James P. Barry, Senior Scientist
Publications (Peer-reviewed)

2015

  • Kim, T., Taylor, J., Lovera, C., and Barry, J.P. (2015) Ocean acidification impairs olfactory behavior in deep sea hermit crabs and increases variation among individuals. ICES J. Mar. Sci., doi: 10.1093/icesjms/fsv019
  • Gattuso, J.P., Kirkwood W., Barry J., Cox E., Gazeau F., Hansson L., Hendriks I., Kline D.I., Mahacek P., Marker M., Martin S., McElhany P., Reeve J., Roberts D., Saderne V., Tait K., Widdicombe S., Brewer, P.G. (2014). FOCE systems: present status and future developments. Biogeosciences, 11, 4057-4075, doi:10.5194/bg-11-4057-2014.
  • Hennige, S., Roberts, M., Williamson, P., Aze, T., Barry, J.P., Bellerby, R., Brander, L., Byrne, M., Gattuso, J.-P., Gibbs, S., Hansson, L., Hattam, C., Hauton, C., Havenhand, J., Helge Fosså, J., Kavanagh, C., Kurihara, H., Matear, R., Mark, R., Melzner, F., Munday, P., Niehoff, B., Pearson, P., Rehdanz, K., Tambutté, S., Turley, C., Venn, A., Warnau, M.,Young, J. (2014). An updated synthesis of the impacts of ocean acidification on marine biodiversity. Convention for Biological Diversity

2014

  • McClain, C., Barry, J.P. Beta-diversity on deep-sea wood falls reflects gradients in energy availability (accepted), Biology Letters
  • Taylor, J.R., DeVogelaere, A.P., Burton, E.J., Frey, O., Lundsten, L., Kuhnz, L.A., Whaling, P.J., Lovera, C., Buck, K.R., Barry, J.P. (accepted) Deep-sea benthic mega- and macrofaunal communities on and around a lost intermodal shipping container in the Monterey Bay National Marine Sanctuary, CA (Marine Pollution Bulletin
  • Taylor, J.R., Lovera, C., Whaling, P.J., Buck, K.R., Pane, E.F., Barry, J.P. (in press) Physiological compensation for environmental acidification is limited in the deep-sea urchinStrongylocentrotus fragilis.  Biogeosciences
  • Walz, K.R., Clague, D.A., Barry, J.P., Vrijenhoek, R.C. (in press). First records and range extensions for two Acesta clam species (Bivalvia, Limidae) in the Gulf of California, Mexico. Mar. Biodiv. Rec.

2013

  • Barry, J.P. Buck, K.R., Lovera, C., Brewer, P.G., Seibel, B.A., Drazen, J.C., Tamburri, M.N., Whaling, P.J., Kuhnz, L., Pane, E. (2013). The response of abyssal organisms to low pH conditions during a series of CO2-release experiments simulating deep-sea carbon sequestration. Deep-Sea Res. II, 92:249-260.
  • Buck, K.R., Barry, J.P., Hallam, S. (2013).  Thioploca spp. Sheaths as niches for bacterial and protistan assemblages.  Marine Ecology,(2013): 1-6, ISSN 0173-9565.
  • Dayton, P.K., Kim, S., Jarrell, S., Oliver, J.S., Hammerstrom, K., Fisher, J.L., O’Connor, K., Barber, J.S., Robilliard, G., Barry, J., Thurber, A.R., Conlan, K. (2013). Recruitment, growth, and mortality of an Antarctic hexactinellid sponge, Anoxycalyx joubini, PLoS-1, 8(2): e56939 doi:10.1371/journal.pone.0056939.
  • Kim, T., Barry, J.P., Micheli, F. (2013). The effects of intermittent exposure to low pH and oxygen conditions on survival and growth of juveniles red abalone. Biogeosciences, 10: 7255-7262.
  • National Research Council Committee (2013; J. Barry, Member).  Review of the Federal Ocean Acidification Research and Monitoring Plan. The Nat. Acad. Press, Washington D.C.
  • Ruckelshaus, M., Doney, S.C., Galindo, H.M., Barry, J.P., Chan, F., Duffy, E., English, C., Gaines, S., Grebmeier, J.M., Holowed, A., Knowlton, N., Polovina, J., Rabalais, N.N., Sydeman, W.J., Talley, L.D. (2013). Securing ocean benefits in the face of climate change, Mar. Policy, 40:154-159.
  • Sedlacek, L, Thistle, D., Fernandez-Leborans, G., Carman, K.R., Barry, J.P. (in press). First report of ciliate (Protozoa) epibionts on deep-sea harpacticoid copepods.  Deep-Sea Res., 92: 165-171.
  • Tang, Q., Chen, Z., Dai Min, H, Zhao, M., Ke Cai, H., Huang, T., Chaifei, T., Zhou, L., Chen, L., Song, J., Barry, J., Wu, Y., Gao, K. (2013). Ocean acidification and its marine life and ecosystems relationship. Chinese Science Bulletin, 58(14): 1307-1314.
  • Xu, J.P., Barry, J.P., Paull, C.K. (2013). Small-scale turbidity currents in a big submarine canyon.Geology, 41(2): 143-146.

2012

  • Buck, K.R., Rabalais, N., Bernhard, J.M., Barry, J.P.  (2012) Living assemblages from the ‘dead zone’ and naturally occurring hypoxic zones.  Cellular Origin, Life in Extreme Habitats, and Astrobiology 21: 343-352.
  • Doney, S. C., Ruckelshaus, M., Duffy, J.E., Barry, J.P., Chan, F., English, C.A., Galindo, H.M., Grebmeier, J.M., Hollowed, A.B., Knowlton, N., Polovina, J., Rabalais N., Sydeman, W.J., Talley, L.D. (2012).  Climate change impacts on marine ecosystems.  Annual Reviews of Marine Science, 4, 11-37.

2011

  • Barry, J.P., Widdicombe, S., Hall-Spencer, J. (2011).  Effects of ocean acidification on marine biodiversity and ecosystem function.  Pages 192-209 in, Ocean Acidification, J.P. Gattuso, ed., Oxford Univ. Press,
  • Johnson, K.J., Barry, J.P., Coletti, L.J., Fitzwater, S.E., Jannasch, H.W., Lovera, C.F. (2011).  Nitrate and oxygen flux across the sediment-water interface observed by eddy correlation measurements on the open continental shelf.  Limnol. & Oceanogr. Methods 9, 543-553..
  • Levin, L.A., Gambi, M.C., Barry, J.P., Genin, A., Thrush, S.  The Dayton legacy: baselines, benchmarks, climate, disturbance, and proof.  Mar. Ecol., 32(3): 261-265.
  • McClain, C.R., Nekola, J.C., Kuhnz, L., Barry, J.P. (2011).  Local-scale faunal turnover on the deep Pacific floor.  Mar. Ecol. Prog. Ser., 422: 193-200.

2010

  • Barry, J.P., Hall-Spencer, J.M., Tyrrell, T. (2010) In situ perturbation experiments: natural venting sites, spatial/temporal gradients in ocean pH, manipulative in situ p(CO2) perturbations.  Pages 123-136 in, Best Practices for Ocean Acidification Research, U. Riebesell, V.J. Fabry, L. Hansson, J.-P. Gattuso, eds., European Commission, Luxembourg, 258p.
  • Barry, J.P., Tyrrell, T., Hansson, L., Plattner, G.-K., Gattuso, J.-P. (2010).  Atmospheric CO2 targets for ocean acidification perturbation experiments. Pages 53-63 in, Best Practices for Ocean Acidification Research, U. Riebesell, V.J. Fabry, L. Hansson, J.-P. Gattuso, eds., European Commission, Luxembourg, 258p.
  • Fleeger, J.W., Johnson, D.S., Carman, K.R., Weisenhorn, P.B., Gabriele, A., Thistle, D., Barry, J.P.  (2010).  The response of nematodes to deep-sea CO2 sequestration: A quantile regression approach.  Deep-Sea Res. I, 57:696-707.
  • Hofmann, G.E., Barry, J.P., Edmunds, P.J., Gates, R.D., Hutchins, D.A., Klinger, T., Sewell, M.A. (2010).  The effects of ocean acidification on calcifying organisms in marine ecosystems: an organism to ecosystem perspective. (2010)  Ann. Rev. of Ecol., Evol. & Syst. 41: 127-47.
  • McClain, C.R., Barry, J.P. (2010).  The Role of Abrupt Topography on Species Diversity in the Deep-Sea Benthos, Ecology, 91(4): 964-976.
  • McClain, C.R., Lundsten, L., Barry, J.P., and DeVogelaere, A. (2010).  Assemblage structure, but no diversity or density, change with depth on a northeast Pacific seamount.  Mar. Ecol.,31(Suppl. 1: 114-25.
  • National Research Council Committee (J. Barry – member), (2010).  Ocean Acidification: A national strategy to meet the challenges of a changing ocean.  The Nat. Acad. Press, Washington, D.C.
  • Paull, C.K., Schlining, B., Ussler, W. III, Lundsten, E., Barry, J.P., Caress, D.W., Johnson, J., McGann, M.  (2010) Submarine mass transport within Monterey Canyon: Benthic disturbance controls the distribution of chemosynthetic biological communities.  In: D.C. Mosher et al. (eds.), Submarine Mass Movements and Their Consequences, Advances in Natural and Technological Hazards Research, Vol. 28: 229-246.

2009

  • Barry, J.P., and Hashimoto, J.  (2009). Revisiting the Challenger Deep using the ROV Kaiko.  Mar. Tech. Soc., 43(5):1-2.
  • Bernhard, J.M., Barry, J.P., Buck, K.R., Starczak, V.R. (2009) Impact of intentionally injected carbon dioxide hydrate on deep-sea benthic foraminiferal survival.  Global Change Biology, doi: 10.111/j.1365-2486.2008.01822.x
  • Lundsten, L., Barry, J.P., Cailliet, G.M. Clague, D.A., DeVogelaere, A.P., Geller, J.B. (2009). Benthic invertebrate communities on three seamounts off southern and central California, USA, Mar. Ecol. Prog. Ser. 374: 23-32
  • Lundsten, L., McClain, C.R., Barry, J.P., Cailliet, G.M., Clague, D.A., DeVogelaere, A.P. (2009).  Ichthyofauna on three seamounts off southern and central California, USA.  Mar. Ecol. Prog. Ser. 389: 223-232.
  • McClain, C.R., Lundsten, L., Ream, M., Barry, J.P., DeVogelaere, A.  (2009). Endemicity, Biogeography, Composition, and Community Structure on a Northeast Pacific Seamount.  PLoS ONE 4(1): e4141
  • Ricketts, E.R., Kennett, J.P., Hill, T.M., and Barry J.P.  (2009). Effects of carbon dioxide sequestration on California margin deep-sea foraminiferal assemblages.  Mar. Micropaleontology 72: 165-175.
  • Sedlacek, L., Thistle, D., Carman, K.R., Fleeger, J.W., Barry, J.P. (2009).  Effects of carbon dioxide on deep-sea harpacticoids revisited.  Deep-Sea Res. I, 56: 1018-1025.

2008

  • Barry, J.P., Lovera, C., Okuda, C., Nelson, E., Pane, E.F. (2008)  A gas-controlled aquarium system for ocean acidification studies.  IEEE Xplore, 978-4244-2126-08/08
  • Pane, E.F., Grosell, M., Barry J.P. (2008).  Comparison of enzyme activities linked to acid-base regulation in a deep-sea and a sublittoral decapod crab species.  Aquatic Biology, 4: 23-32.

2007

  • Barry, J.P. & 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., Whaling, P.J., Kochevar, R.K. (2007).  Growth, production, and mortality of the chemosynthetic vesicomyid bivalve, Calyptogena kilmeri, from cold seeps off central California. Marine Ecology, 28: 169-182
  • Caldeira, K, Archer, D., Barry, J.P., Bellerby, R., Brewer, P., Cao, L, Dickson, A.G., Doney, S.C., Elderfield, H., Fabry, V., Feely, R.A., Gattuso, J.P., Hoegh-Guldberg, O., Haugan, P.M., Kleypas, J.A., Langdon, C., Orr, J.C., Ridgwell, A., Sabine, C.L., Seibel, B., Turley, C., Watson, A., Zeebe, R. (2007).  Comment on “Modern-age buildup of CO2 and its effects on seawater acidity and salinity”  Geophysical Res. Letters, 34, L18608, doi:10.1029/2006GL027288
  • Fujikura, K., Amaki, K., Barry, J.P., Fujiwara, Y., Furushima, Y., Iwase, R., Yamamoto, H., Maruyama, T. (2007).  Direct observations of spawning behavior and synchrony in Calyptogenaclams using an observatory and an estimate of fecundity.  Mar. Ecol. Prog. Ser. 333:185-193.
  • Grebmeier, J.M., and Barry, J.P.  (2007) Benthic processes in polar polynyas.  Pages 262-290 in: Polynyas: Windows into Polar Oceans, Elsevier Oceanography Series, David Halpern, editor.
  • Levin, L.A., Barry, J.P., Felbeck, H., Smith, C.R., Young, C.M. (2007).  Advances in vent, seep, whale-, and wood-fall biology.  Marine Ecology, 28: 1-2.
  • Pane, E.F., Barry, J.P. (2007).  Extracellular acid-base regulation during short-term hypercapnia is effective in a shallow-water crab, but ineffective in a deep-sea crab.  Mar. Ecol. Prog. Ser., 334:1-9.
  • Thistle, D., Sedlacek, L., Carman, K.R., Fleeger, J.W., Barry, J.P.  (2007). Emergence in the deep-sea: evidence from harpacticoid copepods.  Deep-Sea Research, 54: 1008-1014
  • Thistle, D., Sedlacek, L., Carman, K.R., Fleeger, J.W., Brewer, P.G., Barry, J.P.  (2007). Exposure to carbon dioxide-rich seawater is stressful for deep-sea species: an in situ, behavioral study.  Mar. Ecol. Prog. Ser., 340: 9-16.

2006

  • Fleeger, J.W., Carman, K.R., Weisenhorn, P.B., Sofranko, H., Marshall, T., Thistle, D., and Barry, J.P. (2006).  Simulated sequestration of anthropogenic carbon dioxide at a deep-sea site: effects on nematode abundance and biovolume.  Deep-Sea Research I, 53: 1135-1147.
  • Kogan, I., Paull, C.K., Kuhnz, L.A., Burton, E.J., VonThun, S., Greene, H.G., Barry, J.P.  (2006) ATOC/Pioneer Seamount cable after 8 years on the seafloor: Observations and environmental impact.  Continental Shelf Research, 26: 771-787.
  • Stein, D.L., Drazen, J.C., Schlining, K.L., Barry, J.P., Kuhnz, L. (2006).  Snailfishes of Monterey Canyon: video, photographic, and morphological observations.  J. Fish Biology, 69: 970-986.
  • Thistle, D., Sedlacek, L., Carman, K.R., Fleeger, J.W., Brewer, P.G., Barry, J.P. (2006).  Simulated sequestration of anthropogenic carbon dioxide at a deep-sea site: effects on harpacticoid-copepod species.  J. Exp. Mar. Biol. Ecol., 330: 141-158

2005

  • Barry, J.P., Buck, K.R., Lovera, C., Kuhnz, L, Whaling, P.J. (2005) Utility of deep-sea CO2release experiments in understanding the biology of a high CO2 ocean: Effects of hypercapnia on deep-sea meiofauna.  Journal of Geophysical Research, Oceans, 110, C09S12.
  • Caldeira, K., Brewer, P.G., Chen, B., Hansen, L., Haugan, P., Iwama, T., Johnston, P., Kheshgi, H., Li, Q., Ohsumi, T., Pörtner, H., Sabine, C., Shirayama, Y., Thomson, J. (authors), Barry, J.P. (contributing author) (2005).  Chapter 6: Ocean Storage.  In IPCC Special Report on Carbon Dioxide Capture and Storage, Intergovernmental Panel on Climate Change, Cambridge University Press, Cambridge
  • Drazen, J.C., Bird, L.E., Barry, J.P.  2005.  Development of a hyperbaric trap-respirometer for the capture and maintenance of live deep-sea organisms.  Limnol. and Ocean. Methods, 3, 48849
  • Paull, C.K., Ussler, W., III., Barry, J.P., Greene, H.G., and Keaten, R., 2005, Bioerosion by chemosynthetic biological communities on Holocene slide scars, Geo-Marine Letters, 25: 11-19.
  • Kirkwood, W., Graves, D., Conway, M., Pargett, D., Scholfield, J., Walz, P., Dunk, R., Peltzer, E., Barry, J., Brewer, P. (2005).  Engineering development of the free ocean CO2 enrichment (FOCE) experiment.  Oceans, 2005, Proceedings of MTS/IEEE DOI: 10.1109/Oceans.2005.1640013
  • Thistle, D., Carman, K.R., Sedlacek, L., Brewer, P.G., Fleeger, J.W., Barry, J.P.  (2005) Deep-ocean, sediment-dwelling animals are sensitive to sequestered carbon dioxide. Mar. Ecol. Prog. Ser., 289:

2004

  • Barry, J.P., Kurt R. Buck, Chris F. Lovera, Linda Kuhnz, Patrick J. Whaling, Edward T. Peltzer, Peter Walz, and Peter G. Brewer (2004)  Effects of Direct Ocean CO2 Injection on Deep-Sea Meiofauna.  Journal of Oceanography, 60: 759-766
  • Carman, K.R., Thistle, D., Fleeger, J., Barry, J.P. (2004)  The influence of introduced CO2 on Deep-Sea metazoan meiofaunal, Journal of Oceanography, 60(4): 767-772
  • Goffredi, S.K., Barry, J.P., and Buck, K.R., (2004)  Vesicomyid symbioses from Monterey Bay (Central California) Cold Seeps.  Symbiosis, 36, 1-27.

2003

  • Barry, J.P., Grebmeier, J., Smith, J., & Dunbar, R.B. (2003)  Bathymetric versus seafloor-habitat control of benthic megafaunal patterns in the Ross Sea, Antarctica, Ant. Res. Series, 78: 327-354.
  • Grebmeier, J.G., DiTullio, G.R., Barry, J.P., & Cooper, L.W.  (2003)  Benthic carbon cycling in the Ross Sea polynya, Antarctica:  Benthic community metabolism and sediment tracers. Antarctic Research Series, 78: 301-326
  • Paull, C.K., Ussler, W III., Greene, H.G., Keaten, R., Mitts, P., Barry, J.P. (2003)  Caught in the Act: The December 20th, 2001 Gravity Flow Event in Monterey Canyon.  Geo-Mar. Let., 22: 227-232.
  • Yoklavich, M, Cailliet, G., Oxman, D., Barry, J.P., Lindquist, D.C. (2003) Fishes.  Pages 163-185 in Caffrey, J. (Ed.).  Ecosystem Changes in a California Estuary: a Characterization of Elkhorn Slough.  Elkhorn Slough Foundation, Moss Landing, CA

2002

  • Barry, J.P., Buck, K.R., Kochevar, R.K., Nelson, D.C., Fujiwara, Y., Goffredi, S.K., & J. Hashimoto (2002) Methane-based symbiosis in a mussel, Bathymodiolus platifrons, from cold seeps in Sagami Bay, Japan.  Invertebrate Biology, 121(1): 47-54
  • Eastman, J.T. and Barry, J.P.  (2002) Video observation of the Antarctic toothfish, Dissostichus mawsoni (Perciformes: Nototheniidae) in the Ross Sea, Antarctica, Polar Biology, 25: 391-395
  • Goffredi, S.K. & Barry, J.P. (2002)  Species-specific variation in sulfide physiology between closely related vesicomyid clams.  Marine Ecology Progress Series, 225: 227-238.
  • Goffredi, S.K. and Barry, J.P. (2002) Energy acquisition in vesicomyid symbioses.  Cahier de Biologie Marine, 43: 345-350
  • Orange, D.L., Yun, J., Maher, N., Barry, J., Greene, G. (2002)  Tracking California Seafloor seeps with bathymetry, backscatter and ROVs .  Continental Shelf Research, 22: 2273-2290.

2001

  • Bernhard, J.M., Buck, K.M., Barry, J.P. 2001.  Monterey Bay cold-seep biota: Assemblages, abundance, and ultrastructure of living foraminifera, Deep-Sea Research I, 48: 2233-2249.
  • Johnson, K.S., Paull, C.K., Barry, J.P. & Chavez, F.P. (2001).  A decadal record of turbidity underflows from a coastal river in to the deep-sea.  Geology, 29(11): 1019-1022.
  • Torres, M.E., Barry, J.P., & Suess, E.  (2001)  Reconstructing the history of fluid flow at cold seep sites from Ba/Ca in shells of vesicomyid clams.  Limnology & Oceanography, 46(7): 1701-1708.

2000

  • Barry, J.P. & N. Maher (2000) Observation of the prickly shark, Echinorhinus cookei Pietschmann, 1928 from the O2 minimum zone in Santa Barbara Basin, California.  Calif. Fish & Game, 86:213-215.
  • Barry, J.P., Buck, K.R., Goffredi, S.K., & J. Hashimoto (2000) Ultrastructure studies of two chemosynthetic invertebrate-bacterial symbioses (Lamellibrachia sp. and Acharax sp.) from the Hatsushima cold seeps in Sagami Bay, Japan.  JAMSTEC J. Deep-Sea Research, 16: 91-99
  • Buck, K.R., Barry, J.P., Simpson, A.G.B. 2000.  Monterey Bay cold seep biota: euglenozoa with chemoautotrophic bacterial epibionts.  Eur. J. Protistology, 36: 117-126.
  • DiTullio, G.R., Grebmeier, J., Arrigo, K.R., Lizotte, M.P., Robinson, D.H., Leventer, A., Barry, J.P., VanWoert, M., & R.B. Dunbar (2000).  Rapid and early export of Phaeocystis antarcticablooms in the Ross Sea, Antarctica, Nature, 404 (6778): 595-598
  • Peek, A.S., Gaut, B.S., Feldman, R.A., Barry, J.P., Kochevar, R.E., Lutz, R.A., & R.C. Vrijenhoek (2000).  Neutral and nonneutral mitochondrial genetic variation in deep sea clams from the family Vesicomyidae.  J. Molecular Evolution, 50(2):141-153

1999

  • Ahmad, A., Barry, J.P., & D.C. Nelson. (1999) Phylogenetic and physiological affinity of wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon with Thioploca spp. Applied and Environmental Microbiology, 65(1):270-277.
  • Barry, J.P.  & R E. Kochevar (1999). Calyptogena diagonalis, a new Vesicomyid Bivalve from subduction zone seeps in the eastern North Pacific.  The Veliger, 42(2): 117-123
  • Orange, D.L., Greene, H.G., Reed, D., Martin, J.B., McHugh, C.M., Ryan, W.B.F., Maher, N, Stakes, D. & J.P. Barry (1999).  Widespread fluid expulsion on a translational continental margin: mud volcanoes, fault zones, headless canyons, and aquifers in Monterey Bay, California.  Bull. Geological Society of America 111(7): 992-1009
  • Pennington, J.T., Tamburri, M.N., and J.P. Barry (1999) Development, temperature tolerance, and settlement preference of embryos and larvae of the articulate brachiopod Laqueus californianus. Biological Bulletin, 196: 245-256.
  • Sagarin, R.D., Barry, J.P., Gilman, S.E., & C.H. Baxter (1999).  Climate-related change in an intertidal community over short and long time scales. Ecological Monographs, 69(4): 465-490.
  • Tamburri, M.N. & J.P. Barry (1999).  Adaptations for scavenging by three diverse bathyal species, Eptatretus stouti, Neptunea amianta and Orchomene obtusus. Deep-Sea Research Part It,46(12):2079-2093
  • Yoklavich, M.M., Cailliet, G.M., Oxman, D.S., Barry, J.P., & D.C. Lindquist (1999).  Fish assemblages of Elkhorn Slough and adjacent habitats.  Elkhorn Slough Res. Res. Profile on Fishes

1998

  • Barry, J.P. & R.E. Kochevar. (1998) A tale of two clams: differing chemosynthetic life styles among vesicomyids in Monterey Bay cold seeps.  Cahier de Biologie Marine 39:329-331
  • Buck, K.R. & J.P. Barry (1998).  Monterey Bay Cold Seep Infauna: Quantitative comparison of bacterial mat meiofauna with non-seep control sites. Cahier de Biologie Marine, 39:333-336.

1997

  • Barry, J.P., Kochevar, R.E., J. Hashimoto, Y. Fujiwara, K. Fujikura, & H.G. Greene. (1997)  Studies of the physiology of chemosynthetic fauna at Cold Seeps in Sagami Bay, Japan JAMSTEC Journal of Deep Sea Research, 13: 417-423
  • Barry, J.P., R.E. Kochevar, & C.H. Baxter (1997).  The influence of pore-water chemistry and physiology in the distribution of vesicomyid clams at cold seeps in Monterey Bay: Implications for patterns of chemosynthetic community organization.  Limnology and Oceanography, 42(2):318-328.
  • Barry, J.P., R.E. Kochevar, C.H. Baxter, C. Harrold. (1997). Calyptogena packardana, a new species of Vesicomyid Bivalve from Cold Seeps in Monterey Bay, California.  Veliger, 40(4): 341-349
  • Greene, H.G., Barry, J.P. & B.H. Robison. (1997). A submersible-based comparison of cold seep regions in Sagami and Monterey Bays.  JAMSTEC Journal of Deep-Sea Research, 13: 395-415.
  • Lisin, S.E., E.E. Hannan, R.E. Kochevar, C. Harrold, & J.P. Barry (1997) Temporal variation in gametogenic cycles of vesicomyid clams.  Invertebrate Reproduction and Development, 31(1-3): 307-318.

1996

  • Barry, J.P., H.G. Greene, D.L. Orange,  C.H. Baxter, B.H. Robison, R.E. Kochevar, J.W. Nybakken, D.L. Reed, C.M. McHugh (1996).  Biologic and Geologic Characteristics of Cold Seeps in Monterey Bay, California.  Deep-Sea Research, I, 43(11-12): 1739-1762
  • Barry, J.P., Yoklavich, M.M., Cailliet, G.M., Ambrose, D.A., Antrim, B.S. (1996). Trophic ecology of the dominant fishes in Elkhorn Slough, California.  Estuaries, 19: 115-138
  • McHatton, S.C., J.P. Barry, H.W. Jannasch, & D.C. Nelson (1996).  High nitrate concentrations in vacuolate, autotrophic marine Beggiatoa spp.  Appl. and Enviro. Micro. 62: 954-958.

1995

  • Barry, J.P., Baxter, C.H., Sagarin, R.D., Gilman, S.E. (1995).  Climate-related, long-term faunal changes in a California rocky intertidal community.  Science, 267: 672-675
  • Stoker, C.R., D.R. Barch, B.P. Hine III, & J.P. Barry (1995).  Antarctic undersea exploration using a robotic submarine with a telepresence user interface.  IEEE Expert Intelligent systems & their Applications, 10(6): 14-23.

1994

  • Stoker, C., Barry, J.P., Barch, D.R., Hine B.P. III.  (1994) Use of telepresence and virtual reality in undersea exploration: 1993 Antarctic telepresence experiment.  Pages 37-44 in: Proceedings of AAAI workshop AI technologies in environmental applications, Seattle WA, July 30-31, 1994.

1993

  • Barry, J.P. & Ehret, M.J. (1993) Diet, food preference, and algal availability for fishes and crabs on intertidal reef communities in southern California.  Env. Biol. Fish., 37: 75-95.
  • McFeters, G.A., Barry, J.P., Howington, J.P. (1993)  Distribution of enteric bacteria in Antarctic seawater surrounding a sewage outfall.  Water Res., 27: 645-650.

1992

  • Barry, J.P., & Baxter, C.H.  (1992)  Survey design considerations for deep-sea benthic communities using ROVs.  Mar. Tech. Soc., 26(4):20-26.
  • Howington, J.P., McFeters, G.A., Barry, J.P., Smith, J.J.  (1992)  Mapping the McMurdo Station sewage plume.  Mar. Poll. Bull., 25: 9-12

1991

  • Barry, J.P. & Dayton, P.K.  (1991)  Physical Heterogeneity and the Community Organization of Marine Systems.  Pp 270-320 in: Ecological Heterogeneity, Springer Verlag, J. Kolasa & S. Pickett (eds.)
  • Grebmeier, J.M. & Barry, J.P.  (1991)  The influence of oceanographic processes on pelagic-benthic coupling in polar regions: a benthic perspective.  J. Mar. Sys., 2: 495-518.
  • Yoklavich, M.M., Cailliet, G.M., Barry, J.P., Ambrose, D.A., Antrim, B.S.  (1991)  Temporal and spatial patterns in abundance and diversity of fishes in Elkhorn Slough, California. Estuaries, 14:465-480

<1991

  • Barry, J.P.  (1988)  Hydrographic patterns in McMurdo Sound, Antarctica and their relationship to biological productivity.  Polar Biol.,  8:377-391.
  • Barry, J.P.  (1989)  Reproductive response of a marine annelid to winter storms: an analog to fire adaptation in plants?  Mar. Ecol. Prog. Ser., 54:99-107
  • Barry, J.P. & Cailliet, G.M.  (1981)  The utilization of shallow marsh habitats by commercially important fishes in Elkhorn Slough, California.  Cal-Neva Wildlife Trans. 1981:38-47.
  • Barry, J.P. & Dayton, P.K.  (1988)  Current patterns in McMurdo Sound, Antarctica and their relationship to local biotic communities.  Polar Biol., 8:367-376.
  • Barry, J.P. & Tegner, M.J.  (1990)  Inferring demographic processes from size frequency distributions: simple models indicate specific patterns of growth and mortality.  Fish. Bull., 88;13-19
  • Cailliet, G.M. & Barry, J.P.  (1978)  Com­parison of food array overlap measures useful in fish feeding habit analysis.  From the Proc.­ Second Pacific Northwest Tech. Work., October 10-13, 1978.  Maple Valley, Washington.
  • Dayton, P.K., Watson, D., Pal­misano, A., Barry, J.P., Oliver, J.S., Rivera, D.  (1986)  Benthic microalgal standing stock and primary production at McMurdo Sound, Antarctica.  Polar Biol., 6:207-213.

Publications (Un-refereed Contributions)

  • Barry, J.P. (2013).  The sustainability of ocean resources.  Pages 201-205 in, Practicing Sustainability, G. Madhavan, B. Oakley, D. Green, D. Koon, P. Low (eds.) Springer, New York.
  • Cooley, S., Mathis, J., Yates, K., Turley, C. (eds.) (J. Barry, contrib. author). Frequently asked questions about ocean acidification (2013).  U.S. Ocean Carbon and Biogeochemistry Program and the UK. Ocean Acidification Research Programme, Version 2 (WHOI OA FAQs).
  • Kuhnz, L.A., Barry, J.P., Buck, K., Lovera, C., Whaling, P.J. (2011).  Potential impacts of the Monterey Accelerated Research System (MARS) cable on the seabed and benthic faunal assemblages. Report to Monterey Bay National Marine Sanctuary.
  • Cooley, S., Riebesell, U., Gattuso, J.-P., and others (including Barry, J.P.  2010.  FAQ on ocean acidification.  Ocean Biogeochemistry Program.
  • U.S. Senate, Transcript of Hearing before the Subcommittee on Oceans, Atmosphere, Fisheries, and Coast Guard on the Committee on Commerce, Science, and Transportation, U.S. Senate, 111th Congress, April 22, 2010.  The Environmental and Economic Impacts of Ocean Acidification. Senate Hearing Link
  • Barry, J.P. (2010). Marine organisms and ecosystems in a high-CO2 ocean, and An overview of recommendations from the NRC Committee Report on Development of an integrated science strategy for ocean acidification monitoring , research, and impacts assessment.  Written testimony for the April 22, 2010 U.S. Senate Hearing on The environmental and economic impacts of ocean acidification, held by the U.S. Senate Committee on Commerce, Science and Transportation (Oceans,  Atmosphere, Fisheries and Coast Guard Subcommittee)
  • Barry, J.P. (2010). Response to questions for the record (A), The environmental and economic impacts of ocean acidification, April 22, 2010
  • Barry, J.P. (2010). Response to questions for the record (B), The environmental and economic impacts of ocean acidification, April 22, 2010
  • Barry, J.P., Kuhnz, L., Buck, K., Lovera, C., Whaling, P.J. (2010).  Potential Impacts of the MARS Cable on the seabed and benthic faunal assemblages.  Report to: Monterey Bay National Marine Sanctuary.
  • Brewer, P.G. and Barry, J.P.  (2008)  Ocean acidification: The Other Carbon Dioxide Problem, Scientific American, commentary
  • Barry, J.P., Pane, E.F., Brewer, P.G. (2006) Ocean Ecosystems and the Carbon Dioxide Invasion. Ecosystems Observations for the Monterey Bay National Marine Sanctuary. NOAA Monterey Bay National Marine Sanctuary.
  • Ricketts, E.R., Kennett, J.P., Hill, T.M., and Barry, J.P (2005).  Effects of CO2 hydrate on deep-sea foraminiferal assemblages.  Proceedings of the Fifth International Conference on Gas Hydrates, Trondheim, Norway, 3, (3020): 839-847.
  • Barry, J.P., Seibel, B.A., Drazen, J.C., Tamburri, M.N., Buck, K.R., Lovera, C., Kuhnz, L., Peltzer, E.T., Osborn, K., Whaling, P.J, Walz, P., Brewer, P.G. (2003) Deep-sea field experiments on the biological impacts of direct deep-sea CO2 injection.  Proceedings of the Second Annual Conference on Carbon Sequestration, May 5-8, 2003, Alexandria, VA.
  • Barry, J.P., Young, C., and Nelson, D.  (2001). Biological impacts of deep-sea CO2 sequestration, Report for CO2 sequestration workshop, MBARI, 2001.
  • Smith, K.L. Jr., Barry, J.P., Beaulieu, S.E., Priede, I.G., Robison, B.H., Shank, T.M., Wakefield, W.W. (2001), Real-time, long-term ecological studies in the deep ocean, report of working group for deep-sea ecological studies for NEPTUNE
  • DeVogelaere, A., Tamburri, M., Clague, D., Barry, J., and Benson, S. (2000).  Exploring the Davidson Seamount.  Pages 8 in: Ecosystem Observations for the Monterey Bay National Marine Sanctuary, NOAA Monterey Bay National Marine Sanctuary.
  • Dawe, T.C., D.S. Stakes, P.R. McGill, J. Barry, S. Etchemendy (1998).  Subsea Instrument deployments: methodology and techniques using a work class remotely operated vehicles (ROV).  Proceedings, 1998 Oceans Conference, Nice, France
  • Barry, J.P.  (1995). Ocean current observations near McMurdo Station, Antarctica, 1993 to 1994: Relation to wastewater discharge dispersal.  Idaho National Engineering Laboratory Report 95/0362, 104p.
  • Barry, J.P.  (1994). Ocean Current Observations near McMurdo Station, Antarctica from 1991 to 1993: Relation to Wastewater Discharge Dispersal.  Idaho National Engineering Laboratory Report EGG-CIET-11280, 100p
  • Barry, J.P. Robison, B.H., Greene, H.G., Baxter, C.H., Harrold, C., Kochevar, R.E., Orange, D., Lisin, S., Whaling, P.J., Nybakken, J.  (1993)  Investigations of cold seep communities in Monterey Bay, California, using a remotely operated vehicle.  American Academy of Underwater Science, 1993 Symposium Volume.
  • Lissner, A., Barry, J.P., Heilprin, D., Davison, D.  (1992)  Trawl and remotely operated vehicle ocean studies report for detailed physical and biological oceanographic studies for an ocean site designation effort under the marine protection, research and sanctuaries act of 1972 (MPRSA).  Prepared for U.S. Environmental Protection agency, EPA contract number 68-C8-0062.
  • Howington, J.P., Barry, J.P., Smith, J.J. & McFeters, G.A.  (1992)  Mapping the McMurdo Station sewage plume using bacterial indicators.  Ant. J. U. S.
  • Barry, J.P., Dunbar, R, Leventer-Reed, A., Dayton, P.K.  (1991)  Measurements of Ocean Currents in McMurdo Sound, Antarctica during the austral winter, 1989.  Ant. J. U. S.
  • Foster, M, Stellar, D., Barry J.P. (1990) Review of San Diego Gas and Electric Company (1989) Notice of Intention: The effects on the Marine Environment of the Proposed Changes (Combined Cycle) to Power Plants at Encina or South Bay.  Final report for the California Energy Commission on Agreements 700-89-012 and 700-89-014.  Report to: Mr. Richard Anderson, The California Energy Commission, 3600 Ashe Road, #17, Bakersfield, Ca.  93309.
  • Barry, J.P.  (1988)  Pattern and Process: Patch Dynamics in a Rocky Intertidal Community in Southern California.  Ph.D. Dissertation, Scripps Inst. of Oceanography, Univ. of California, San Diego, 335 pp.
  • Barry, J.P., Dayton, P.K.  (1986)  Oceanographic Influences on Marine Benthic Communities in McMurdo Sound, Antarctica.  Ant. J. U. S., 21:78.
  • Dayton, P.K., Kooyman, G., Barry, J.P.  (1984)  Benthic life under thick ice.  Ant. J. U. S., 19(5):128
  • Barry, J.P. (1983) Utilization of shallow marsh habitats by fishes in Elkhorn Slough, California.  Master’s thesis, San Jose State University, San Jose, CA 95 pp;