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2008

Vrijenhoek, R.C. 2008. Valuing what most will never see. Trends in Ecology & Evolution, 23: 10–11.

Vrijenhoek, R.C., P.C. Collins, and C.L. Van Dover. 2008. Bone-eating marine worms: Habitat specialists or generalists?. Proceedings of the Royal Society B, 275: 1963–1964. http://dx.doi.org/10.1098/rspb.2008.0350

Walz, P.M., W.J. Kirkwood, E.T. Peltzer, K.C. Hester, and P.G. Brewer. 2008. Creating controlled CO2 perturbation experiments on the seafloor — Development of FOCE techniques. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Kobe Techno Meeting.

Wang, K., D. Klimov, and Z. Kolber. 2008. Long period grating-based ocean pH sensor in an SMS fiber. Proceedings of SPIE, 6932.

Wheat, C.G., P. Fryer, A.T. Fisher, S. Hulme, H. Jannasch, M.J. Mottl, and K. Becker. 2008. Borehole observations of fluid flow from South Chamorro Seamount, an active serpentinite mud volcano in the Mariana forearc.. Earth and Planetary Science Letters, 267: 401–409. http://dx.doi.org/10.1016/j.epsl.2007.11.057

Won, Y.J., W.J. Jones, and R.C. Vrijenhoek. 2008. Absence of co-speciation between deep-sea mytilids and their thiotrophic endosymbionts. Journal of Shellfish Research, 27: 129–138.

Worden, A.Z., and F. Not. 2008. Ecology and diversity of picoeukaryotes. Microbial Ecology of the Oceans, Second Edition, 159–206.

Zedlitz, J., J. Graybeal, and N. Luttenberger. 2008. Using XML-based formats for marine data. Proceedings of the Ocean Sensors Workshop.

Zeidberg, L. D., and B. Robison. 2008. Reply to Watters et al.: Range expansion by the Humboldt squid. Proceedings of the National Academy of Sciences Online, 105. http://dx.doi.org/10.1073/pnas.0710602105

Zhang, Y., and J.G. Bellingham. 2008. An efficient method of selecting ocean observing locations for capturing the leading modes and reconstructing the full field. Journal of Geophysical Research, 113. http://dx.doi.org/10.1029/2007JC004327

2007

Adams, L., and G.I. Matsumoto. 2007. Investigating coastal processes and nitrate levels in the Elkhorn Slough using real-time data. Oceanography, 20: 200–204.

Allison, N., A.A. Finch, J.M. Webster, and D.A. Clague. 2007. Paleoenvironmental records from fossil corals: The effects of submarine diagenesis on temperature and climate estimates. Geochimica et Cosmochimica Acta, 71: 4693–4703.

Barde, J., D.R. Edgington, and J.C. Desconnets. 2007. A generic approach to manage metadata standards. OSGeo Journal, 3: 24–30.

Barry, J.P., and J.C. Drazen. 2007. Response of deep-sea scavengers to mild hypercapnia and the odor from a dead grenadier. Marine Ecology Progress Series, 350: 193–207.

Barry, J.P., P.J. Whaling, and R.K. Kochevar. 2007. Growth, production, and mortality of the chemosynthetic vesicomyid bivalve, Calyptogena kilmeri, from cold seeps off central California. Marine Ecology, 28: 169–182. http://dx.doi.org/10.1111/j.1439-0485.2007.00119.x

Bird, L.E., A.D. Sherman, and J. Ryan. 2007. Development of an active, large volume, discrete seawater sampler for autonomous underwater vehicles. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Bird, L.E., C.K. Paull, and B. Hobson. 2007. Instrumentation for investigating submarine canyons: The development of a self-triggering event detector to investigate sediment transport events. Sea Technology, 48: 17–21.

Braby, C.E., G.W. Rouse, S.B. Johnson, W.J. Jones, and R.C. Vrijenhoek. 2007. Bathymetric and temporal variation among Osedax boneworms and associated megafauna on whale-falls in Monterey Bay, California. Deep-Sea Research Part I, 54: 1773–1791. http://dx.doi.org/10.1016/j.dsr.2007.05.014

Browne, W.E., S.H.D. Haddock, and M.Q.Martindale. 2007. Phylogenetic analysis of lineage relationships among hyperiid amphipods as revealed by examination of the mitochondrial gene, cytochrome oxidase I (COI). Integrative and Comparative Biology, 47: 815–830. http://dx.doi.org/10.1093/icb/icm093

Caffrey, J.M., T.P. Chapin, H. Jannasch, and J.C. Haskins. 2007. High nutrient pulses, tidal mixing and biological response in a small California estuary: Variability in nutrient concentrations from decadal to hourly time scales. Estuaries, Coastal and Shelf Science, 71: 368–380. http://dx.doi.org/10.1016/j.ecss.2006.08.015

Caldeira, K, D. Archer, J.P. Barry, R. Bellerby, P.G. Brewer, L. Cao, A.G. Dickson, S.C. Doney, H. Elderfield, V. Fabry, R.A. Freely, J.P. Gattuso, O. Hoegh-Guldberg, P.M. Haugan, J.A. Kleypas, C. Langdon, J.C. Orr, A. Ridgwell, C.L. Sabine, B.A. Seibel, C. Turley, A. Watson, and R. Zeebe. 2007. Comment on "Modern-age buildup of CO2 and its effects on seawater acidity and salinity". Geophysical Research Letters, 34: 1–3. http://dx.doi.org/10.1029/2006GL027288

Chai, F., M.S. Jiang, Y. Chao, R.C. Dugdale, F.P. Chavez, and R.T. Barber. 2007. Modeling responses of diatom productivity and biogenic silica export to iron enrichment in the equatorial Pacific Ocean. Global Biogeochemical Cycles, 21: 1–16. http://dx.doi.org/10.1029/2006GB002804

Chavez, F.P., T. Takahashi, W.J. Cai, G.E. Friederich, B. Hales, R. Wanninkhof, and R.A. Feely. 2007. Coastal Oceans, Lakes, and Rivers. The First State of the Carbon Cycle Report (SOCCR): The North American carbon budget and implications for the global carbon cycle: 157–166.

Cline, D., D.R. Edgington, and J. Mariette. 2007. An automated visual event detection system for cabled observatory video. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Comeau, A.J., M.R. Lewis, J. Cullen, R.S. Adams, J. Andrea, S. Feener, S.D. McLean, K.S. Johnson, L.J. Coletti, H. Jannasch, S. Fitzwater, C. Moore, and A.H. Barnard. 2007. Monitoring the spring bloom in an ice-covered fjord with the Land/Ocean Biogeochemical Observatory (LOBO). Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Davis, A.S., D.A. Clague, and J.B. Paduan. 2007. Diverse origins of zenoliths from seamounts at the continental margin, offshore central California. Journal of Petrology, 48: 829–852.

Dolenc, D., B. Romanowicz, R. Uhrhammer, P. McGill, D. Neuhauser, and D. Stakes. 2007. Identifying and removing noise from the Monterey ocean bottom broadband seismic station (MOBB) data. Geochemistry, Geophysics, Geosystems, 8: 1–17. http://dx.doi.org/10.1029/2006GC001403

Drazen, J.C., K.R. Reisenbichler, and B.H. Robison. 2007. A comparison of absorption and assimilation efficiencies between four species of shallow- and deep-living fishes. Marine Biology, 151: 1551–1558. http://dx.doi.org/10.1007/s00227-006-0596-6

Edgington, D.R., D. Cline, J. Mariette, and I. Kerkez. 2007. Detecting and tracking events automatically in underwater video. ASLO Aquatic Sciences Meeting.

Foster, M.S., L.M. McConnico, L. Lundsten, T. Wadsworth, T. Kimball, L.B. Brooks, M. Medina-Lopez, R. Riosmena-Rodriguez, G. Hernandez-Carmona, R.M. Vasquez-Elizondo, S. Johnson, and D.L. Steller. 2007. Diversity and natural history of a Lithothamnion muelleri-Sargassum horridum community in the Gulf of California. Ciencias Marinas, 33: 367–384.

Fox, M., D. Long, F. Py, K. Rajan, and J. Ryan. 2007. In-situ analysis for intelligent control. Oceans 2007.

Fujikura, K., K. Amaki, J.P. Barry, Y. Fujiwara, Y. Furushima, R. Iwase, H. Yamamoto, and T. Maruyama. 2007. Direct observations of spawning behavior and synchrony in Calyptogena clams using an observatory and an estimate of fecundity. Marine Ecology Progress Series, 333: 185–193.

Godhea, A., C. Cusack, J. Pedersen, P. Andersen, D. Anderson, E. Bresnan, A. Cembella, E. Dahl, S. Diercks, M. Elbrächter, L. Edler, L. Galluzzi, C. Gescher, M. Gladstone, B. Karlson, D. Kulis, M. LeGresley, O. Lindahl, R. Marin III, G. McDermott, L.K. Medlin, L.J. Naustvoll, A. Penna, and K. Töbef. 2007. Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities. Harmful Algae, 6: 56–72.

Godin, M.A., and J.G. Bellingham. 2007. Data exploration for multidisciplinary research. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Goffredi, S.K., S.B. Johnson, and R.C. Vrijenhoek. 2007. Genetic and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Applied and Environmental Microbiology, 73: 2314–2323. http://dx.doi.org/10.1128/AEM.01986-06

Gomes, K., J. Graybeal, and T.  O'Reilly. 2007. Data management issues on operational ocean observatories. Sea Technology, 48: 17–20.

Graybeal, J., S. Watson, A. Isenor, and L. Bermudez. 2007. Sensor metadata interoperability workshop report. The Marine Metadata Workshop: Sensor Metadata Interoperability.

Grebmeier, J.M., and J.P. Barry. 2007. Benthic processes in polar polynyas. Polynyas: Windows into polar oceans, Elsevier Oceanography Series: 262–290.

Grech, C., and S.M. Rock. 2007. Rediscovery of the USS Macon - First archeological survey of the last flying aircraft carrier using advanced imaging and offshore technology. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Haywood, A.J., C.A. Scholin, R. Marin III, K.A. Steidinger, C. Heil, and J. Ray. 2007. Molecular detection of the brevetoxin-producing dinoflagellate Karenia brevis and closely related species using rRNA-targeted probes and a semiautomated sandwich hybridization assay. Journal of Phycology, 43: 1271–1286. http://dx.doi.org/10.1111/j.1529-8817.2007.00407.x

Hester, K.C., R.M. Dunk, P. Walz, E.T. Peltzer, E.D. Sloan, and P.G. Brewer. 2007. Direct measurements of multi-component hydrates on the seafloor: Pathways to growth. Fluid Phase Equilibria, 261: 396–406.

Hester, K.C., R.M. Dunk, S.N. White, P.G. Brewer, E.T. Peltzer, and E.D. Sloan. 2007. Gas hydrate measurements at Hydrate Ridge using Raman spectroscopy. Geochimica et Cosmochimica Acta, 71: 2947–2959. http://dx.doi.org/10.1016/j.gca.2007.03.032

Hobson, B., R. McEwen, J. Erickson, T. Hoover, L.R. McBride, F. Shane, and J.G. Bellingham. 2007. The development and ocean testing of an AUV docking station for a 21-inch AUV. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Huffard, C.L. 2007. Ethogram of Abdopus aculeatus (Cephalopoda: Octopodidae): Can behavioral characters inform octopod taxonomy and systematics?. Journal of Molluscan Studies, 73: 185–193.

Huffard, C.L. 2007. Four new species of shallow water pygmy octopus (Mollusca: Cephalopoda) from the Kingdom of Tonga. Molluscan Studies, 27: 147–170.

Johnson, K.S., E. Boyle, K. Bruland, K. Coale, C. Measures, J. Moffett, A. Aguilar-Islas, K. Barbeau, B. Bergquist, A. Bowie, K. Buck, Y. Cai, Z. Chase, J. Cullen, T. Doi, V. Elrod, S. Fitzwater, M. Gordon, A. King, P. Laan, L. Laglera-Baquer, W. Landing, M. Lohan, J. Mendez, A. Milne, H. Obata, L. Ossiander, J. Plant, G. Sarthou, P. Sedwick, G.J. Smith, B. Sohst, S. Tanner, S. Van den Berg, and J. Wu. 2007. The SAFe Iron Intercomparison Cruise: An international collaboration to develop dissolved iron in seawater standards. EOS, Transactions of the American Geophysical Union, 88: 131–132.

Johnson, K.S., J.A. Needoba, S.C. Riser, and W.J. Showers. 2007. Chemical sensor networks for the aquatic environment. Chemical Reviews, 107: 623–640. http://dx.doi.org/10.1021/cr050354e

Jones, W.J., and E. Macpherson. 2007. Molecular phylogeny of the East Pacific Rise squat lobsters of the genus Munidopsis (Decapoda: Galitheidae) with the descriptions of seven new species. Journal of Crustacean Biology, 27: 477–501.

Kirkwood, W.J. 2007. Development of the DORADO mapping vehicle for multibeam, subbottom, and sidescan science missions. Journal of Field Robotics, 24: 487–495.

Kirkwood, W.J., and D.W. Caress. 2007. Comparison of MBARI autonomous underwater mapping results for ORION Monterey Accelerated Research System (MARS) and Neptune Canada. Underwater Technology Conference.

Kirkwood, W.J., E.T. Peltzer, and P.G. Brewer. 2007. In situ ocean acidification environmental observations: MBARI's cabled observatory technology for controlled studies of changing ocean pH. Underwater Technology Conference.

Kitts, C., G. Wheat, and W. Kirkwood. 2007. Robotic system applications for fisheries research. American Fisheries Society 137th Annual Meeting.

Kolber, Z.S. 2007. Energy cycle in the ocean: Powering the microbial world. Oceanography, 20: 82–91.

Lundsten, L. 2007. The biogeography and distribution of megafauna at three California seamounts.

McBride, L.R., and J.T. Scholfield. 2007. Solid-state pressure-tolerant illumination for MBARI's Underwater Low-Light Imaging System. Journal of Display Technology, 3: 149–154. http://dx.doi.org/10.1109/Jdt.2007.895344

McDonald, S.M., D. Sarno, and A. Zingone. 2007. Identifying Pseudo-nitzschia species in natural samples using genus-specific PCR primers and clone libraries. Harmful Algae, 6: 849–860. http://dx.doi.org/10.1016/j.hal.2007.03.003

McDonald, S.M., D. Sarno, D.J. Scanlan, and A. Zingone. 2007. Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle. Aquatic Microbial Ecology, 50: 75–89. http://dx.doi.org/10.3354/ame01148

McEwen, R., B. Hobson, and J.G. Bellingham. 2007. Docking control system for a 21-inch diameter AUV. Proceedings of the Unmanned Untethered Systems Submersible Technology Conference.

McGann, C., F. Py, K. Rajan, H. Thomas, R. Henthorn, and R. McEwen. 2007. T-REX: A deliberative system for AUV control. International Conference on Automated Planning and Scheduling.

McGill, P., A.D. Sherman, B. Hobson, R. Henthorn, A.C. Chase, and K.L. Smith Jr. 2007. Initial deployments of the Benthic Rover, an autonomous bottom-transecting instrument platform for long-term measurements in deep benthic environments. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

McNutt, M., and D.W. Caress. 2007. Hotspots and hotspot swells in seismology and the structure of the Earth. Treatise on Geophysics, Volume 1.

Mills, C.E., and S.H.D. Haddock. 2007. Key to the ctenophora. Light and Smith's Manual: Intertidal invertebrates of the central California coast: 189–199.

Mills, C.E., S.H.D. Haddock, C.W. Dunn, and P.R. Pugh. 2007. Key to the siphonophora. Light and Smith's Manual: Intertidal invertebrates of the central California coast: 150–166.

Møller, P.R., and W.J. Jones. 2007. Eptatratus strickrotti n. sp. (Myxinidae): First hagfish from a hydrothermal vent. Biological Bulletin, 212: 55–66.

Morgan, J.K., D.A. Clague, D.C. Borchers, A.S. Davis, and K.L. Milliken. 2007. Mauna Loa's submarine western flank: Landsliding, deep volcanic spreading, and hydrothermal alteration. Geochemistry, Geophysics, Geosystems, 8: 1–42. http://dx.doi.org/10.1029/2006GC001420

Naehr, T.H., P. Eichhubl, V.J. Orphan, M. Hovland, C.K. Paull, W. Ussler III, T. Lorenson, and H.G. Greene. 2007. Authigenic carbonate formation at hydrocarbon seeps in continental margin sediments: A comparative study. Deep-Sea Research Part II, 54: 1268–1291. http://dx.doi.org/10.1016/j.dsr2.2007.04.010

Needoba, J.A., R.A. Foster, C.M. Sakamoto, J.P. Zehr, and K.S. Johnson. 2007. N2-fixation by unicellular cyanobacterial diazotrophs in the temperate, oligotrophic North Pacific. Limnology and Oceanography, 52: 1317–1327.

Not, F., R. Gausling, F. Azam, J.F. Heidelberg, and A.Z. Worden. 2007. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environmental Microbiology, 9: 1233–1252.

O'Reilly, T., R.A. Herlien, K. Headley, B. Kieft, M. Chaffey, and K.A. Salamy. 2007. Satellite link management for an ocean observing network. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference.

Osborn, D.A., M.W. Silver, C.G. Castro, S.M. Bros, and F.P. Chavez. 2007. The habitat of mesopelagic scyphomedusae in Monterey Bay, California. Deep Sea Research Part I, 54(8): 1241–1255. doi.org/10.1016/j.dsr.2007.04.015

Osborn, K.J., G.W. Rouse, S.K. Goffredi, and B.H. Robison. 2007. Description and relationships of Chaetopterus pugaporcinus, an unusual pelagic polychaete (Annelida, Chaetopteridae). Biological Bulletin, 212: 40–54. http://dx.doi.org/10.2307/25066579

Paduan, J.B., D.A. Clague, and A.S. Davis. 2007. Erratic continental rocks on volcanic seamounts off the U.S. West Coast. Marine Geology, 246: 1–8.

Pane, E.F., and J.P. Barry. 2007. Inefficient acid-base regulation in the deep-sea decapod crab (Chionoecetes tanneri) during short-term hypercapnia. Marine Ecology Progress Series, 334: 1–9.

Paul, J., C.A. Scholin, G. Van den Engh, and M.J. Perry. 2007. In-situ instrumentation. Oceanography, 20: 58–66.

Paull, C.K., W. Ussler III, and W.S. Holbrook. 2007. Assessing methane release for the colossal Storegga submarine landslide. Geophysical Research Letters, 34.

Paull, C.K., W. Ussler III, E.T. Peltzer, P.G. Brewer, R. Keaten, P. Mitts, J. Nealon, J. Greinert, J.C. Herguera, and E. Perez. 2007. Authigenic carbon entombed in methane-soaked sediments from the northeastern transform margin of the Guaymas Basin, Gulf of California. Deep-Sea Research Part II, 54: 1240–1267. http://dx.doi.org/10.1016/j.dsr2.2007.04.009

Paull, C.K., W. Ussler III, S. Dallimore, S. Blasco, T. Lorenson, H. Melling, F. McLaughlin, and F.M. Nixon. 2007. Origin of pingo-like features on the Beaufort Sea shelf and their possible relationship to decomposing methane gas hydrates. Geophysical Research Letters, 34: 1–5. http://dx.doi.org/10.1029/2006gl027977

Paull, C.K., W. Ussler III, W.S. Holbrook, T.M. Hill, R. Keaten, H. Haflidason, J.E. Johnson, W. Winters, and T. Lorenson. 2007. Origin of pockmarks and chimney structures on the flanks of the Storegga Slide, offshore Norway. Geo-Marine Letters, 28: 43–1.

Pennington, J.T., and F.P. Chavez. 2007. Project Report. MBARI Time Series (MBTS) Program.

Pennington, J.T., R. Michisaki, D. Johnston, and F.P. Chavez. 2007. Ocean observing in the Monterey Bay National Marine Sanctuary: CalCOFI and the MBARI time series: 24.

Rago, T.A., R. Michisaki, B. Marinovic, M. Blum, and K. Whitaker. 2007. Physical, nutrient, and biological measurements of coastal water off Central California in June/July 2006: 87.

Rago, T.A., R. Michisaki, B. Marinovic, M. Blum, and K. Whitaker. 2007. Physical, nutrient, and biological measurements of coastal water off Central California in October 2006: 93.

Rajan, K., C. McGann, F. Py, and H. Thomas. 2007. Robust mission planning using deliberative autonomy for autonomous underwater vehicles. International Conference on Robotics and Automation.

Raymond, E.H., and E.A. Widder. 2007. Behavioral responses of two deep-sea fishes to red, far-red and white light. Marine Ecology Progress Series, 350: 291–298. http://dx.doi.org/10.3354/meps07196

Reimers,C.E., H.A. Stecher III, J.C. Westall, Y. Alleau, K.A. Howell, L. Soule, H.K. White, and P.R. Girguis. 2007. Substrate degradation kinetics, microbial diversity and the current efficiency of microbial fuel cells supplied with marine plankton. Applied and Environmental Microbiology, 73: 7029–7040. http://dx.doi.org/10.1128/AEM.01209-07

Roman, B., C.A. Scholin, S. Jensen, E. Massion, R. Marin III, C. Preston, D. Greenfield, W. Jones, and K. Wheeler. 2007. Controlling a robotic marine water sampler with the Ruby scripting language. Journal of American Laboratory Automation, 12: 56–61.

Ruhl, H.A. 2007. Abundance and size distribution dynamics of abyssal epibenthic megafauna in the northeast Pacific. Ecology, 88: 1250–1262.

Sherr, B.F., E.B. Sherr, D.A. Caron, D. Vaulot, and A.Z. Worden. 2007. Oceanic protists. Oceanography, 20: 130–134.

Shulman, I., J. Kindle, P. Martin, S. deRada, J. Doyle, B. Penta, S. Anderson, F.P. Chavez, J. Paduan, and S.R. Ramp. 2007. Modeling of upwelling/relaxation events with the Navy Coastal Ocean Model. Journal of Geophysical Research, 112: 1–12. http://dx.doi.org/10.1029/2006JC003946

Smith Jr., K.L., B.H. Robison, J.J. Helly, R.S. Kaufmann, H.A. Ruhl, T.J. Shaw, B.S. Twining, and M. Vernet. 2007. Free-drifting icebergs: Hot spots of chemical and biological enrichment in the Weddell Sea. Science, 317: 478–485.