society (Vol. 1), Venice, Italy, 21–25 September 2009, ed. J. Hall, D.E. Harrison, and D. Stammer, ESA Publication WPP-306, doi:10.5270/OceanObs09.pp.24,  http://www.oceanobs09.net/

Luo, Y., H.W. Ducklow, M.A.M. Friedrichs, S.C. Doney, and M.J. Church, 2010: Oceanic heterotrophic bacterial nutrition by semilabile DOM as revealed by data assimilative modeling, Aquatic Microbial Ecology, 60, 273-287.

Mahowald, N.M., S. Kloster, S. Engelstaedter, J.K. Moore, S. Mukhopadhyay, J.R. McConnell, S. Albani, S.C. Doney, A. Bhattacharya, M.A. J. Curran, M.G. Flanner, F.M. Hoffman, D.M. Lawrence, K. Lindsay, P.A. Mayewski, J. Neff, D. Rothenberg, E. Thomas, P.E. Thornton, and C.S. Zender, 2010: Observed 20th century desert dust variability: impact on climate and biogeochemistry, Atmosp. Chem. Physics, 10, 10875-10893, doi:10.5194/acp-10-10875-2010.

* Marinov, I., S.C. Doney and I.D. Lima, 2010: Response of ocean phytoplankton community structure to climate change over the 21st century: partitioning the effects of nutrients, temperature and light, Biogeosciences, 7, 3941-3959, doi:10.5194/bg-7-3941-2010

McGillicuddy, D.J. Jr., B. de Young, S.C. Doney, P.M. Glibert, D. Stammer, and F.E. Werner, 2010: Models: tools for synthesis in international oceanographic research programs, Oceanography, 23, 126-139.

Montes-Hugo, M., C. Sweeney, S.C. Doney, H. Ducklow, R. Frouin, D.G. Martinson, S. Stammerjohn, and O. Schofield, 2010: Seasonal forcing of summer dissolved inorganic carbon and chlorophyll a on the western shelf of the Antarctic Peninsula, J. Geophys. Res. Oceans, 115, C03024, doi:10.1029/2009JC005267.

National Research Council, 2010: Ocean Acidification: A National Strategy to Meet the Challenges of a Changing Ocean, National Academies Press, Washington DC, ISBN 0-309-15360-3, 175pp.

Oschlies, A., J. Blackford, S.C. Doney, and M. Gehlen, 2010: Modelling Considerations, Chapter 14, Guide to Best Practices for Ocean Acidification Research and Data Reporting, ed. U. Riebesell, V.J. Fabry, L. Hansson, and J.-P. Gattuso, Publications Office of the European Union, Luxembourg, 233-242. (http://www.epoca-project.eu/index.php/Home/Guide-to-OA-Research/)

Park, G.-H., R. Wanninkhof, S.C. Doney, T. Takahashi, K. Lee, R.A. Feely, C.L. Sabine, J. Triñanes, and I.D. Lima, 2010: Variability of global net air-sea CO2 fluxes over the last three decades using empirical relationships, Tellus, 62B, 352-368, doi:10.1111/j.1600-0889.2010.00498.x.

Saba, V.S., M.A.M. Friedrichs, M.-E. Carr, D. Antoine, R.A. Armstrong, I. Asanuma, O. Aumont, N.R. Bates, M.J. Behrenfeld, V. Bennington, L. Bopp, J. Bruggeman, E.T. Buitenhuis, M.J. Church, A.M. Ciotti, S.C. Doney, M. Dowell, J. Dunne, S. Dutkiewicz, W. Gregg, N. Hoepffner, K.J.W. Hyde, J. Ishizaka, T. Kameda, D.M. Karl, I. Lima, M.W. Lomas, J. Marra, G.A. McKinley, F. Mélin, J.K. Moore, A. Morel, J. O’Reilly, B. Salihoglu, M. Scardi, T.J. Smyth, S. Tang, J. Tjiputra, J. Uitz, M. Vichi, K. Waters, T.K. Westberry, and A. Yool, 2010: Challenges of modeling depth-integrated marine primary productivity over multiple decades:  A case study at BATS and HOT, Global Biogeochem. Cycles, 24, GB3020, doi:10.1029/2009GB003655

Steinacher, M., F. Joos, T.L. Frölicher, L. Bopp, P. Cadule, V. Cocco, S.C. Doney, M. Gehlen, K. Lindsay, J.K. Moore, B. Schneider, and J. Segschneider, 2010: Projected 21st century decrease in marine productivity: a multi-model analysis, Biogeosciences, 7, 979-1005, www.biogeosciences.net/7/979/2010/ (chosen for Nature Research Highlights (http://www.nature.com/nature/journal/v464/n7288/full/464469a.html)

Swann, A.L., I.Y. Fung, S. Levis, G.B. Bonan, and S.C. Doney, 2010: Changes in Arctic vegetation amplify high-latitude warming through the greenhouse effect, Proc. Nat. Acad. Sci. USA, 107, 1295-1300, doi:10.1073/pnas.0913846107.

Udovydchenkov, I.A., T.F. Duda, S.C. Doney, and I.D. Lima, 2010: Modeling deep ocean shipping noise in varying acidity conditions, J. Acoustical Soc. America, 128(3), EL130-EL136, doi:10.1121/1.3402284.

Wanninkhof, R., S.C. Doney, J.L. Bullister, N.M. Levine, M. Warner, and N. Gruber, 2010: Detecting anthropogenic CO2 changes in the interior Atlantic Ocean between 1989 and 2005, J. Geophys. Res. Oceans, 115, C11028, doi:10.1029/2010JC006251.

Yoder, J.A., S.C. Doney, D.A. Siegel, and C. Wilson, 2010: Study of marine ecosystems and biogeochemistry now and in the future: examples of the unique contributions from space, Oceanography, 23(4), 104-117.

Yoder, J.A., M.A. Kennelly, S.C. Doney, I.D. Lima, 2010: Are trends in SeaWiFS chlorophyll time-series unusual relative to historic variability? Acta Oceanologica Sinica, 29(2), 1-4.


2009

Behrenfeld, M.J., T.K. Westberry, E.S. Boss, R.T. O’Malley, D.A. Siegel, J.D. Wiggert, B.A. Franz, C.R. McClain, G.C. Feldman, S.C. Doney, J.K. Moore, G. Dall’Olmo, A.J. Milligan, I. Lima, N. Mahowald, 2008. Satellite-detected fluorescence reveals global physiology of ocean phytoplankton. Biogeosciences, 6, 779-794.(www.biogeosciences.net/6/779/2009)

Birdsey, R., N. Bates, M. Behrenfeld, K. Davis, S.C. Doney, R. Feely, D.Hansell, L. Heath, E. Kasischke, H. Kheshgi, B. Law, C. Lee, A.D. McGuire, P. Raymond, and C.J. Tucker, 2009: Carbon cycle observations: gaps threaten climate mitigation policies, EOS, Trans.  American Geophys. Union, 90(34), 292-293.

Cooley, S.R. and S.C. Doney, 2009: Anticipating ocean acidification’s economic consequences for commercial fisheries, Environ. Res. Lett., 4, 024007, doi:10.1088/1748-9326/4/2/024007.

Cooley, S.R. and S.C. Doney, 2009: Ocean acidification’s impact on fisheries and societies: a U.S. perspective, Current-the Journal of Marine Education, 25(1), 15-19, National Marine Educators Association.

Cooley, S., H.L. Kite-Powell, S.C. Doney, 2009: Ocean acidification’s potential to alter global marine ecosystem services, Oceanography, 22(4), 172-180.

Doney, S., 2009: The consequences of human-driven ocean acidification for marinelife, F1000 Biology Reports 2009, 1:36, 4pp., doi: 10.3410/B1-36 http://www.f1000biology.com/f1000reports/articles/10.3410/b1-36/article.html

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Doney, S.C. and R.A. Feely, 2009: Ocean acidification, Education in Chemistry (Royal Society of Chemistry), 46(6), 182-187.

Doney, S.C. and D.M. Glover, 2009: Ocean carbon system, modeling of, in Encyclopedia of Ocean Sciences (second edition), ed. J. Steele, K.K. Turekian, and S.A. Thorpe, Elseiver, 4121-4130, doi:10.1016/B978-012374473-9.00631-7 (expanded and updated version of Doney and Glover, 2001).

Doney, S.C., W.M. Balch, V.J. Fabry, and R.A. Feely, 2009: Ocean acidification: a critical emerging problem for the ocean sciences, Oceanography, 22(4), 16-25.

Doney, S.C., V.J. Fabry, R.A. Feely, J.A. Kleypas, 2009: Ocean acidification: the other CO2 problem, Ann. Rev. Mar. Sci., 1, 169-192, 10.1146/annurev.marine.010908.163834
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Doney, S.C., I. Lima, R.A. Feely, D.M. Glover, K. Lindsay, N. Mahowald, J.K. Moore, and R. Wanninkhof, 2009: Mechanisms governing interannual variability in upper-ocean inorganic carbon system and air-sea CO2 fluxes: physical climate and atmospheric dust, Deep-Sea Res. II, 56, 640-655.

Doney, S.C
., I. Lima, J.K. Moore, K. Lindsay, M.J. Behrenfeld, T.K. Westberry, N. Mahowald, D.M. Glover, and T. Takahashi, 2009: Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data, J. Mar. Systems, 76, 95-112, doi:10.1016/j.jmarsys.2008.05.015.

Doney, S.C., B. Tilbrook, S. Roy, N. Metzl, C. Le Quéré, M. Hood, R.A. Feely,and D. Bakker, 2009: Surface ocean CO2 variability and vulnerability, Deep-Sea Res. II, 56, 504-511.

Ducklow, H.W., S.C. Doney, D.K. Steinberg 2009: Contributions of Long-Term Research and Time-Series Observations to Marine Ecology and Biogeochemistry.  Annual Review of Marine Science, (1), 279-302, doi:10.1146/annurev.marine.010908.163801
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Feely, R.A., S.C. Doney and S.R. Cooley, 2009: Ocean acidification: present conditions and future changes in a high-CO2 world, Oceanography, 22(4), 36-47.

Friedrichs, M.A.M., M.-E. Carr, R.T. Barber, M. Scardi, D. Antoine, R.A. Armstrong, I. Asanuma, M.J. Behrenfeld, E.T. Buitenhuis, F. Chai, J.R. Christian, A.M. Ciotti, S.C. Doney, M. Dowell, J. Dunne, B. Gentili, W. Gregg, N. Hoepffner, J. Ishizaka, T. Kameda, I. Lima, J. Marra, F. Mélin, J.K. Moore, A. Morel, R.T. O’Malley, J. O’Reilly, V.S. Saba, M. Schmeltz, T.J. Smyth, J. Tjiputra, K. Waters, T.K. Westberry, A. Winguth, 2009: Assessing the uncertainties of model estimates of primary productivity in the tropical Pacific Ocean, J. Mar. Systems, 76, 113-133, doi:10.1016/j.jmarsys.2008.05.010.

Frölicher, T.L., F. Joos, G.-K. Plattner, M. Steinacher, and S.C. Doney, 2009: Natural variability and anthropogenic trends in oceanic oxygen in a coupled carbon cycle-climate model ensemble, Global Biogeochem. Cycles, 23, GB1003, doi:10.1029/2008GB003316.

Gregg, W.W., M.A.M. Friedrichs, A.R. Robinson, K.A. Rose, R. Schlitzer, K.R. Thompson, and S.C. Doney, 2009: Skill assessment in ocean biological data assimilation, J. Mar. Systems, 76, 16-33, doi:10.1016/j.jmarsys.2008.05.006.

Gruber, N. and S.C. Doney, 2009: Modeling of ocean biogeochemistry and ecology, in Encyclopedia of Ocean Sciences (second edition), ed. J. Steele, K.K. Turekian, and S.A. Thorpe, Elseiver, 4105-4120, doi:10.1016/B978-012374473-9.00741-4.

Gruber, N., M. Gloor, S.E. Mikaloff Fletcher, S.C. Doney, S. Dutkiewicz, M.J. Follows, M. Gerber, A.R. Jacobson, F. Joos, K. Lindsay, D. Menemenlis, A.  Mouchet, S.A. Müller, J.L. Sarmiento, and T. Takahashi, 2009: Oceanic sources, sinks, and transport of atmospheric CO2, Global Biogeochem. Cycles, 23, GB1005, doi:10.1029/2008GB003349.

Hynes, A.M., P.D. Chappell, S.T. Dyhrman, S.C. Doney, and E.A. Webb, 2009: Cross-basin comparison of phosphorus stress and nitrogen fixation in Trichodesmium, Limnol. Oceanogr., 54, 1438-1448.

Intergovernmental Oceanographic Commission of UNESCO and the International CLIVAR Project Office, 2009: Hood, M. (ed.), Ship-based Repeat Hydrography: A Strategy for a Sustained Global Programme. IOC Technical Series, 89. IOCCP Reports, 17. ICPO Publication 142. UNESCO.

Krishnamurthy, A., J.K. Moore, N. Mahowald, C. Luo, S.C. Doney, K. Lindsay, C.S. Zender, 2009: Impacts of increasing anthropogenic soluble iron and nitrogen deposition on ocean biogeochemistry, Global Biogeochem. Cycles, 23, GB3016, doi:10.1029/2008GB003440.

Joint, I., D.M. Karl, S.C. Doney, E.V. Armbrust, W. Balch, M. Berman, C. Bowler, M. Church, A. Dickson, J. Heidelberg, D.  Iglesias-Rodriguez, D. Kirchman, Z. Kolber, R. Letelier, C. Lupp, S. Maberly, S. Park, J. Raven, D.J. Repeta, U. Riebesell, G. Steward, P. Tortell, R.E. Zeebe and J.P. Zehr, 2009: Consequences of high CO2 and ocean acidification for microbes in the global ocean, Report of expert meeting at U. Hawaii, 24-26 February 2009 organized by Plymouth Marine Laboratory and Center for Microbial Oceanography Research and Education, 23pp.

Le Quéré, C., M.R. Raupach, J.G. Canadell, G. Marland, L. Bopp, P. Ciais, T.J. Conway, S.C. Doney, R.A. Feely, P. Foster, P. Friedlingstein, K. Gurney, R.A. Houghton, J.I. House, C. Huntingford, P.E. Levy, M.R. Lomas, J. Majkut, N. Metzl, J.P. Ometto, G.P. Peters, I.C. Prentice, J.T. Randerson, S.W. Running, J.L. Sarmiento, U. Schuster, S. Sitch, T. Takahashi, N. Viovy, G.R. van der Werf, and F.I. Woodward, 2009: Trends in the sources and sinks carbon dioxide, Nat. Geosci., 2, 831-836, doi:10.1038/ngeo689.

Levine, N.M., M.L. Bender, and S.C. Doney, The δ18O of dissolved O2 as a tracer of mixing and respiration in the mesopelagic ocean, Global Biogeochem. Cycles, 23, GB1006, doi:10.1029/2007GB003162.

Marshall, J., A. Andersson, N. Bates, W. Dewar, S. Doney, J. Edson, R. Ferrari, G. Forget, D. Fratantoni, M. Gregg, T. Joyce, K. Kelly, S. Lozier, R. Lumpkin, G. Maze, J. Palter, R. Samelson, K. Silverthorne, E. Skyllingstad, F. Straneo, L. Talley, L. Thomas, J. Toole, and R. Weller, 2009: The CLIMODE field campaign: observing the cycle of convection and restratification over the Gulf Stream, Bull. Amer. Meteor. Soc., 90, 1337-1350.

Montes-Hugo, M., H. Ducklow, S. Doney, W. Fraser, D. Martinson, S. Stammerjohn, and O. Schofield, 2009: Recent changes in phytoplankton communities associated with rapid regional climate change along the western Antarctic Peninsula, Science, 323, 1470-1473.

Paytan, A., K.R.M. Mackey, Y. Chen, I.D. Lima, S.C. Doney, N. Mahowald, R. Labiosa, and A.F. Post, 2009: Toxicity of atmospheric aerosols on marine phytoplankton, Proc. Nat. Acad. Sci. USA, 106, 4601-4605, 10.1073/pnas.0811486106.

Randerson, J.T., F.M. Hoffman, P.E. Thornton, N.M. Mahowald, K. Lindsay, Y.-H. Lee, C.D. Nevison, S.C. Doney, G. Bonan, R. Stöckli, C. Covey, S.W. Running,and I.Y. Fung, 2009: Systematic assessment of terrestrial biogeochemistry in coupled climate-carbon models, Global Change Biology, 15, 2462-2484, doi:10.1111/j.1365-2486.2009.01912.x   http://www3.interscience.wiley.com/cgi-bin/fulltext/122374110/PDFSTART .

Rodgers, K.B., R.M. Key, A. Gnanadesikan, J.L. Sarmiento, O. Aumont, L. Bopp, S.C. Doney, J.P. Dunne, D.M. Glover, A. Ishida, M. Ishii, A.R. Jacobson, C. Lo Monaco, E. Maier-Reimer, H. Mercier, N. Metzl, F.F. Pérez, A.F. Rios, R. Wanninkhof, P. Wetzel, C.D. Winn, and Y. Yamanaka, 2009: Using altimetry to help explain patchy changes in hydrographic carbon measurements, J. Geophys. Res. Oceans, 114, C09013, doi:10.1029/2008JC005183.

Stanley, R.H.R., W.J. Jenkins, D.E. Lott III, and S.C. Doney, 2009: Noble gas constraints on air-sea gas exchange and bubble fluxes, J. Geophys. Res. Ocean, 114, C11020, doi:10.1029/2009JC005396.

Steinacher, M., F. Joos, T.L. Frölicher, G.-K. Plattner, and S.C. Doney, 2009: Imminent ocean acidification in the Arctic projected with the NCAR global coupled carbon cycle-climate model, Biogeosciences, 6, 515-533.

Stow, C.A. J. Jolliff, D.J. McGillicuddy Jr., S.C. Doney, J.I. Allen, M.A.M. Friedrichs, K.A. Rose, and P. Wallhead, 2009: Skill assessment for coupled biological/physical models of marine systems, J. Mar. Systems, 76, 4-15, doi:10.1016/j.jmarsys.2008.03.011.

Thornton, P.E., S.C. Doney, K. Lindsay, J.K. Moore, N. Mahowald, J.T. Randerson, I. Fung, J.-F. Lamarque, J.J. Feddema, and Y.-H. Lee, 2009: Carbon-nitrogen interactions regulate climate-carbon cycle feedbacks: results from an atmosphere-ocean general circulation model, Biogeosciences, 6, 2099-2120.



2008

Boyd, P., S.C. Doney, R. Strzepek, J. Dusenberry, K. Lindsay, and I. Fung, 2008: Climate-mediated changes to mixed-layer properties in the Southern Ocean: assessing the phytoplankton response Biogeosciences, 5, 847-864.  http://www.biogeosciences.net/5/847/2008/bg-5-847-2008.pdf

Buesseler, K.O., S.C. Doney, D.M. Karl, P.W. Boyd, K. Caldeira, F. Chai, K. Coale, H.J.W. de Baar, P.G. Falkowski, K.S. Johnson, R.S. Lampitt, A.F. Michaels, S.W.A. Naqvi, V. Smetacek, S. Takeda, and A.J. Watson, 2008: Ocean iron fertilization:  moving forward in a sea of uncertainty, Science, 319, 162, DOI: 10.1126/science.1154305.

Casciotti, K.L., T. Trull, D.M. Glover, and D. Davies, 2008, Constraints on nitrogen cycling at the subtropical North Pacific Station ALOHA from isotopic measurements of nitrate and particulate nitrogen, Deep-Sea Res. II, doi:10.1016/j.dsr2.2008.04.017, 55, 1661–1672.

Goodkin, N.F., K.A. Hughen, W.B. Curry, S.C. Doney, and D.R. Ostermann, 2008: Sea surface temperature and salinity variability at Bermuda during the end of the Little Ice Age, Paleoceanography, 23, PA3203, doi:10.1029/2007PA001532.

Goodkin, N.F., K.A. Hughen, S.C. Doney, and W.B. Curry, 2008: Increased multidecadal variability of the North Atlantic Oscillation since 1781, Nature Geosciences, 1, 844 - 848, doi: 10.1038/ngeo352.

Jin, X., N. Gruber, H. Frenzel, S.C. Doney, and J.C. McWilliams, 2008: The impact on atmospheric CO2 of iron fertilization induced changes in the ocean’s biological pump, Biogeosciences, 5, 385-406.  http://www.biogeosciences.net/5/385/2008/bg-5-385-2008.pdf

Krishnamurthy, A., J.K. Moore, and S.C. Doney, 2008: The effects of dilution and mixed layer depth on deliberate ocean iron fertilization: 1-D simulations of the southern ocean iron experiment (SOFeX), J. Mar. Systems, 71, 112-130.  DOI:10.1016/j.jmarsys.2007.07.002

Levine, N.M, S.C. Doney, R. Wanninkhof, K. Lindsay, and I. Fung, 2008: Impact of ocean carbon system variability on the detection of temporal increases in anthropogenic CO2, J. Geophys. Res. Oceans, 113, C03019, DOI:10.1029/2007JC004153.

Lovenduski, N.S., N. Gruber, and S.C. Doney, 2008: Toward a mechanistic understanding of the decadal trends in the Southern Ocean carbon sink, Global Biogeochem. Cycles, 22, GB3016, doi:10.1029/2007GB003139.

Nevison, C.D., N.M. Mahowald, S.C. Doney, I.D. Lima, 2008: Impact of variable air-sea O2 and CO2 fluxes on atmospheric potential oxygen (APO) and land-ocean carbon sink partitioning, Biogeosciences, 5, 875-889.

Nevison, C.D., N.M. Mahowald, S.C. Doney, I.D. Lima, G.R. van der Werf, J.T. Randerson, D.F. Baker, P. Kasibhatla, and G.A. McKinley, 2008: Contribution of ocean, fossil fuel, land biosphere and biomass burning carbon fluxes to seasonal and interannual variability in atmospheric CO2, J. Geophys. Res. Biogeosci., 113, G01010, DOI:10.1029/2007JG000408.

Schneider, B., L. Bopp, M. Gehlen, J. Segschneider, T.L. Frölicher, P. Cadule, P. Friedlingstein, S.C. Doney, M.J. Behrenfeld, and F. Joos, 2008:  Climate-induced interannual variability of marine primary and export production in three global coupled climate carbon cycle models, Biogeosciences, 5, 597-614.  http://www.biogeosciences.net/5/597/2008/bg-5-597-2008.pdf

Thomas, H., A.E. Friederike Prowe, I.D. Lima, S.C. Doney, R. Wanninkhof, R.J. Greatbatch, U. Schuster, and A. Corbière, 2008: Changes in the North Atlantic Oscillation influence CO2 uptake in the North Atlantic over the past two decades, Global Biogeochem. Cycles, 22, GB4027, doi:10.1029/2007GB003167.

Toole, D.A., D.A. Siegel, and S.C. Doney, 2008: An ultraviolet light-driven 1-D DMS biogeochemcial cycling model for the Sargasso Sea, J. Geophys. Res. Biogeosci., 113, G02009, doi:10.1029/2007JG000426.


2007

Caldeira, K., D. Archer, J.P. Barry, R.G.J. Bellerby, P.G. Brewer, L. Cao, A.G. Dickson, S.C. Doney, H. Elderfield, V.J. Fabry, R.A. Feely, J.-P. Gattuso, P.M. Haugan, O. Hoegh-Guldberg, A.K. Jain, J.A. Kleypas, C. Langdon, J.C. Orr, A. Ridgwell, C.L. Sabine, B.A. Seibel, Y. Shirayama, C. Turley, A.J. Watson, and R.E. Zeebe,  Comment on “Modern-age buildup of CO2 and its effects on seawater acidity and salinity” by Hugo A. Loaiciga, Geophys. Res. Lett., 34, L18608, doi:10.1029/2006GL027288.

Doney, S.C. and D.S. Schimel, 2007: Carbon and climate system coupling on timescales from the Precambrian to the Anthropocene, Ann. Rev. Environ. Resources, 32, 31-66, doi:10.1146/annurev.energy.32.041706.124700.
This chapter's eprint is available at the following URL:
http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.energy.32.041706.124700

Doney, S.C., and D.S. Schimel, 2007: Climate change and biogeochemical impacts, Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester http://www.els.net/, doi:10.1002/9780470015902.a0003242.pub2 (updated and revised version of Doney and Schimel, ELS, 2001).

Doney, S.C., N. Mahowald, I. Lima, R.A. Feely, F.T. Mackenzie, J.-F. Lamarque, and P.J. Rasch, 2007: The impact of anthropogenic atmospheric nitrogen and sulfur deposition on ocean acidification and the inorganic carbon system, Prod. Nat. Acad. Sci. USA, 104, 14580-14585, doi:10.1073/pnas.0702218104.

Doney, S.C., S. Yeager, G. Danabasoglu, W.G. Large, and J.C. McWilliams, 2007: Mechanisms governing interannual variability of upper ocean temperature in a global hindcast simulation, J. Phys. Oceanogr., 37, 1918-1938.  http://ams.allenpress.com/archive/1520-0485/37/7/pdf/i1520-0485-37-7-1918.pdf

Frew, N.M., D.M. Glover, E.J. Bock, and S.J. McCue, 2007, A new approach to estimation of global air-sea gas transfer velocity fields using dual-frequency altimeter backscatter, J. Geophys. Res., 112, C11003, doi:10.1029/2006JC003819.

Friedrichs, M.A.M., J.A. Dusenberry, L.A. Anderson, R. Armstrong, F. Chai, J.R. Christian, S.C. Doney, J. Dunne, M. Fujii, R. Hood, D. McGillicuddy, J.K. Moore, M. Schartau, Y.H. Spitz, and J.D. Wiggert, 2007: Assessment of skill and portability in regional marine biogeochemical models: the role of multiple planktonic groups, J. Geophys. Res. Oceans, 112, C08001, doi:10.1029/2006JC003852.

Glover, D.M., N.M. Frew, and S.J. McCue, 2007, Air-sea gas transfer velocity estimates from the Jason-1 and TOPEX altimeters: Prospects for a long-term global time series, J. Mar. Systems, 66, doi:10.1016/j.jmarsys.2006.03.020, 173–181.

Jin, X., R.G. Najjar, F. Louanchi, and S.C. Doney, 2007: A modeling study of the seasonal oxygen budget of the global ocean, J. Geophys. Res. Oceans, 112, C05017, doi:10.1029/2006JC003731.

Lovenduski, N.S., N. Gruber, S.C. Doney, and I.D. Lima, 2007: Enhanced CO2 outgassing in the Southern Ocean from a positive phase of the Southern Annular Mode, Global Biogeochem. Cycles, 21, GB2026, doi:10.1029/2006GB002900.

Mikaloff Fletcher, S.E., N. Gruber, A.R. Jacobson, M. Gloor, S.C. Doney, S. Dutkiewicz, M. Gerber, M. Follows, F. Joos, K. Lindsay, D. Menemenlis, A. Mouchet, S.A. Muller, and J.L. Sarmiento, 2007: Inverse estimates of the oceanic sources and sinks of natural CO2 and their implied oceanic transport, Global Biogeochem. Cycles, 21, GB1010, 10.1029/2006GB002751.

Miller, C.E., D. Crisp, P.L. DeCola, S.C. Olsen, J.T. Randerson, A. Michalak, A. Alkhaled, P. Rayner, D.J. Jacob, P. Suntharalingam, D.B.A. Jones, A.S. Denning, M.E. Nicholls, S.C. Doney, S. Pawson, H. Boesch, B.J. Connor, I.Y. Fung, D. O’Brien, R.J. Salawitch, S.P. Sander, B. Sen, P. Tans, G.C. Toon, P.O. Wennberg, S.C. Wofsy, Y.L. Yung, and R.M. Law, 2007: Precision requirements for space-based XCO2 data, J. Geophys. Res. Atmos., 112, D10314, doi:10.1029/2006JD007659.

Moore, J.K., and S.C. Doney, 2007: Iron availability limits the ocean nitrogen inventory stabilizing feedbacks between marine denitrification and nitrogen fixation, Global Biogeochem. Cycl., 21, GB2001, doi:10.1029/2006GB002762.

Najjar, R.G., X. Jin, F. Louanchi, O. Aumont, K. Caldeira, S.C. Doney, J.-C. Dutay, M. Follows, N. Gruber, F. Joos, K. Lindsay, E. Maier-Reimer, R.J. Matear, K. Matsumoto, P. Monfray, A. Mouchet, J.C. Orr, G.K. Plattner, J.L. Sarmiento, R. Schlitzer, R.D. Slater, M.-F. Weirig, Y. Yamanaka and A. Yool, 2007: Impact of circulation on export production, dissolved organic matter and dissolved oxygen in the ocean:  Results from Phase II of the Ocean Carbon-cycle Model Intercomparison Project (OCMIP-2), Global Biogeochem. Cycles, 21, GB3007, doi:10.1029/2006GB002857.

Patra, P.K., J.K. Moore, N. Mahowald, M. Uematsu, S.C. Doney, and T. Nakazawa, 2007: Exploring the sensitivity of interannual basin-scale air-sea CO2 fluxes to variability in atmospheric dust deposition using ocean carbon models and atmospheric CO2 inversions, J. Geophys. Res. Biogeosci., 112, G02012, doi:10.1029/2006JG000236.

Thomas, H., A.E.F. Prowe, S. van Heuven, Y. Bozec, H.J.W. de Baar, L.-S. Schiettecatte, K. Suykens, M. Koné, A.V. Borges, I.D. Lima, and S.C. Doney, 2007: Rapid decline of the CO2 buffering capacity in the North Sea and implications for the North Atlantic Ocean, Global Biogeochem. Cycles, 21, GB4001, doi:10.1029/2006GB002825.

2006

Bryan, F., G. Danabasoglu, N. Nakashiki, Y. Yoshida, D.-H. Kim, J. Tsutsui, and S. Doney, 2006: Response of the North Atlantic thermohaline circulation and ventilation to increasing carbon dioxide in CCSM3, J. Climate, 19(11), 2382-2397.  http://ams.allenpress.com/archive/1520-0442/19/11/pdf/i1520-0442-19-11-2382.pdf

Collins, W.D., M. Blackmon, C.M. Bitz, G.B Bonan, C.S. Bretherton, J.A. Carton, P. Chang, S. Doney, J.J. Hack, J.T. Kiehl, T. Henderson, W.G. Large, D. McKenna, and B.D. Santer, 2006: The Community Climate System Model: CCSM3, J. Climate, 19(11), 2122-2143.  http://ams.allenpress.com/archive/1520-0442/19/11/pdf/i1520-0442-19-11-2122.pdf

Doney, S.C., 2006: Plankton in a warmer world, Nature, 444, 695-696.  DOI:10.1038/444695a
Baker, D.F., S.C. Doney, and D.S. Schimel, 2006: Variational data assimilation for atmospheric CO2, Tellus B, 58, 359-365.  DOI: 10.1111/j.1600-0889.2006.00218.x

Doney, S.C. and H.W. Ducklow, 2006: A decade of synthesis and modeling in the U.S. Joint Global Ocean Flux Study, Deep-Sea Res. II, 53(5-7), 451-458.  doi:10.1016/j.dsr2.2006.01.019 

Doney, S.C., K. Lindsay, I. Fung and J. John, 2006: Natural variability in a stable 1000 year coupled climate-carbon cycle simulation, J. Climate, 19(13), 3033-3054.  http://ams.allenpress.com/archive/1520-0442/19/13/pdf/i1520-0442-19-13-3033.pdf

Friedlingstein, P., P. Cox, R. Betts, L. Bopp, W. von Bloh, V. Brovkin, P. Cadule, S. Doney, M. Eby, I. Fung, G. Bala, J. John, C. Jones, F. Joos, T. Kato, M. Kawamiya, W. Knorr, K. Lindsay, H.D. Matthews, T. Raddatz, P. Rayner, C. Reick, E. Roeckner, K.-G. Schnitzler, R. Schnur, K. Strassmann, A.J. Weaver, C. Yoshikawa, and N. Zeng, 2006: Climate–carbon cycle feedback analysis: Results from the C4MIP model intercomparison, J. Climate, 19(14), 3337-3353.  http://ams.allenpress.com/archive/1520-0442/19/14/pdf/i1520-0442-19-14-3337.pdf

Gent, P.R., F.O. Bryan, G. Danabasoglu, K. Lindsay, D. Tsumune, M.W. Hecht, and S.C. Doney, 2006: Ocean chlorofluorocarbon and heat uptake during the twentieth century in the CCSM3, J. Climate, 19(11), 2366-2381.  http://ams.allenpress.com/archive/1520-0442/19/11/pdf/i1520-0442-19-11-2366.pdf

Glover, D.M., C.L. Chandler, S.C. Doney, K.O. Buesseler, G. Heimerdinger, J.K.B. Bishop, and G.R. Flierl, 2006: The U.S. JGOFS data management experience, Deep-Sea Res. II, 53(5-7), 793-802.  doi:10.1016/j.dsr2.2006.01.018

Gruber, N., H. Frenzel, S.C. Doney, P. Marchesiello, J.C. McWilliams, J.R. Moisan, J.J. Oram, G.-K. Plattner, and K.D. Stolzenbach, 2006: Eddy-resolving simulation of plankton ecosystem dynamics in the California Current System, Deep-Sea Res. I, 53, 1483-1516, doi:10.1016/j.dsr.2006.06.005.

Hood, R.R., E.A. Laws, R.A. Armstrong, N.R. Bates, C.W. Brown, C.A. Carlson, F. Chai, S.C. Doney, P.G. Falkowski, R.A. Feely, M.A.M. Friedrichs, M.R. Landry, J.K. Moore, D.M. Nelson, T.L. Richardson, B. Salihoglu, M. Schartau, D.A. Toole, and J.D. Wiggert, 2006: Pelagic functional group modeling: progress, challenges and prospects, Deep-Sea Res. II, 53(5-7), 459-512.  doi:10.1016/j.dsr2.2006.01.025 

Johnson, G.C., and S.C. Doney, 2006: Recent western South Atlantic bottom water warming, Geophys. Res. Lett., 33(14), L14614, doi:10.1029/2006GL026769.

McKinley, G.A., T. Takahashi, E. Butenhuis, F. Chai, J.R. Christian, S.C. Doney, M.-S. Jiang, K. Lindsay, J.K. Moore, C. Le Quere, I. Lima, R. Murtugudde, L. Shi, and P. Wetzel, 2006: North Pacific carbon cycle response to climate variability on seasonal to decadal timescales, J. Geophys. Res. Oceans, 111, C07S06, doi:10.1029/2005JC003173.

Mikaloff Fletcher, S.E., N. Gruber, A.R. Jacobson, S.C. Doney, S. Dutkiewicz, S. Gerber, M. Follows, F. Joos, K. Lindsay, D. Menemenlis, A. Mouchet, S.A. Muller, and J.L. Sarmiento, 2006: Inverse estimates of anthropogenic CO2 uptake, transport, and storage by the ocean, Global Biogeochem. Cycles, 20, GB2002, doi:10.1029/2005GB002530.

Moore, J.K., and S.C. Doney, 2006: Remote sensing observations of ocean physical and biological properties in the region of the SOFeX iron fertilization experiment, 2006: J. Geophys. Res. Oceans, 111, C06026, doi:10.1029/2005JC003289.

Moore, J.K., S.C. Doney, K. Lindsay, N. Mahowald, and A.F. Michaels, 2006: Nitrogen fixation amplifies the ocean biogeochemical response to decadal timescale variations in mineral dust deposition, Tellus B, 58, 560-572.  DOI: 10.1111/j.1600-0889.2006.00209.x

Rothstein, L., M. Abbott, E. Chassignet, J. Cullen, K. Denman, S. Doney, H. Ducklow, K. Fennel, M. Follows, D. Haidvogel, E. Hofmann, D. Karl, J. Kindle, I. Lima, M. Maltrud, C. McClain, D. McGillicuddy, J. Olascoa, Y. Spitz, J. Wiggert, and J. Yoder, 2006: Modeling ocean ecosystems: The PARADIGM Program, Oceanography, 19, 16-45. http://www.tos.org/oceanography/issues/issue_archive/issue_pdfs/19_1/19.1_rothstein_et_al.pdf

Stanley, R.H.R., W.J. Jenkins, and S.C. Doney, 2006: Quantifying seasonal air-sea gas exchange processes using noble gas time-series: a design experiment, J. Mar. Res., 64(2), 267-295.  DOI: 10.1357/002224006777606452 

2005

Bonfils, C., A. Angert, C. Henning, S. Biraud, S.C. Doney, and I. Fung, 2005: Extending the record of photosynthetic activity over the eastern United States into the pre-satellite period using surface diurnal temperature range, Geophysical Res. Lett., 32, L08405, doi:10.1029/2005GL022583.

Fung, I., S.C. Doney, K. Lindsay, and J. John, 2005: Evolution of carbon sinks in a changing climate, Proc. Nat. Acad. Sci. (USA), 102, 11201-11206, doi:10.1073/pnas.0504949102.

Orr, J.C., V.J. Fabry, O. Aumont, L. Bopp, S.C. Doney, R.A. Feely, A. Gnanadesikan, N. Gruber, A. Ishida, F. Joos, R.M. Key, K. Lindsay, E. Maier-Reimer, R. Matear, P. Monfray, A. Mouchet, R.G. Najjar, G.-K. Plattner, K.B. Rodgers, C.L. Sabine, J.L. Sarmiento, R. Schlitzer, R.D. Slater, I.J. Totterdell, M.-F. Weirig, Y. Yamanaka, and A. Yool, 2005: Anthropogenic ocean acidification over the twenty-first century and its impact on marine calcifying organisms, Nature, 437, 681-686, doi:10.1038/nature04095.

2004

Bailey, B.A., S.C. Doney, and I.D. Lima, 2004: Quantifying the effects of dynamical noise on the predictability of simple ecosystem model, Environmetrics, 15, 337-355, doi:10.1002/env.645.

Bonfils, C., I. Fung, S. Doney, and J. John, 2004: On the detection of summertime terrestrial photosynthetic variability from its atmospheric signature, Geophys. Res. Lett., 31, L09207, doi: 10.1029/2004GL019453.

Crisp, D., R.M. Atlas, F.-M. Breon, L.R. Brown, J.P. Burrows, P. Ciais, B.J. Connor, S.C. Doney, I.Y. Fung, D.J. Jacob, C.E. Miller,  D. O'Brien, S. Pawson, J.T. Randerson, P. Rayner, R.J. Salawitch, S.P. Sander, B. Sen, G.L. Stephens, P.P. Tans, G.C. Toon, P. O. Wennberg, S.C. Wofsy, Y.L. Yung, Z. Kuang, B. Chudasama, G. Sprague, B. Weiss, R. Pollock, D. Kenyon, S. Schroll, 2004: The Orbiting Carbon Observatory (OCO) Mission, Advanc. Space Res., 34, 700-709. DOI:10.1016/j.asr.2003.08.062

Doney, S.C., M.R. Abbott, J.J. Cullen, D.M. Karl, and L. Rothstein, 2004: From genes to ecosystems: the ocean’s new frontier, Frontiers Ecology Environ., 2, 457-466.

Doney, S.C., K. Lindsay, K. Caldeira, J.-M. Campin, H. Drange, J.-C. Dutay, M. Follows, Y. Gao, A. Gnanadesikan, N. Gruber, A. Ishida, F. Joos, G. Madec, E. Maier-Reimer, J.C. Marshall, R.J. Matear, P. Monfray, A. Mouchet, R. Najjar, J.C. Orr, G.-K. Plattner, J. Sarmiento, R. Schlitzer, R. Slater, I.J. Totterdell, M.-F. Weirig, Y. Yamanaka, A. Yool, 2004: Evaluating global ocean carbon models: the importance of realistic physics, Global Biogeochem. Cycles, 18, GB3017, doi:10.1029/2003GB002150.

Geels, C., S.C. Doney, R. Dargaville, J. Brandt, and J.H. Christensen, 2004: Investigating the sources of synoptic variability in atmospheric CO2 measurements over the Northern Hemisphere continents: A regional model study. Tellus B, 56, 35-50.  DOI: 10.1111/j.1600-0889.2004.00084.x

Lima, I. and S.C. Doney, 2004: A three-dimensional, multi-nutrient, size-structured ecosystem model for the North Atlantic, Global Biogeochem. Cycles, 18, GB3019, doi:10.1029/2003GB002146.

Matsumoto, K., J.L. Sarmiento, R.M. Key, J.L. Bullister, K. Caldeira, J.-M. Campin, S.C. Doney, H. Drange, J.-C. Dutay, M. Follows, Y. Gao, A. Gnanadesikan, N. Gruber, A. Ishida, F. Joos, K. Lindsay, E. Maier-Reimer, J.C. Marshall, R.J. Matear, P. Monfray, R. Najjar, G.-K. Platter, R. Schlitzer, R. Slater, P.S. Swathi, I.J. Totterdell, M.-F. Weirig, Y. Yamanaka, A. Yool, and J.C. Orr, 2004: Evaluation of ocean carbon cycle models with data-based metrics, Geophys. Res. Lett., 31, L07303, doi:10.1029/2003GL018970.

Moore, J.K., S.C. Doney and K. Lindsay, 2004: Upper ocean ecosystem dynamics and iron cycling in a global 3-D model, Global Biogeochem. Cycles, 18, 4, GB4028, 10.1029/2004GB002220.

Sarmiento, J., R. Slater, R .Barber, L. Bopp, S.C. Doney, A.C. Hirst, J. Kleypas, R. Matear, U. Mikolajewicz, P. Monfray, V. Soldatov, S. Spall, R. Slater, and R. Stouffer, 2004: Response of ocean ecosystems to climate warming, Global Biogeochem. Cycles, 18, GB3003, doi:10.1029/2003GB002134.

Stark, S., W.J. Jenkins, and S.C. Doney, 2004: Deposition and recirculation of tritium in the North Pacific Ocean, J. Geophys. Res., Oceans, 109 (C6), C06009, 10.1029/2003JC002150.

2003

Boyd, P. and S.C. Doney, 2003: The impact of climate change and feedback process on the ocean carbon cycle. Ocean Biogeochemistry, ed. M. Fasham, Springer, 157-193.

Dargaville, R.J., S.C. Doney, and I.Y. Fung, 2003: Inter-annual variability in the interhemispheric atmospheric CO2 gradient: Contributions from transport and the seasonal rectifier. Tellus B, 55, 711-722.  DOI: 10.1034/j.1600-0889.2003.00038.x

Dilling, L., S.C. Doney, J. Edmonds, K.R. Gurney, R. Harriss, D. Schimel, B. Stephens, G. Stokes, 2003: The role of carbon cycle observations and knowledge in carbon management, Ann. Rev. Environ. Resourc., 28, 521-558, doi: 10.1146/annurev.energy.28.011503.163443.

Doney, S.C., D.M. Glover, M. Fuentes, and S. McCue, 2003: Mesoscale variability of Sea-viewing Wide Field-of-view Sensor (SeaWiFS) satellite ocean color: Global patterns and spatial scales, J. Geophys. Res., Oceans., 108(C2), 3024, doi:10.1029/2001JC000843.

Doney, S.C., K. Lindsay, J.K. Moore, 2003: Global ocean carbon cycle modeling, Ocean Biogeochemistry, ed. M. Fasham, Springer, 217-238.

Jenkins, W.J. and S.C. Doney, 2003: The subtropical nutrient spiral, Global Biogeochem. Cycles,17(4), 1110, doi:10.1029/2003GB002085.

McGillicuddy, D.J., Jr., L.A. Anderson, S.C. Doney, and M.E. Maltrud, 2003: Eddy-driven sources and sinks of nutrients in the upper ocean: Results from a 0.1 resolution model of the North Atlantic, Global Biogeochem. Cycles, 17(2), 1035, doi:10.1029/2002GB001987.

2002

Boyd, P.W., S.C. Doney, 2002: Modelling regional responses by marine pelagic ecosystems to global climate change, Geophys. Res. Lett., 29(16), 1806, doi:10.1029/2001GL014130.

Doney, S.C. and M.W. Hecht, 2002: Antarctic Bottom Water formation and deep water chlorofluorocarbon distributions in a global ocean climate model, J. Phys. Oceanogr., 32, 1642-1666.  http://ams.allenpress.com/archive/1520-0485/32/6/pdf/i1520-0485-32-6-1642.pdf

Doney, S.C., J.A. Kleypas, J.L. Sarmiento, and P.G. Falkowski, 2002: The US JGOFS Synthesis and Modeling Project-An introduction, Deep-Sea Res. II, 49, 1-20.  doi:10.1016/S0967-0645(01)00092-3

Dutay, J.-C., J.L. Bullister, S.C. Doney, J.C. Orr, R. Najjar, K. Caldeira, J.-M. Champin, H. Drange, M. Follows, Y. Gao, N. Gruber, M.W. Hecht, A. Ishida, F. Joos, K. Lindsay, G. Madec, E. Maier-Reimer, J.C. Marshall, R.J. Matear, P. Monfray, G.-K. Plattner, J. Sarmiento, R. Schlitzer, R. Slater, I.J. Totterdell, M.-F. Weirig, Y. Yamanaka, and A. Yool, 2002: Evaluation of ocean model ventilation with CFC-11: comparison of 13 global ocean models. Ocean Modelling, 4, 89-120.  doi:10.1016/S1463-5003(01)00013-0 

Glover, D.M., S.C. Doney, A.J. Mariano, R.H. Evans, and S.J. McCue, 2002: Mesoscale variability in time-series data: Satellite-based estimates for the U.S. JGOFS Bermuda Atlantic Time-Series Study (BATS) site, J. Geophys. Res., Oceans, 107(C8), 3092, doi:10.1029/2000JC000589.

Glover, D.M., N.M. Frew, S.J. McCue, and E.J. Bock, 2002a, A Multi-year Time Series of Global Gas Transfer Velocity from the TOPEX Dual Frequency, Normalized Radar Backscatter Algorithm, In: Gas Transfer at Water Surfaces, M. Donelan, W. Drennan, E. Saltzman, and R. Wanninkhof (eds), Geophysical Monograph 127, American Geophysical Union, Washington, DC, 325–331.

Iglesias-Rodriguez, M.D., C.W. Brown, S.C. Doney, J. Kleypas, D. Kolber, Z. Kolber, P.K. Hayes, and P.G. Falkowski, 2002: Representing key phytoplankton functional groups in ocean carbon cycle models: coccolithophores, Global Biogeochem. Cycles, 16(4), 1100, doi:10.1029/2001GB001454.

Lima, I.D., D.B. Olson, and S.C. Doney, 2002: Biological response to frontal dynamics and mesoscale variability in oligotrophic environments: a numerical modeling study, J. Geophys. Res., Oceans, 107(C8), 3111, doi: 10.1029/2000JC000393

Lima, I, D.B. Olson and S.C. Doney, 2002:  Intrinsic dynamics and stability properties of size-structured pelagic ecosystem models. J. Plankton Res., 24, 533-556.  doi:10.1093/plankt/24.6.533

Moore, J.K., S.C. Doney, D.M. Glover, and I.Y. Fung, 2002: Iron cycling and nutrient limitation patterns in surface waters of the world ocean. Deep-Sea Res., II, 49, 463-507.  doi:10.1016/S0967-0645(01)00109-6 

Moore, J.K., S.C. Doney, J.A. Kleypas, D.M. Glover, and I.Y. Fung, 2002: An intermediate complexity marine ecosystem model for the global domain. Deep-Sea Res., II, 49, 403-462.  doi:10.1016/S0967-0645(01)00108-4 

Randerson, J.T., C.J. Still, J.J. Ballé, I.Y. Fung, S.C. Doney, P.P. Tans, T.J. Conway, J.W.C. White, B. Vaugn, N. Suits and A.S. Denning, 2002: Carbon isotope discrimination of arctic and boreal biomes inferred from remote atmospheric measurements and a biosphere-atmosphere model. Global Biogeochem. Cycles, 16(3), 1028, doi:0.1029/2001GB001435.

Siegel, D.A., S.C. Doney, and J.A. Yoder, 2002: The North Atlantic spring phytoplankton bloom and Sverdrup's critical depth hypothesis, Science, 296, 730-733.  DOI: 10.1126/science.1069174

Zedler, S. E., T. D. Dickey, S. C. Doney, J. F. Price, X. Yu, and G. L. Mellor, 2002: Analyses and simulations of the upper ocean’s response to Hurricane Felix at the Bermuda Testbed Mooring site: 13–23 August 1995, J. Geophys. Res., Oceans, 107(C12), 3232, doi:10.1029/2001JC000969. 

2001

Blackmon, M., B. Boville, F. Bryan, R. Dickinson, P. Gent, K. Kiehl, R. Moritz, D. Randall, J. Shukla, S. Solomon, G. Bonan, S. Doney, I. Fung, J. Hack, E. Hunke, J. Hurrell, J. Kutzbach, J. Meehl, B. Otto-Bliesner, R. Saravanan, E.K. Schneider, L.Sloan, M. Spall, K. Taylor, J. Tribbia and W. Washington, 2001: The Community Climate System Model, Bull. Amer. Meteorol. Soc., 82, 2357-2376.  http://ams.allenpress.com/archive/1520-0477/82/11/pdf/i1520-0477-82-11-2357.pdf

Dickey, T., S. Zedler, X. Yu, S.C. Doney, D. Frye, H. Jannasch, D. Manov, D. Sigurdson, J.D. McNeil, L. Dobeck, T. Gilboy, C. Bravo, D.A. Siegel, and N. Nelson, 2001: Physical and biogeochemical variability from hours to years at the Bermuda testbed mooring: June 1994--March 1998, Deep-Sea Res. II, 48, 2105-2140.  DOI:10.1016/S0967-0645(00)00173-9 

Doney, S.C. and D.M. Glover, 2001: Modelling the ocean carbon system, in Encyclopedia of Ocean Sciences, Vol. 4, 1929-1935, ed. J. Steele, S.A. Thorpe, and K.K. Turekian, Academic Press, London, UK.

Doney, S.C., and D.S. Schimel, 2001: Global Change---the future and the greenhouse effect, Encyclopedia of Life Sciences, Nature Publishing Group, http://www.els.net.

Doney, S.C., I. Lima, K. Lindsay, J.K. Moore, S. Dutkiewicz, M.A.M. Friedrichs, and R.J. Matear, 2001: Marine biogeochemical modeling, Oceanography, 14 (4), 93-107.  http://www.tos.org/oceanography/issues/issue_archive/issue_pdfs/14_4/14_4_doney_et_al.pdf

Fasham, M.J.R., B.M. Balino, M.C. Bowles, R. Anderson, D. Archer, U. Bathmann, P. Boyd, K. Buesseler, P. Burkill, A. Bychkov, C. Carlson, C.T.A. Chen, S. Doney, H. Ducklow, S. Emerson, R. Feely, G. Feldman, V. Garcon, D. Hansell, R. Hanson, P. Harrison, S. Honjo, C. Jeandel, D. Karl, R. Le Borgne, K.K. Liu, K. Lochte, F. Louanchi, R. Lowry, A. Michaels, P. Monfray, J. Murray, A. Oschlies, T. Platt, J. Priddle, R. Quinones, D. Ruiz-Pino, T. Saino, E. Sakshaug, G. Shimmield, S. Smith, W. Smith, T. Takahashi, P. Treguer, D. Wallace, R. Wanninkhof, A. Watson, J. Willebrand, C.S. Wong, 2001: A new vision of ocean biogeochemistry after a decade of the Joint Global Ocean Flux Study (JGOFS), AMBIO, Sp. Iss. 10, 4-31.

Garcon, V.C., A. Oschlies, S.C. Doney, D. McGillicuddy, J. Waniek, 2001: The role of mesoscale variability on plankton dynamics in the North Atlantic, Deep-Sea Res. II, 48, 2199-2226.  DOI: 10.1016/S0967-0645(00)00183-1

Rosenbloom, N.A., S.C. Doney, and D.S. Schimel, 2001: Geomorphic evolution of soil texture and organic matter in eroding landscapes, Global Biogeochem. Cycles, 15, 365-381.  DOI:10.1029/1999GB001251

Wanninkhof, R., S.C. Doney, T. Takahashi, and W.R. McGillis, 2001: The effect of using time-averaged winds on regional air-sea CO2 fluxes, in Gas Transfer at Water Surfaces, ed. M. Donelan, W. Drennan, E. Saltzman, and R. Wanninkhof, pp. 351-357, AGU, Geophysical Monograph 127, Washington, DC.

2000

Bailey, B.A., and S. Doney, 2000: Quantifying the effects of noise on biogeochemical models, Computing Science and Statistics, 32, 447-453.

Doney, S.C. and D.M. Glover, 2000, Ocean process tracers: modelling the ocean carbon cycle, In: Encyclopedia of Ocean Sciences, ed. J. Steele, Academic Press, London, UK, pp 1929–1935.

Doney, S.C., D.W.R. Wallace, H.W. Ducklow, 2000: The North Atlantic Carbon Cycle: New Perspectives from JGOFS and WOCE. in The Changing Ocean Carbon Cycle: A Midterm Synthesis of the Joint Global Ocean Flux Study, ed. R.B. Hanson, H.W. Ducklow, and J.G. Field, Cambridge University Press, 373-391.

Fuentes, M., S.C. Doney, D.M. Glover, and S.J. McCue, 2000: Spatial structure of the SeaWiFS ocean color data for the North Atlantic Ocean, Studies in the Atmospheric Sciences (Lecture notes in Statistics Vol. 144), ed. M. Berliner, D. Nychka, and T. Hoar, Springer-Verlag, New York, 153-171.

Fung, I.Y., S.K. Meyn, I. Tegen, S.C. Doney, J.G. John, and J.K.B. Bishop, 2000: Iron supply and demand in the upper ocean. Global Biogeochem. Cycles, 14, 281-295.  DOI:10.1029/1999GB900059

Saravanan, R., G. Danabasoglu, S.C. Doney, and J.C. McWilliams, 2000: Decadal variability and predictability in the midlatitude ocean-atmosphere system, J. Climate, 13, 1073-1097.  http://ams.allenpress.com/archive/1520-0442/13/6/pdf/i1520-0442-13-6-1073.pdf

1999

Doney, S.C., 1999: Major challenges confronting marine biogeochemical modeling, Global Biogeochem. Cycles, 13, 705-714.  DOI: 10.1029/1999GB900039

Wanninkhof, R., S.C. Doney, T.-H. Peng, J. Bullister, K. Lee, and R.A. Feely, 1999: Comparison of methods to determine the anthropogenic CO2 invasion into the Atlantic Ocean, Tellus, 51B, 511-530.  DOI: 10.1034/j.1600-0889.1999.00027.x

1998

Doney, S.C., J.L. Bullister, and R. Wanninkhof, 1998: Climatic variability in upper ocean ventilation diagnosed using chlorofluorocarbons, Geophys. Res. Lett., 25, 1399-1402.  DOI: 10.1029/98GL00844

Doney, S.C., W.G. Large, and F.O. Bryan, 1998: Surface ocean fluxes and water-mass transformation rates in the coupled NCAR Climate System Model, J. Climate, 6, 1420-1441.  http://ams.allenpress.com/archive/1520-0442/11/6/pdf/i1520-0442-11-6-1420.pdf

Gent, P.R., F.O. Bryan, G. Danabasoglu, S.C. Doney, W.R. Holland, W.G. Large, J.C. McWilliams, 1998: The NCAR Climate System Model global ocean component, J. Climate, 6, 1287-1306.  http://ams.allenpress.com/archive/1520-0442/11/6/pdf/i1520-0442-11-6-1287.pdf

Keeling, R.F., B.B. Stephens, R.G. Najjar, S.C. Doney, D. Archer, M. Heimann, 1998: Seasonal variations in the atmospheric O2/N2 ratio in relation to the kinetics of air-sea gas exchange, Global Biogeochem. Cycles, 12, 141-163.  DOI: 10.1029/97GB02339

Lee, K., R. Wanninkhof, T. Takahashi, S.C. Doney, and R.A. Feely, 1998: Low interannual variability in recent oceanic uptake of atmospheric carbon dioxide, Nature, 396, 155-159.  DOI:10.1038/24139

Lee-Taylor, J.M., S.C. Doney, G. Brasseur, and J.-F. Muller, 1998: A global three-dimensional atmosphere-ocean model of methyl bromide distributions, J. Geophys. Res., 103, 16,039-16,059.  DOI: 10.1029/98JD00970

1997

Doney, S.C., 1997: The ocean's productive deserts, Nature, 389, 905-906.  DOI: doi:10.1038/39993

Doney, S.C., W.J. Jenkins, and J.L. Bullister, 1997. A comparison of ocean tracer dating techniques on a meridional section in the eastern North Atlantic. Deep-Sea Res. I, 44, 603-626.  DOI:10.1016/S0967-0637(96)00105-7

Goyet, C., R. Healy, S. McCue, and D.M. Glover, 1997, Interpolation of TCO2 data on 1◦ × 1◦ grid throughout the water column below 500 m depth in the Atlantic Ocean, Deep-Sea Res. I, 44(12), 1945–1955.

Howell, E.A., S.C. Doney, R.A. Fine, D.B. Olson, 1997: Geochemical estimates of denitrification rates for the Arabian Sea and Bay of Bengal during WOCE. Geophys. Res. Lett., 24, 2549-2552.  DOI: 10.1029/97GL01538

Large, W.G., G. Danabasoglu, S.C. Doney, and J.C. McWilliams, 1997: Sensitivity to surface forcing and boundary layer mixing in a global ocean model: annual-mean climatology. J. Phys. Oceanogr., 27, 2418-2447.  http://ams.allenpress.com/archive/1520-0485/27/11/pdf/i1520-0485-27-11-2418.pdf

1996

Ayotte, K.W., P.P. Sullivan, A. Andren, S.C. Doney, A.A.M. Holtslag, W.G. Large, J.C. McWilliams, C.-H. Moeng, M.J. Otte, J.J. Tribbia, and J.C. Wyngaard, 1996. An evaluation of neutral and convective planetary boundary-layer parameterizations relative to large eddy simulations. Bound. Layer Meteorol., 79, 131-175.  DOI: 10.1007/BF00120078

Doney, S.C., 1996. A synoptic atmospheric surface forcing data set and physical upper ocean model for the U.S. JGOFS Bermuda Atlantic Time-Series Study (BATS) site. J. Geophys. Res., Oceans, 101, 25,615-25,634.  DOI: 10.1029/96JC01424

Doney, S.C., D.M. Glover, and R.G. Najjar, 1996. A new coupled, one-dimensional biological--physical model for the upper ocean: applications to the JGOFS Bermuda Atlantic Time Series (BATS) site. Deep-Sea Res. II, 43, 591-624.  DOI:10.1016/0967-0645(95)00104-2

1995

Brewer, P.G., D.M. Glover, C.M. Goyet, and D.K. Shafer. 1995. The pH of the North Atlantic Ocean: Improvements to the global model for sound absorption in sea water. J. Geophys. Res. 100(C5), 8761–8776.

Doney, S.C., 1995. Comment on "Experimental demonstration of coupling of heat and matter fluxes at a gas-water interface'' by Leon F. Phillips. J. Geophys. Res., Atmospheres, 100, 14,347-14,350.  DOI: 10.1029/95JD01075

Doney, S.C., 1995. Irreversible thermodynamics and air-sea exchange. J. Geophys. Res., Oceans, 100, 8541-8553. DOI: 10.1029/95JC00685

Doney, S.C., R.G. Najjar, and S. Stewart, 1995. Photochemistry, mixing, and diurnal cycles in the upper ocean. J. Mar. Res., 53, 341-369.  DOI: 10.1357/002224095321313

1994

Doney, S.C., 1994. Irreversible thermodynamic coupling between heat and mass fluxes across a gas/liquid interface. J. Chem. Society, Faraday Trans., 90, 1865-1874.  DOI: 10.1039/FT9949001865

Doney, S.C. and W.J. Jenkins, 1994. Ventilation of the deep western boundary current and the abyssal western North Atlantic: estimates from tritium and 3He distributions. J. Phys. Oceanogr., 24, 638-659.  http://ams.allenpress.com/archive/1520-0485/24/3/pdf/i1520-0485-24-3-638.pdf

Glover, D.M., J.S. Wroblewski and C.R. McClain. 1994. Dynamics of the transition zone in coastal zone color scanner-sensed ocean color in the North Pacific during oceanographic spring. J. Geophys. Res., Oceans 99(C4), 7501–7511.

Large, W.G., J.C. McWilliams, and S.C. Doney, 1994. Oceanic vertical mixing: A review and a model with a nonlocal boundary layer parameterization. Rev. Geophys., 32, 363-403.  DOI: 10.1029/94RG01872

1993

Doney, S.C., W.J. Jenkins, and H.G. Östlund, 1993. A tritium budget for the North Atlantic, observations and model results.  J. Geophys. Res., Oceans, 98, 18,069-18,081.  DOI: 10.1029/93JC00917

1992

Doney, S.C., 1992. Bomb tritium in the deep North Atlantic. Oceanography, 5, 169-170.  http://www.tos.org/oceanography/issues/issue_archive/issue_pdfs/5_3/5.3_doney.pdf

Doney, S.C. and J.L. Bullister, 1992. A chlorofluorocarbon section in the eastern North Atlantic. Deep-Sea Res., 39, 1857-1883.  http://dx.doi.org/10.1016/0198-0149(92)90003-C

Doney, S.C., D.M. Glover, and W.J. Jenkins, 1992. A model function of the global bomb-tritium distribution in precipitation, 1960-1986. J. Geophys. Res., Oceans, 97, 5481-5492.  http://www.agu.org/journals/jc/v097/iC04/92JC00015/92JC00015.pdf

1991

Wanninkhof, R.K., L.F. Bliven, and D.M. Glover. 1991. Gas transfer velocities and radar backscatter from the water surface. In: Air-Water Mass Transfer: Selected Papers from the Second International Symposium on Gas Transfer at Water Surfaces. S.C. Wilhelms and J.S. Gulliver (eds.) pp. 294–308.

1988

Doney, S.C. and W.J. Jenkins, 1988. The effect of boundary conditions on tracer estimates of thermocline ventilation rates. J. Mar. Res., 46, 947-965.  DOI: 10.1357/002224088785113414.

Glover, D.M. and Brewer, P.G. 1988. Estimates of wintertime mixed layer nutrient concentrations in the North Atlantic. Deep-Sea Res. 35(9): 1525–1546.

1987

Brewer, P.G. and D.M. Glover. 1987. Ocean chemical fluxes 1983–1986. Reviews Geophys. 25(6): 1376–1386.

Glover, D.M. and W.S. Reeburgh. 1987. Radon-222 and radium-226 in southeastern Bering Sea shelf waters and sediments. Contin. Shelf Res. 7(5): 433–456.

 

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