Publications

Mackey, K.R.M., C.E. Mioni, J.P. Ryan, and A. Paytan. 2012. Phosphorus cycling in the red tide incubator region of Monterey Bay in response to upwelling. Frontiers in Microbiology, 3: 1–14. http://dx.doi.org/10.3389/fmicb.2012.00033

Maier, K.L., A. Fildani, C.K. Paull, T.R. McHargue, S.A. Graham, and D.W. Caress. 2012. Deep-sea channel evolution and stratigraphic architecture from inception to abandonment from high-resolution autonomous underwater vehicle surveys offshore central California. Sedimentology, 60(4): 935–960. http://dx.doi.org/10.1111/j.1365-3091.2012.01371.x

Maier, K.L., A. Fildani, T.R. McHargue, C.K. Paull, S.A. Graham, and D.W. Caress. 2012. Deep-marine punctuated channel migration: High-resolution subsurface data from the Lucia Chica channel system, offshore California. Journal of Sedimentary Research (SEPM), 82: 1–8.

McGillivary, P., K. Rajan, J.B. de Sousa, F. Leroy, and R. Martins. 2012. Integrating autonomous underwater vessels, surface vessels and aircraft as persistent surveillance components of ocean observing studies. In: Proceedings of Oceanic Engineering Society/IEEE Autonomous Underwater Vehicles, 2012: 1–5. http://dx.doi.org/10.1109/AUV.2012.6380734

Messié, M., and F.P. Chavez. 2012. A global analysis of ENSO synchrony: The oceans' biological response to physical forcing. Journal of Geophyiscal Research, 117(C9): 1–19. http://dx.doi.org/10.1029/2012JC007938

Moeseneder, M.M., K.L. Smith Jr., H.A. Ruhl, D.O.B. Jones, U. Witte, and J.I. Prosser. 2012. Temporal and depth-related differences in prokaryotic communities in abyssal sediments associated with particulate organic carbon flux. Deep Sea Research I, 70: 26–35. http://dx.doi.org/10.1016/j.dsr.2012.07.010

Monier, A., R.M. Welsh, C. Gentemann, G. Weinstock, E. Sodergren, E.V. Armbrust, J.A. Eisen, and A.Z. Worden. 2012. Phosphate transporters in marine phytoplankton and their viruses: Cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology, 14: 162–176. http://dx.doi.org/10.1111/j.1462-2920.2011.02576.x

Patterson, J., J. Thomas, L. Rosenfeld, J. Newton, L. Hazard, J. Scianna, R. Kudela, E. Mayorga, C. Cohen, M. Cook, M. Otero, and J. Adelaars. 2012. Addressing ocean and coastal issues at the West Coast scale through regional ocean observing system collaboration. Oceans 2012, 2012: 1–8. http://dx.doi.org/10.1109/OCEANS.2012.6404937

Paull, C.K., D.W. Caress, E. Lundsten, R. Gwiazda, K. Anderson, M. McGann, J. Conrad, B. Edwards, and E.J. Sumner. 2012. Anatomy of the La Jolla Submarine Canyon system; offshore southern California. Marine Geology, 335: 16–34. http://dx.doi.org/10.1016/j.margeo.2012.10.003

Pfeil, B., A. Olsen, D.C.E. Bakker, S. Hankin, H. Koyuk, A. Kozyr, J. Malczyk, A. Manke, N. Metzl, C.L. Sabine, J. Akl, S.R. Alin, R.G.J. Bellerby, A. Borges, J. Boutin, P.J. Brown, W.J. Cai, F.P. Chavez, A. Chen, C. Cosca, A.J. Fassbender, R.A. Feely, M. González-Dávila, C. Goyet, N. Hardman-Mountford, C. Heinze, M. Hood, M. Hoppema, C.W. Hunt, D. Hydes, M. Ishii, T. Johannessen, S.D. Jones, R.M. Key, A. Körtzinger, P. Landschützer, S.K. Lauvset, N. Lefèvre, A. Lenton, A. Lourantou, L. Merlivat, T. Midorikawa, L. Mintrop, C. Miyazaki, A. Murata, A. Nakadate, Y. Nakano, S. Nakaoka, Y. Nojiri, A.M. Omar, X.A. Padin, G.H. Park, K. Paterson, F.F. Perez, D. Pierrot, A. Poisson, A.F. Ríos, J.M. Santana-Casiano, J. Salisbury, V.V.S.S. Sarma, R. Schlitzer, B. Schneider, U. Schuster, R. Sieger, I. Skjelvan, T. Steinhoff, T. Suzuki, T. Takahashi, K. Tedesco, M. Telszewski, H. Thomas, B. Tilbrook, J. Tjiputra, D. Vandemark, T. Veness, R. Wanninkhof, A.J. Watson, R. Weiss, C.S. Wong, and H. Yoshikawa-Inoue. 2012. A uniform, quality controlled Surface Ocean CO2 Atlas (SOCAT). Earth System Science Data Discussions, 5: 735–780. http://dx.doi.org/10.5194/essdd-5-735-2012

Pinto, J., J.B. de Sousa, F. Py, and K. Rajan. 2012. Experiments with deliberative planning on autonomous underwater vehicles. IROS 2012 Workshop on Robotics for Environmental Monitoring, Vilamoura, Algarve, Portugal, 7–12 October 2012.

Powers, M.L., A.G. McDermott, N. Shaner, and S.H.D. Haddock. 2012. Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: Insights into light-sensitive photoproteins. Biochemical and Biophysical Research Communications, 431(2): 360–366. http://dx.doi.org/10.1016/j.bbrc.2012.12.026

Py, F., and K. Rajan. 2012. Towards Distributed Decision-Making in Situated Agents. Conference on Advances in Cognitive Systems, Palo Alto, California, 6–8 December 2012.

Rago, T.A., R. Michisaki, B. Marinovic, and M. Blum. 2012. Physical, Nutrient, and Biological Measurements of Coastal Waters off Central California in March 2012. Calhoun, 63.

Rajan, K., and F. Py. T-REX: Partitioned inference for AUV mission control. In Further Advances in Unmanned Marine Vehicles, edited by G.N. Roberts and R. Sutton, 171–199. London, Institution of Electrical Engineers: 2012. http://dx.doi.org/10.1049/PBCE077E_ch9

Robidart, J.C., C.M. Preston, R.W. Paerl, K.A. Turk, A.C. Mosier, C.A. Francis, C.A. Scholin, and J.P. Zehr. 2012. Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal, 6: 513–523. http://dx.doi.org/10.1038/ismej.2011.127

Rosenfeld, L., Y. Chao, and R. Signell. 2012. IOOS modeling subsystem: vision and implementation strategy. Integrated Ocean Observing System Summit, Herndon, Virginia, 13–16 November 2012.

Rubin, K.H., S.A. Soule, W.W. Chadwick Jr., D.J. Fornari, D.A. Clague, R.W. Embley, E.T. Baker, M.R. Perfit, D.W. Caress, and R.P. Dziak. 2012. Volcanic eruptions in the deep sea. Oceanography, 25: 142–157. http://dx.doi.org/10.5670/oceanog.2012.12

Ryan, H.F., J.E. Conrad, C.K. Paull, and M. McGann. 2012. Slip rate on the San Diego Trough Fault Zone, inner California Borderland, and the 1986 Oceanside earthquake swarm revisited. Bulletin of the Seismological Society of America, 102: 2300–2312. http://dx.doi.org/10.1785/0120110317

Sabine, C.L., S. Hankin, H. Koyuk, D.C.E. Bakker, B. Pfeil, A. Olsen, N. Metzl, A. Kozyr, A. Fassbender, A. Manke, J. Malczyk, J. Akl, S.R. Alin, R.G.J. Bellerby, A. Borges, J. Boutin, P.J. Brown, W.J. Cai, F.P. Chavez, A. Chen, C. Cosca, R.A. Feely, M. González-Dávila, C. Goyet, N. Hardman-Mountford, C. Heinze, M. Hoppema, C.W. Hunt, D. Hydes, M. Ishii, T. Johannessen, R.M. Key, A. Körtzinger, P. Landschützer, S.K. Lauvset, N. Lefèvre, A. Lenton, A. Lourantou, L. Merlivat, T. Midorikawa, L. Mintrop, C. Miyazaki, A. Murata, A. Nakadate, Y. Nakano, S. Nakaoka, Y. Nojiri, A.M. Omar, X.A. Padin, G.H. Park, K. Patterson, F.F. Perez, D. Pierrot, A. Poisson, A.F. Ríos, J. Salisbury, J.M. Santana-Casiano, V.V.S.S. Sarma, R. Schlitzer, B. Schneider, U. Schuster, R. Sieger, I. Skjelvan, T. Steinhoff, T. Suzuki, T. Takahashi, K. Tedesco, M. Telszewski, H. Thomas, B. Tilbrook, D. Vandemark, T. Veness, A.J. Watson, R. Weiss, C.S. Wong, and H. Yoshikawa-Inoue. 2012. Surface Ocean CO2 Atlas (SOCAT) gridded data products. Earth System Science Data Discussions, 5: 781–804. http://dx.doi.org/10.5194/essdd-5-781-2012

Salathé, R.M., and R.C. Vrijenhoek. 2012. Temporal variation and lack of host specificity among bacterial endosymbionts of Osedax bone worms (Polychaeta: Siboglinidae). BMC Evolutionary Biology, 12: 189. http://dx.doi.org/10.1186/1471-2148-12-189

Schnitzler, C.E., K. Pang, M.L. Powers, A.M. Reitzel, J.F. Ryan, D. Simmons, T. Tada, M. Park, J. Gupta, S.Y. Brooks, R.W. Blakesley, S. Yokoyama, S.H.D. Haddock, M.Q. Martindale, and A.D. Baxevanis. 2012. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biology, 10: 1–26. http://dx.doi.org/10.1186/1741-7007-10-107

Secor, S.M., J.R. Taylor, and M. Grosell. 2012. Selected regulation of gastrointestinal acid-base secretion and tissue metabolism for the diamondback water snake and Burmese python. Journal of Experimental Biology, 215: 185–196. http://dx.doi.org/10.1242/jeb.056218

Shulman, I., B. Penta, M.A. Moline, S.H.D. Haddock, S. Anderson, M.J. Oliver, and P. Sakalaukus. 2012. Can vertical migrations of dinoflagellates explain observed bioluminescence patterns during an upwelling event in Monterey Bay, California?. Journal of Geophysical Research, 117: C01016. http://dx.doi.org/10.1029/2011JC007480

Sumner, E.J., P.J. Talling, L.A. Amy, R.B. Wynn, C.J. Stevenson, and M. Frenz. 2012. Facies architecture of individual basin-plain turbidites: Comparison with existing models and implications for flow processes. Sedimentology, 59: 1850–1887. http://dx.doi.org/10.1111/j.1365-3091.2012.01329.x

Talling, P.J., D.G. Masson, E.J. Sumner, and G. Malgesini. 2012. Subaqueous sediment density flows: Depositional processes and deposit types. Sedimentology, 59: 1937–2003. http://dx.doi.org/10.1111/j.1365-3091.2012.01353.x

Talling, P.J., G. Malgesini, E.J. Sumner, L.A. Amy, F. Felletti, G. Blakbourn, C. Nutt, C. Wilcox, I.C. Harding, and S. Akbari. 2012. Planform geometry, stacking pattern, and extrabasinal origin of low strength and intermediate strength cohesive debris flow deposits in the Marnoso-arenacea Formation, Italy. Geosphere, 8: 1207–1230. http://dx.doi.org/10.1130/GES00734.1

Vernet, M., K.L. Smith Jr., A.O. Cefarelli, J.J. Helly, R.S. Kaufmann, H. Lin, D.G. Long, A.E. Murray, B.H. Robison, H.A. Ruhl, T.J. Shaw, A.D. Sherman, J. Sprintall, G.R. Stephenson Jr., K.M. Stuart, and B.S. Twining. 2012. Islands of ice: Influence of free-drifting Antarctic icebergs on pelagic marine ecosystems. Oceanography, 25: 38–39. http://dx.doi.org/10.5670/oceanog.2012.72

Vrijenhoek, R.C. Fitness loss and genetic rescue in stream-dwelling topminnows. In Conservation and the Genetics of Populations, 2nd Edition, edited by F.W. Allendorf, G. Luikart, S.N. Aitken, 313. West Sussex, UK, Wiley-Blackwell: 2012.

Vrijenhoek, R.C., and R.S. Waples. 2012. Popular misconceptions. Molecular Ecology, 21: 4155–4156. http://dx.doi.org/10.1111/j.1365-294X.2012.05658.x

Weiss-Penzias, P.S., C. Ortiz Jr., R.P. Acosta, W. Heim, J.P. Ryan, D. Fernandez, J.L. Collett Jr., and A.R. Flegal. 2012. Total and monomethyl mercury in fog water from the central California coast. Geophysical Research Letters, 39: 1–5. http://dx.doi.org/10.1029/2011GL050324

Wheat, C.G., K.J. Edwards, T. Pettigrew, H.W. Jannasch, K. Becker, E.E. Davis, H. Villinger, and W. Bach. 2012. CORK-lite: bringing legacy boreholes back to life. Scientific Drilling Journal, 14: 39–43. http://dx.doi.org/10.2204/iodp.sd.14.05.2012

Worden, A.Z., J. Janouskovek, D. McRose, A. Engman, R.M. Welsh, S. Malfatti, S.G. Tringe, and P.J. Keeling. 2012. Global distribution of a wild alga revealed by targeted metagenomics. Current Biology, 22: R675–R677. http://dx.doi.org/10.1016/j.cub.2012.07.054

Xu, J.P., J.P. Barry, and C.K. Paull. 2012. Small-scale turbidity currents in a big submarine canyon. Geology, 41: 143–146. http://dx.doi.org/10.1130/G33727.1

Zhang, H., and M.P. Hare. 2012. Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters. Heredity, 108: 616–625. http://dx.doi.org/10.1038/hdy.2011.132

Zhang, X., W.J. Kirkwood, P.M. Walz, E.T. Peltzer, and P.G. Brewer. 2012. A review of advances in deep-ocean Raman spectroscopy. Applied Spectroscopy, 66: 237–249. http://dx.doi.org/10.1366/11-06539

Zhang, Y., J.G. Bellingham, M.A. Godin, and J.P. Ryan. 2012. Using an autonomous underwater vehicle to track the thermocline based on peak-gradient detection. IEEE Journal of Oceanic Engineering, 37: 544–553. http://dx.doi.org/10.1109/JOE.2012.2192340

Zhang, Y., J.P. Ryan, J.G. Bellingham, J.B.J. Harvey, and R.S. McEwen. 2012. Autonomous detection and sampling of water types and fronts in a coastal upwelling system by an autonomous underwater vehicle. Limnology and Oceanography: Methods, 10: 934–951. http://dx.doi.org/10.4319/lom.2012.10.934

Zhang, Y., M.A. Godin, J.G. Bellingham, and J.P. Ryan. 2012. Using an autonomous underwater vehicle to track a coastal upwelling front. IEEE Journal of Oceanic Engineering, 37: 338–347. http://dx.doi.org/10.1109/JOE.2012.2197272

Zhu, Z., T.W. Kim, and J.C. Choe. 2012. Is female preference for large sexual ornaments due to the bias to escape predation risk? BMC Evolutionary Biology, 12: 1–7. http://dx.doi.org/10.1186/1471-2148-12-33

Adams, L.G., and G.I. Matsumoto. 2011. The benefits and challenges of using real-time data in the classroom: Perspectives from the students, educators, and researchers. Marine Technology Society Journal, 45: 55–58.

Barry, J.P., S. Widdicombe, and J.M. Hall-Spencer. Effects of ocean acidification on marine biodiversity and ecosystem function. In Ocean Acidification, edited by J.P. Gattuso, L. Hansson, 192–209. Oxford, UK, Oxford University Press: 2011.

Becker, M., D. Crichton, E. Deelman, Y. Gil, T. Harmon, S. Granger, Q. Guo, P. Hanson, A. Hofmann, B. Jones, C. Knoblock, M. McCann, T. Stough, P. Szekely, R. Utz, and S. Villamizar. 2011. Information Sciences Institute Technical Report Number ISI-TR-674. Workshop on Aquatic Ecosystem Sustainability, 2011: 34.

Bertrand, A., A. Chaigneau, S. Peraltilla, J. Ledesma, M. Graco, F. Monetti, and F.P. Chavez. 2011. Oxygen: A fundamental property regulating pelagic ecosystem structure in the Coastal Southeastern Tropical Pacific. PLoS ONE, 6: E29558. http://dx.doi.org/10.1371/journal.pone.0029558

Bolstad, K.S.R., and H.J.T. Hoving. 2011. Spermatangium structure and implantation sites in onychoteuthid squid (Cephalopoda: Oegopsida). Marine Biodiversity Records, 4: E5. http://dx.doi.org/10.1017/S175526721000120X

Brewer, P.G., W. Ussler III, E.T. Peltzer, P. Walz, W. Kirkwood, and K.C. Hester. 2011. Accurate in situ observation of deep-sea sediment dissolved methane profiles in hydrate bearing provinces. 7th International Conference on Gas Hydrates, Edinburgh, Scotland, 17–21 July 2011.

Caress, D.W., and D.N. Chayes. 2011. MB-System Version 5.3.1909. Open source software distributed from the MBARI and L-DEO web sites.

Castro, C.G., C.A. Collins, J.T. Pennington, D. Zuniga, and F.P. Chavez. 2011. Spatial distribution and offshore export of total organic carbon along the eastern boundary of the Subtropical North Pacific. Advances in Oceanography and Limnology, 2: 93–106. http://dx.doi.org/10.1080/19475721.2011.626941

Cazenave, F., R. Zook, D. Carroll, M. Flagg, and S. Kim. 2011. Development of the ROV SCINI and deployment in McMurdo Sound, Antarctica. Journal of Ocean Technology, 6: 39–58.

Cazenave, F., Y. Zhang, E. McPhee-Shaw, J.G. Bellingham, and T.P. Stanton. 2011. High-resolution surveys of internal tidal waves in Monterey Bay, California, using an autonomous underwater vehicle. Limnology and Oceanography: Methods, 9: 571–581. http://dx.doi.org/10.4319/lom.2011.9.571

Ceballos, A., S. Bensalem, A. Cesta, L. de Silva, S. Fratini, F. Ingrand, J. Ocón, A. Orlandini, F. Py, K. Rajan, R. Rasconi, and M. van Winnendael. 2011. A goal-oriented autonomous controller for space exploration. 11th Symposium on Advanced Space Technologies in Robotics and Automation (ASTRA 2011), Noordwijk, Netherlands, 12–14 April 2011.

Chavez, F.P., M. Messié, and J.T. Pennington. 2011. Marine primary production in relation to climate variability and change. Annual Review of Marine Science, 3: 227–260. http://dx.doi.org/10.1146/annurev.marine.010908.163917

Clague, D.A., J.B. Paduan, D.W. Caress, H. Thomas, W.W. Chadwick Jr., and S.G. Merle. 2011. Volcanic morphology of West Mata Volcano, NE Lau Basin, based on high-resolution bathymetry and depth changes. Geochemistry, Geophysics, Geosystems, 12: QOAF03. http://dx.doi.org/10.1029/2011GC003791

Clague, G.E., W.J. Jones, J.B. Paduan, D.A. Clague, and R.C. Vrijenhoek. 2011. Phylogeography of Acesta clams from submarine seamounts and escarpments along the western margin of North America. Marine Ecology, 33: 75–87. http://dx.doi.org/10.1111/j.1439-0485.2011.00458.x

Coykendall, D.K., S.B. Johnson, S.A. Karl, R.A. Lutz, and R.C. Vrijenhoek. 2011. Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents. BMC Evolutionary Biology, 11: 96. http://dx.doi.org/10.1186/1471-2148-11-96

Das, J., T. Maughan, M. McCann, M. Godin, T. O'Reilly, M. Messié, F. Bahr, K. Gomes, F. Py, J.G. Bellingham, G.S. Sukhatme, and K. Rajan. 2011. Towards mixed-initiative, multi-robot field experiments: Design, deployment, and lessons learned. Proceedings of the International Conference on Intelligent Robots and Systems, San Francisco, California, 25–30 September 2011.

del Rio, J., D.M. Toma, T.C. O'Reilly, A.H. Broring, A. Manuel, K.L. Headley, and D. Edgington. 2011. Interoperable data management and instrument control experiences at OBSEA. OCEANS 2011, 2011: 1–4. http://dx.doi.org/10.1109/Oceans-Spain.2011.6003616

Demir-Hilton, E., S. Sudek, M.L. Cuvelier, C.L. Gentemann, J.P. Zehr, and A.Z. Worden. 2011. Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. The ISME Journal, 5: 1095–1107. http://dx.doi.org/10.1038/ismej.2010.209

Edgington, D.R., R. Butler, T. Fleury, K. Gomes, J. Graybeal, R.A. Herlien, and V. Welch. 2011. Observatory Middleware Framework (OMF). In Remote Instrumentation Services on the e-Infrastructure, edited by F. Davoli, N. Meyer, R. Pugliese, and S. Zappatore, 231–240. New York: Springer, 2011.

Faichney, I.D.E., J.M. Webster, D.A. Clague, J.C. Braga, W. Renema, and D.C. Potts. 2011. The impact of the Mid-Pleistocene Transition on the composition of submerged reefs of the Maui Nui Complex, Hawaii. Palaeogeography, Palaeoclimatology, Palaeoecology, 299: 493–506. http://dx.doi.org/10.1016/j.palaeo.2010.11.027

Ferrario, M.E., A.O. Cefarelli, B. Robison, and M. Vernet. 2011. Thalassioneis signyensis (Bacillariophyceae) from northwest Weddell Sea icebergs, an emendation of the generic description. Journal of Phycology, 48: 222–230. http://dx.doi.org/10.1111/j.1529-8817.2011.01097.x

Field, D.B., F. Chavez, C.B. Lange, and P.E. Smith. 2011. Variations in fisheries and complex ocean environments. Shifting Baselines, 2: 59–76. http://dx.doi.org/10.5822/978-1-61091-029-3_5

Fredericks, J.J., and C. Rueda. 2011. Content-infused OGC web services enabling dynamic quality assessment in observing systems. Workshop on Sensor Web Enablement 2011, Banff, Alberta, Canada, 6–7 October 2011.

Gilmour, K.M., S.F. Perry, A.J. Esbaugh, J. Genz, J.R. Taylor, and M. Grosell. 2011. Compensatory regulation of acid-base balance during salinity transfer in rainbow trout (Oncorhynchus mykiss). Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, 182: 259–274. http://dx.doi.org/10.1007/s00360-011-0617-8

Godin, M.A., Y. Zhang, J.P. Ryan, T.T. Hoover, and J.G. Bellingham. 2011. Phytoplankton bloom patch center localization by the Tethys autonomous underwater vehicle. OCEANS’11 MTS/IEEE KONA, Hilton Waikoloa Village, Kona, Hawai'i, 19–22 September 2011.

Gray, S.E.C., M.D. DeGrandpre, T.S. Moore, T.R. Martz, G.E. Friederich, and K.S. Johnson. 2011. Applications of in situ pH measurements for inorganic carbon calculations. Marine Chemistry, 125: 82–90. http://dx.doi.org/10.1016/j.marchem.2011.02.005

Graybeal, J., A.W. Isenor, and C. Rueda. 2011. Semantic mediation of vocabularies for ocean observing systems. Computers & Geosciences, 40: 120–131. http://dx.doi.org/10.1016/j.cageo.2011.08.002

Greenberg, J.A., C. Rueda, E.L. Hestir, M.J. Santos, and S.L. Ustin. 2011. Least cost distance analysis for spatial interpolation. Computers & Geosciences, 37: 272–276. http://dx.doi.org/10.1016/j.cageo.2010.05.012

Haddock, S.H.D., and C.W. Dunn. Practical computing for biologists. Sunderland, Massachusetts: Sinauer Associates, 2011.

Helo, C., M. Longpre, N. Shimizu, D.A. Clague, and J. Stix. 2011. Explosive eruptions at mid-ocean ridges driven by CO2-rich magmas. Nature Geoscience, 4: 260–263. http://dx.doi.org/10.1038/ngeo1104

Hill, T.M., C.K. Paull, and R.B. Critser. 2011. Glacial and deglacial seafloor methane emissions from pockmarks on the northern flank of the Storegga Slide complex. Geo-Marine Letters, 32: 73–84. http://dx.doi.org/10.1007/s00367-011-0258-7

Hill, T.M., H.J. Spero, T. Guilderson, M. LaVigne, D. Clague, S. Macalello, and N. Jang. 2011. Temperature and vital effect controls on bamboo coral (Isididae) isotope geochemistry: A test of the “lines method”. Geochemistry, Geophysics, Geosystems, 12: Q04008. http://dx.doi.org/10.1029/2010GC003443

Hobson, B.W., A.D. Sherman, and P.R. McGill. 2011. Imaging and sampling beneath free-drifting icebergs with a remotely operated vehicle. Deep-Sea Research II, 58: 1311–1317. http://dx.doi.org/10.1016/j.dsr2.2010.11.006

Hofmann, A.F., E.T. Peltzer, P.M. Walz, and P.G. Brewer. 2011. Hypoxia by degrees: Establishing definitions for a changing ocean. Deep-Sea Research I, 58: 1212–1226. http://dx.doi.org/10.1016/j.dsr.2011.09.004

Hofmann, G.E., J.E. Smith, K.S. Johnson, U. Send, L.A. Levin, F. Micheli, A. Paytan, N.N. Price, B. Peterson, Y. Takeshita, P.G. Matson, E.D. Crook, K.J. Kroeker, M.C. Gambi, E.B. Rivest, C.A. Frieder, P.C. Yu, and T.R. Martz. 2011. High-frequency dynamics of ocean pH: a multi-ecosystem comparison. PLoS ONE, 6: e28983. http://dx.doi.org/10.1371/journal.pone.0028983

Hoving, H.J.T., S.L. Bush, and B.H. Robison. 2011. A shot in the dark: same-sex sexual behavior in a deep-sea squid. Biology Letters, 8(2): 287–290. http://dx.doi.org/10.1098/rsbl.2011.0680

Hull, P.M., K.J. Osborn, R.D. Norris, and B.H. Robison. 2011. Seasonality and depth distribution of a mesopelagic foraminifer, Hastigerinella digitata, in Monterey Bay, California. Limnology and Oceanography, 56: 562–576. http://dx.doi.org/10.4319/lo.2011.56.2.0562

Johnson, K.S., J.P. Barry, L.J. Coletti, S.E. Fitzwater, H.W. Jannasch, and C.F. Love. 2011. Nitrate and oxygen flux across the sediment-water interface observed by eddy correlation measurements on the open continental shelf. Limnology and Oceanography Methods, 9: 543–553. http://dx.doi.org/10.4319/lom.2011.9.543

Kaufmann, R.S., B.H. Robison, R.E. Sherlock, K.R. Reisenbichler, and K.J. Osborn. 2011. Composition and structure of macrozooplankton and micronekton communities in the vicinity of free-drifting Antarctic icebergs. Deep-Sea Research II, 58: 1469–1484. http://dx.doi.org/10.1016/j.dsr2.2010.11.026

Kecy, C.D., E.T. Peltzer, P.M. Walz, K. Headley, B. Herlien, W. Kirkwood, T. O'Reilly, K.A. Salamy, F. Shane, J. Scholfield, and P.G. Brewer. 2011. Design and development of the CO2 enriched Seawater Distribution System. OCEANS 2011, 2011: 1–8.

Kieft, B., J. Bellingham, M. Godin, B. Hobson, T. Hoover, R. McEwen, and E. Mellinger. 2011. Fault Detection and Failure Prevention on the Tethys Long-Range Autonomous Underwater Vehicle. 17th International Symposium on Unmanned Untethered Submersible Technology 2011, Portsmouth, New Hampshire, 21–24 August 2011.

Kim, E., J.W. Harrison, S. Sudek, M.D.M. Jones, H.M. Wilcox, T.A. Richards, A.Z. Worden, and J.M. Archibald. 2011. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences, 109: 1469–1500. http://dx.doi.org/10.1073/pnas.1013337108

Kirkwood, W.J., E.T. Peltzer, P. Walz, K. Headley, B. Herlien, C.D. Kecy, T. Maughan, T. O'Reilly, K.A. Salamy, F. Shane, J. Scholfield, and P.G. Brewer. 2011. Cabled instrument technologies for ocean acidification research — FOCE (free ocean CO2 enrichment). Underwater Technology, 2011 IEEE Symposium on and 2011 Workshop on Scientific Use of Submarine Cables and Related Technologies, 2011: 1–8. http://dx.doi.org/10.1109/UT.2011.5774089

Klapp, S.A., M.M. Murshed, T. Pape, G. Bohrmann, P. Brewer, and W.F. Kuhs. 2011. Dual hydrate structures sI and sII at the Chapopote Knoll, southern Gulf of Mexico. 7th International Conference on Gas Hydrates, 2011: 10.

Kuhnz, L.A., J.P. Barry, K. Buck, C. Lovera, and P.J. Whaling. Potential impacts of the Monterey Accelerated Research System (MARS) on the seabed and benthic faunal assemblages. Moss Landing, California: Monterey Bay Aquarium Research Institute, 2011.

Kumar, S., S.J. Celorrio, F. Py, D. Khemani, and K. Rajan. 2011. Optimizing hidden Markov models for ocean feature detection. Proceedings of the 24th Florida Artificial Intelligence Research Society (FLAIRS) Conference, Palm Beach, Florida, 18–20 May 2011.

Levin, L.A., M.C. Gambi, J.P. Barry, A. Genin, and S. Thrush. 2011. The Dayton legacy: baselines, benchmarks, climate, disturbance, and proof. Marine Ecology, 32: 261–265. http://dx.doi.org/10.1111/j.1439-0485.2011.00473.x

Maier, K.L., A. Fildani, C.K. Paull, S.A. Graham, T.R. McHargue, D.W. Caress, and M. McGann. 2011. The elusive character of discontinuous deep-water channels: New insights from Lucia Chica channel system, offshore California. Geology, 39: 327–330. http://dx.doi.org/10.1130/G31589.1

Matsumoto, G.I., and T.A. Potts. 2011. Two ways of researching the underwater world. Brooks/Cole Enrichment Module: 1–27.

Mazillo, F.F.M., J.P. Ryan, and M.W. Silver. 2011. Parasitism as a biological control agent of dinoflagellate blooms in the California Current System. Harmful Algae, 10: 763–773. https://doi.org/10.1016/j.hal.2011.06.009

McClain, C.R., J.C. Nekola, L. Kuhnz, and J.P. Barry. 2011. Local-scale faunal turnover on the deep Pacific seafloor. Marine Ecology Progress Series, 422: 193–200. http://dx.doi.org/10.3354/meps08924

McGill, P.R., K.R. Reisenbichler, S.A. Etchemendy, T.C. Dawe, and B.W. Hobson. 2011. Aerial surveys and tagging of free-drifting icebergs using an unmanned aerial vehicle (UAV). Deep-Sea Research II, 58: 1318–1326. http://dx.doi.org/10.1016/j.dsr2.2010.11.007

Messié, M., and F.P. Chavez. 2011. Global modes of sea surface temperature variability in relation to regional climate indices. Journal of Climate, 24: 4314–4331. http://dx.doi.org/10.1175/2011JCLI3941.1

Osborn, K.J., L.A. Kuhnz, I.G. Priede, M. Urata, A.V. Gebruk, and N.D. Holland. 2011. Diversification of acorn worms (Hemichordata, Enteropneusta) revealed in the deep sea. Proceedings of the Royal Society B, 279: 1646–1654. http://dx.doi.org/10.1098/rspb.2011.1916

Osborn, K.J., S.H.D. Haddock, and G.W. Rouse. 2011. Swima (Annelida, Acrocirridae), holopelagic worms from the deep Pacific. Zoological Journal of the Linnean Society, 163: 663–678. http://dx.doi.org/10.1111/j.1096-3642.2011.00727.x

Ottesen, E.A., R. Marin III, C.M. Preston, C.R. Young, J.P. Ryan, C.A. Scholin, and E.F. DeLong. 2011. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5: 1881–1895. http://dx.doi.org/10.1038/ismej.2011.70

Paerl, R.W., K.A. Turk, R.A. Beinart, F.P. Chavez, and J.P. Zehr. 2011. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR. Environmental Microbiology, 14: 580–593. http://dx.doi.org/10.1111/j.1462-2920.2011.02594.x

Paerl, R.W., K.S. Johnson, R.M. Welsh, A.Z. Worden, F.P. Chavez, and J.P. Zehr. 2011. Differential distributions of Synechococcus subgroups across the California current system. Frontiers in Aquatic Microbiology, 2: 1–22. http://dx.doi.org/10.3389/fmicb.2011.00059

Paull, C.K., D.W. Caress, W. Ussler III, E. Lundsten, and M. Meiner-Johnson 2011. High-resolution bathymetry of the axial channels within Monterey and Soquel submarine canyons, offshore central California. Geosphere, 7: 1077–1101. http://dx.doi.org/10.1130/GES00636.1

Paull, C.K., S. Dallimore, J. Hughes-Clarke, S. Blasco, E. Lundsten, W. Ussler III, D. Graves, A.D. Sherman, K. Conway, H. Melling, S. Vagle, and T. Collett. 2011. Tracking the decomposition of submarine permafrost and gas hydrate under the shelf and slope of the Beaufort Sea. 7th International Conference on Gas Hydrates, 2011: 12.