John is a biological oceanographer studying the ecology of plankton, fish, and mammals—primarily through integration of remote and in situ sensing technologies. Through science–engineering collaborations this research involves advancing methods of sampling and data analysis.


Oestreich, W.K., B. Abrahms, M. McKenna, J. Goldbogen, L. Crowder, J. Ryan (2022) Acoustic signature reveals blue whales tune life history transitions to oceanographic conditions.  Functional Ecology, 36: 882-895. DOI: 10.1111/1365-2435.14013

Smith, K.B., P. Leary, T. Deal, J. Joseph, J. Ryan, C. Miller, C. Dawe, B. Cray (2022) Acoustic vector sensor analysis of the Monterey Bay region soundscape and the impact of COVID-19. Journal of the Acoustical Society of America 151, 2507. DOI: 10.1121/10.0010162


Cade, D.E., J.A. Fahlbusch, W.K. Oestreich, J. Ryan, J. Calambokidis, K.P. Findlay, A.S. Friedlaender, E.L. Hazen, S. Mduduzi Seakamela, J.A. Goldbogen (2021) Social exploitation of extensive, ephemeral, environmentally controlled prey patches by supergroups of rorqual whales. Animal Behaviour 182: 251-266.  DOI:10.1016/j.anbehav.2021.09.013

Harvey, J.B.J., J.P. Ryan, Y. Zhang (2021) Influences of Extreme Upwelling on a Coastal Retention Zone.  Frontiers in Marine Science. DOI:10.3389/fmars.2021.648944

Krumpel, A., A. Rice, K.E. Frasier, F. Reese, J.S. Trickey, A.E. Simonis, J.P. Ryan, S.M. Wiggins, A. Denzinger, H. Schnitzler, S. Baumann-Pickering (2021) Long-Term Patterns of Noise From Underwater Explosions and Their Relation to Fisheries in Southern California. Frontiers in Marine Science 8: 1925. DOI:10.3389/fmars.2021.796849    

Ruhl, H.A., J.A. Brown, A.R. Harper, E.L. Hazen, L. deWitt, P. Daniel, A. DeVogelaere, R.M. Kudela, J.P. Ryan,  A.D. Fischer,  F.E. Muller-Karger,  F.P. Chavez (2021) Integrating Biodiversity and Environmental Observations in Support of National Marine Sanctuary and Large Marine Ecosystem Assessments. Oceanography 34(2): 142-155. DOI:10.5670/oceanog.2021.221

Ryan, J.P., J.E. Joseph, T. Margolina, L.T. Hatch, A. Azzara, A. Reyes, B.L. Southall, A. DeVogelaere, L.E. Peavey Reeves, Y. Zhang, D.E. Cline, B. Jones, P. McGill, S. Baumann-Pickering, A.K. Stimpert (2021) Reduction of Low-Frequency Vessel Noise in Monterey Bay National Marine Sanctuary During the COVID-19 Pandemic. Frontiers in Marine Science 8. DOI:10.3389/fmars.2021.656566

Satterthwaite EV, Ryan JP, Harvey JBJ, Morgan SG (2021) Invertebrate larval distributions influenced by adult habitat distribution, larval behavior, and hydrodynamics in the retentive upwelling shadow of Monterey Bay, California, USA. Mar Ecol Prog Ser 661:35-47.

Thys, T.M., Nyegaard, M., Whitney, J.L., Ryan, J.P., Potter, I., Nakatsubo, T., et al. (2021) Ocean Sunfish Larvae: Detections Identification, and Predation. pp. 105-128 in Thys, T.M., Hayes, G.C., Houghton, J.D.R, eds. The Ocean Sunfishes: Evolution, Biology and Conservation. Taylor and Francis, Abingdon.

Zhang, Y., M.A. Godin, B. Kieft, B. Raanan, J.P. Ryan, B.W. Hobson (2021). Finding and Tracking a Phytoplankton Patch by a Long-Range Autonomous Underwater Vehicle. IEEE Journal of Oceanic Engineering. DOI: 10.1109/JOE.2021.3122195

Zhang, Y, Ryan, J. P. Hobson, B. W., Kieft, B., Romano, A., Barone, B., Preston, C. M., Roman, B., Raanan, B-Y, Pargett, D., Dugenne, M., White, A. E., Freitas, F. H., Poulos, S., Wilson, S. T., DeLong, E. F., Karl, D. M., Birch, J. M., Bellingham, J. G., Scholin, C. A. (2021) A system of coordinated autonomous robots for Lagrangian studies of microbes in the oceanic deep chlorophyll maximum. Science Robotics 6(50), eabb9138. doi: 10.1126/scirobotics.abb9138.


Haver SM, Rand Z, Hatch LT, Lipski D, Dziak RP, Gedamke J, Haxel J, Heppell SA, Jahncke J, McKenna MF, Mellinger DK, Oestreich WK, Roche L, Ryan J, Van Parijs SM. Seasonal trends and primary contributors to the low-frequency soundscape of the Cordell Bank National Marine Sanctuary. J Acoust Soc Am. 2020 Aug;148(2):845. doi: 10.1121/10.0001726. PMID: 32873009.

Oestreich, W.K., J.A. Fahlbusch, D.E. Cade, J. Calambokidis, T. Margolina, J. Joseph, A.S. Friedlaender, M.F. McKenna, A.K. Stimpert, B.L. Southall, J.A. Goldbogen, J.P. Ryan (2020). Animal-borne metrics enable acoustic detection of blue whale migration. Current Biology 30(23), 4773-4779. doi 10.1016/j.cub.2020.08.105

Satterthwaite, E.V, Morgan, S.G., Ryan, J.P., Harvey, J.B.J., Vrijenhoek, R.C. (2020) Seasonal and synoptic oceanographic changes influence the larval biodiversity of a retentive upwelling shadow. Progress in Oceanography 182. doi:10.1016/j.pocean.2019.102261

Simonis, A. E., Forney K. A., Rankin S., Ryan J., Zhang Y., DeVogelaere A., Joseph J., Margolina T., Krumpel A., Baumann-Pickering S. (2020). Seal Bomb Noise as a Potential Threat to Monterey Bay Harbor Porpoise. Front. Mar. Sci. 7, 142. doi:10.3389/fmars.2020.00142

Zhang, B. Kieft, B. W. Hobson, J. Ryan, B. Barone, C. Preston, B. Roman, B-Y. Raanan, R. Marin III, T. O’Reilly, C. Rueda, D. Pargett, K. Yamahara, S. Poulos, A. Romano, G. Foreman, H. Ramm, S. Wilson, E. DeLong, D. Karl, J. Birch, J. Bellingham, and C. Scholin (2020) Autonomous Tracking and Sampling of the Deep Chlorophyll Maximum Layer in an Open-Ocean Eddy by a Long Range Autonomous Underwater Vehicle. IEEE Journal of Oceanic Engineering 45(4), 1308-1321. doi: 10.1109/JOE.2019.2920217


Benoit‐Bird, K. J., Waluk, C. M., & Ryan, J. P. ( 2019). Forage species swarm in response to coastal upwelling. Geophysical Research Letters, 46, 1537– 1546.

Fossum, T. O., Ryan, J., Mukerji, T., Eidsvik, J., Maughan, T., Ludvigsen, M., & Rajan, K. (2019). Compact models for adaptive sampling in marine robotics. The International Journal of Robotics Research.

Kiene, R. P., Nowinski, B., Esson, K., Preston, C., Marin, R., Birch, J., Scholin, C., Ryan, J., Moran M. A. (2019). Unprecedented DMSP concentrations in a massive dinoflagellate bloom in Monterey Bay, CA. Geophysical Research Letters, 46, 12279– 12288..

Ryan J. P., Cline D. E., Joseph J. E, Margolina T., Santora J. A., Kudela R. M., Chavez F. P., Pennington J. T., Wahl C., Michisaki R., Benoit-Bird K., Forney K. A., Stimpert A. K., DeVogelaere A., Black N., Fischer M. (2019). Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific. PLoS ONE 14(9): e0222456.

Yamahara, K. M., C. M. Preston, J. Birch, K. Walz, R. Marin III, S. Jensen, D. Pargett, B. Roman, W. Ussler III, Y. Zhang, J. Ryan, B. Hobson, B. Kieft, B. Raanan, K. D. Goodwin, F. P. Chavez, and C. Scholin, “In situ Autonomous Acquisition and Preservation of Marine Environmental DNA Using an Autonomous Underwater Vehicle,” Frontiers in Marine Science, Vol. 6, Article 373, pp. 1-14, 2019, DOI: 10.3389/fmars.2019.00373

Zhang Y., Ryan J. P., Kieft B., Hobson B. W., McEwen R. S., Godin M. A., Harvey J. B., Barone B,, Bellingham J. G., Birch J. M., Scholin C. A., Chavez F. P. (2019) Targeted Sampling by Autonomous Underwater Vehicles. Frontiers in Marine Science 6:415. doi:10.3389/fmars.2019.00415

Zhang, B. Kieft, B. Hobson, J. Ryan, B. Barone, C. Preston, B. Roman, B-Y. Raanan, R. Marin III, T. O’Reilly, C. Rueda, D. Pargett, K. Yamahara, S. Poulos, A. Romano, G. Foreman, H. Ramm, S. Wilson, E. DeLong, D. Karl, J. Birch, J. Bellingham, and C. Scholin, “Autonomous Tracking and Sampling of the Deep Chlorophyll Maximum Layer in an Open-Ocean Eddy by a Long Range Autonomous Underwater Vehicle,” IEEE Journal of Oceanic Engineering, DOI: 10.1109/JOE.2019.2920217

Zhang, Y., C. Rueda, B. Kieft, J. P. Ryan, C. Wahl, T. C. O‘Reilly, T. Maughan, and F. P. Chavez, “Autonomous Tracking of an Oceanic Thermal Front by a Wave Glider,” Journal of Field Robotics, Vol. 36, pp. 940-954, 2019, DOI: 10.1002/rob.21862


Birch, J.M., Barone, B., DeLong, E., Foreman, G., Gomes, K., Hobson, B., Jensen, S., Karl, D.M., Kieft, B., O’Reilly, T., Pargett, D., Preston, C., Roman, B., Romano, A., Ryan, J., Scholin, C.A., Ussler, W., Yamahara, K., Zhang, Y., (2018). Autonomous targeted sampling of the deep chlorophyll maximum layer in a subtropical north Pacific eddy. Oceans 2018 MTS/IEEE : 5.

Bowers, H. A., J. P. Ryan, K. Hayashi, A. L. Woods, R. Marin III, G. J. Smith, K. A. Hubbard, G. J. Doucette, C. M. Mikulski, A. G. Gellene, Y. Zhang, R. M. Kudela, D. A. Caron, J. M. Birch, and C. A. Scholin, “Diversity and Toxicity of Pseudo-nitzschia Species in Monterey Bay: Perspectives from Targeted and Adaptive Sampling,” Harmful Algae, Vol. 78, pp. 129-141, 2018. DOI: 10.1016/j.hal.2018.08.006.

Hobson, B., B. Kieft, B. Raanan, Y. Zhang, J. Birch, J. P. Ryan, and F. P. Chavez, “An Autonomous Vehicle Based Open Ocean Lagrangian Observatory,” Proc. IEEE AUV’2018, pp. 1-5, Porto, Portugal, November 2018.


Caron, D.A., Gellene, A.G., Smith, J., Seubert, E.L., Campbell, V., Sukhatme, G.S., Seegers, B., Jones, B.H., Lie, A.A.Y., Terrado, R., Howard, M.D.A., Kudela, R.M., Hayashi, K., Ryan, J., Birch, J., Demir-Hilton, E., Yamahara, K., Scholin, C., Mengel, M., Robertson, G. (2017). Response of phytoplankton and bacterial biomass during a wastewater effluent diversion into nearshore coastal waters. Estuarine, Coastal and Shelf Science, 186: 223-236.

Chavez, F.P., J.T. Pennington, R.P. Michisaki, M. Blum, G.M. Chavez, J. Friederich, B. Jones, R. Herlien, B. Kieft, B. Hobson, A.S. Ren, J. Ryan, J.C. Sevadjian, C. Wahl, K.R. Walz, K. Yamahara, G.E. Friederich, and M. Messié. 2017. Climate variability and change: Response of a coastal ocean ecosystem. Oceanography 30(4):128–145,

Fischer, A.M., J.P. Ryan, E.V. Rienecker (2017). Fine scale mapping of the structure and composition of the Elkhorn Slough (California, USA) tidal plume. Estuarine, Coastal and Shelf Science, 184, 10-20. doi: 10.1016/j.ecss.2016.10.035

Ryan, J.P., Green, J.R., Espinoza, E., Hearn, A.R. (2017). Association of whale sharks (Rhincodon typus) with thermo-biological frontal systems of the eastern tropical Pacific. PLoS ONE 12(8): e0182599.

Ryan, J. P., R. M. Kudela, J. M. Birch, M. Blum, H. A. Bowers, F. P. Chavez, G. J. Doucette, K. Hayashi, R. Marin III, C. M. Mikulski, J. T. Pennington, C. A. Scholin, G. J. Smith, A. Woods, Y. Zhang (2017). Causality of an extreme harmful algal bloom in Monterey Bay, California, during the 2014–2016 northeast Pacific warm anomaly, Geophys. Res. Lett., 44, doi:10.1002/2017GL072637.

Thys, T. M., A. R. Hearn, K. C. Weng, J. P. Ryan, C. Peñaherrera-Palma (2017). Satellite Tracking and Site Fidelity of Short Ocean Sunfish, Mola ramsayi, in the Galapagos Islands. Journal of Marine Biology, vol. 2017, Article ID 7097965. doi:10.1155/2017/7097965

Zhang, Y., B. Kieft, M. J. Stanway, R. S. McEwen, B. W. Hobson, J. G. Bellingham, J. P. Ryan, T. C. O’Reilly, B. Y. Raanan, M. Messie, J. M. Smith, F. P. Chavez (2017). Isotherm Tracking by an Autonomous Underwater Vehicle in Drift Mode. IEEE Journal of Oceanic Engineering. doi: 10.1109/JOE.2016.2625058


Ryan, J., D. Cline, C. Dawe, P. McGill, Y. Zhang, J. Joseph, T. Margolina, M. Caillat, M. Fischer, A. DeVogelaere, A. Stimpert, B. Southall (2016). New passive acoustic monitoring in Monterey Bay National Marine Sanctuary: exploring natural and anthropogenic sounds in a deep soundscape. OCEANS 2016 MTS/IEEE, Monterey, CA USA, doi: 10.1109/OCEANS.2016.7761363

Thys, T., J. Ryan, K. C. Weng, M. Erdmann, J. Tresnati (2016). Tracking a Marine Ecotourism Star: Movements of the Short Ocean Sunfish Mola ramsayi in Nusa Penida, Bali, Indonesia. J. Mar. Biol. 2016(3):1-6. doi: 10.1155/2016/8750193

Zhang, Y., J. G. Bellingham, J. P. Ryan, B. Kieft, M. J. Stanway (2016). Autonomous 4-D Mapping and Tracking of a Coastal Upwelling Front by an Autonomous Underwater Vehicle. Journal of Field Robotics, 33, 67-81. doi: 10.1002/rob.21617

Zhang, Y., B. Kieft, C. Rueda, T. O’Reilly, J. Ryan, T. Maughan, C. Wahl, F. Chavez (2016). Autonomous front tracking by a Wave Glider. OCEANS MTS/IEEE Monterey. doi: 10.1109/OCEANS.2016.7761070


Brewer, P.G., E.T. Peltzer, J. Ryan, W.J. Kirkwood, A.F. Hofmann (2015) Ocean chemistry and the speed of sound in sea water. Marine Chemistry 177: 591-606.

Das, J., F. Py, J. B.J. Harvey, J. P. Ryan, A. Gellene, R. Graham, D. A. Caron, K. Rajan, G. S. Sukhatme (2015) Data-driven robotic sampling for marine ecosystem monitoring. Int. J. Robotics Res. 1–18. doi: 10.1177/0278364915587723

Lecher, A. L., K. Mackey, R. Kudela, J. Ryan, A. Fisher, J. Murray, and A. Paytan, 2015. Nutrient Loading through Submarine Groundwater Discharge and Phytoplankton Growth in Monterey Bay, CA. Environmental Science & Technology doi: 10.1021/acs.est.5b0090

Pargett, D. M., J. M. Birch, C. M. Preston, J. P. Ryan, Y. Zhang, and C. A. Scholin, “Development of a Mobile Ecogenomic Sensor,” Proc. MTS/IEEE Oceans’15, pp. 1-6, Washington, D.C., U.S.A., October 2015.

Thys, T. M., J. P. Ryan, , H. Dewar, , C. R. Perle, , K. Lyons, , J. O’Sullivan, , C. Farwell, , M. J. Howard, , K. C. Weng, , B. E. Lavaniegos, G. Gaxiola-Castro, , L. E. M. Bojorquez, , E. L. Hazen, , S. J. Bograd (2015) Ecology of the Ocean Sunfish, Mola mola, in the southern California Current System. J. Exp. Mar. Biol. Ecol. 471: 64-76. doi:10.1016/j.jembe.2015.05.005

Varaljay, V. A., J. Robidart, C. M. Preston, S. M. Gifford, B. P. Durham, A. S. Burns, J. P. Ryan, R. Marin III, R. P. Kiene, J. P. Zehr, C. A. Scholin, M. A. Moran (2015) Single-taxon field measurements of bacterial gene regulation controlling DMSP fate, The ISME Journal 9: 1677–1686. doi:10.1038/ismej.2015.23

Zhang, Y. J. G. Bellingham, J. P. Ryan, M. A. Godin (2015) Evolution of a physical and biological front from upwelling to relaxation. Cont. Shelf Res. 108: 55-64. doi:10.1016/j.csr.2015.08.005

Zhang, Y., B. Kieft, R. McEwen, M. J. Stanway, J. Bellingham, J. Ryan, B. Hobson, D. Pargett, J. Birch, and C. Scholin (2015) Tracking and Sampling of a Phytoplankton Patch by an Autonomous Underwater Vehicle in Drifting Mode. Proc. MTS/IEEE Oceans’15, pp. 1-5, Washington, D.C., U.S.A., October 2015.


Berdalet, E, MA McManus, ON Ross, H Burchard, FP Chavez, JS Jaffe, IR Jenkinson, R Kudela, I Lips, U Lips, A Lucas, D Rivas, MC Ruiz-de la Torre, J Ryan, JM Sullivan, H Yamazaki (2014) Understanding harmful algae in stratified systems: Review of progress and future directions. Deep Sea Research II 101: 4-20. doi: 10.1016/j.dsr2.2013.09.042.

Fischer, AM, JP Ryan, C Levesque, N Welschmeyer (2014) Characterizing estuarine plume discharge into the coastal ocean using fatty acid biomarkers and pigment analysis. Marine Environmental Research, DOI: 10.1016/j.marenvres.2014.04.006

Robidart JC, MJ Church, JP Ryan, F Ascani, ST Wilson, D Bombar, R Marin III, KJ Richards, DM Karl, CA Scholin, JP Zehr (2014) Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal, doi:10.1038/ismej.2013.244.

Ryan, JP, MA McManus, RM Kudela, M Lara Artigas, JG Bellingham, FP Chavez, G Doucette, D Foley, M Godin, JBJ Harvey, R Marin III, M Messié, C Mikulski, T Pennington, F Py, K Rajan, I Shulman, Z Wang, Y Zhang (2014) Boundary influences on HAB phytoplankton ecology in a stratification-enhanced upwelling shadow. Deep Sea Research II 101: 63-79. doi: 10.1016/j.dsr2.2013.01.017.

Ryan, JP, JBJ Harvey, Y Zhang, B Woodson (2014) Distributions of invertebrate larvae and phytoplankton in a coastal upwelling system retention zone and peripheral front. J. Exp. Mar. Biol. Ecol., 459:51-60.

Ryan, JP, CO Davis, NB Tufillaro, RM Kudela, BC Gao (2014) Application of the Hyperspectral Imager for the Coastal Ocean to Phytoplankton Ecology Studies in Monterey Bay, CA, USA. Remote Sens. 6: 1007-1025.

Sevadjian, JC, MA McManus, JP Ryan, AT Greer, RK Cowen, CB Woodson (2014) Across-shore variability in plankton layering and abundance associated with physical forcing in Monterey Bay, California. Cont. Shelf Res. 72: 138-151.


Ottesen, EA, CR Young , JM Eppley, JP Ryan, FP Chavez , CA Scholin, EF DeLong (2013) Pattern and synchrony of gene expression among sympatric marine microbial populations, PNAS, doi:10.1073/pnas.1222099110.

Zhang, Y., Bellingham, J.G., Ryan, J.P., Kieft, B., Stanway, M.J., (2013). Two-dimensional mapping and tracking of a coastal upwelling front by an autonomous underwater vehicle. Proceedings of Marine Technology Society/Institute of Electrical and Electronics Engineers Oceans 2013.


Das, J., Py, F., Maughan, T., O’Reilly, T., Messie, M., Ryan J., Sukhatme G., Rajan, K. (2012) Coordinated sampling of dynamic oceanographic features with underwater vehicles and drifters, International Journal of Robotics Research 31,626-646. doi: 10.1177/0278364912440736.

Das, J., Py, F., Maughan, T., O’Reilly, T., Messié, M., Ryan, J., Sukhatme, G.S., Rajan, K., (2012). Simultaneous tracking and sampling of dynamic oceanographic features with AUVs and drifters. Experimental Robotics, 79: 541-555.

Das, J., Harvey, J., Ryan, J., Py, F., Graham, R., Rajan, K., Sukhatme, G., (2012). Multi-stage Bayesian regression for adaptive sampling of marine phenomena. RSS 2012 Workshop on Robotics for Environmental Monitoring.

Frolov, S., J. Ryan, F. Chavez (2012) Predicting euphotic-depth-integrated chlorophyll-a from discrete depth and satellite-observable chlorophyll-a off central California, J. Geophys. Res., in press.

Harvey, J.B.J., J. P. Ryan, R. Marin III, C. M. Preston, N. Alvarado, C. A. Scholin, and R. C. Vrijenhoek (2012) Robotic sampling, in situ monitoring and molecular detection of marine zooplankton. Journal of Experimental Marine Biology and Ecology 413, 60-70.

Harvey, J., Zhang, Y., Ryan, J., (2012). AUVs for ecological studies of marine plankton communities. Sea Technology Magazine, 53: 51-54.

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, 3:33. doi: 10.3389/fmicb.2012.00033.

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, Geophys. Res. Lett., 39, L03804, doi:10.1029/2011GL050324.

Zhang, Y., Ryan, J.P., Bellingham, J.G., Harvey, J.B.J., McEwen, R.S., (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.

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, Vol. 37, No. 3, pp. 338-347, July 2012, DOI: 10.1109/JOE.2012.2197272.

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, Vol. 37, No. 3, pp. 544-553, July 2012, DOI: 10.1109/JOE.2012.2192340.


Godin, M.A., Zhang, Y., Ryan, J.P., Hoover, T.T., Bellingham, J.G., (2011). Phytoplankton bloom patch center localization by the Tethys autonomous underwater vehicle. OCEANS 2011.

Mazzillo, 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, doi:10.1016/j.hal.2011.06.009.

Ottesen, E.A., R. Marin, 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, doi:10.1038/ismej.2011.70.

Preston C.M., A. Harris, J.P. Ryan, B. Roman, R. Marin III, et al. (2011) Underwater Application of Quantitative PCR on an Ocean Mooring. PLoS ONE, doi:10.1371/journal.pone.0022522.

Ryan, J., D. Greenfield, R. Marin III, C. Preston, B. Roman, S. Jensen, D. Pargett, J. Birch, C. Mikulski, G. Doucette and C. Scholin (2011) Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnol. Oceanogr., doi:10.4319/lo.2011.56.4.1255.

Ryan, J. P., Y. Zhang, H. Thomas, E.V. Rienecker, R.K. Nelson and S.R. Cummings (2011) A high-resolution survey of a deep hydrocarbon plume in the Gulf of Mexico during the 2010 Macondo blowout. In: Monitoring and Modeling the Deepwater Horizon Oil Spill: A Record-Breaking Enterprise, Geophys. Monogr. Ser., vol. 195, edited by Y. Liu et al. AGU, doi:10.1029/2011GM001106.

Tkacik, D.S., Y. Luna-Cruz, N. Clinton, S. Spak and J. Ryan (2011) Atmospheric correction for MASTER image data using localized modelled and observed meteorology and trace gases. Remote Sensing Letters, doi:10.1080/01431161.2010.551550.

Woodson, CB, JA Barth, OM Cheriton, MA McManus, JP Ryan, L Washburn, et al. (2011) Observations of internal wave packets propagating along-shelf in northern Monterey Bay, Geophys. Res. Lett., 38, L01605, doi:10.1029/2010GL045453.

Zhang, Y., R.S. McEwen, J.P. Ryan, J.G. Bellingham, H. Thomas, C.H. Thompson, and E. Rienecker (2011) A Peak-Capture Algorithm Used on an Autonomous Underwater Vehicle in the 2010 Gulf of Mexico Oil Spill Response Scientific Survey. Journal of Field Robotics, doi:10.1002/rob.20399.

Zhang, Y., Godin, M., Bellingham, J.G., Ryan, J.P., (2011). Ocean front detection and tracking by an autonomous underwater vehicle. OCEANS 2011 : 1-4.


Das, J., F. Py, T. Maughan, J. Ryan, K. Rajan, and G. Sukhatme (2010) Simultaneous tracking and sampling of dynamic oceanographic features with autonomous underwater vehicles and Lagrangian drifters. Proceedings of the International Symposium on Experimental Robotics, New Delhi, India.

Das, J., K. Rajan, S. Frolov, J. Ryan, F. Py, D. Caron, and G. Sukhatme (2010) Towards marine bloom trajectory prediction for AUV mission planning. Proceedings of the International Conference on Robotics and Automation, Anchorage, Alaska.

Mackey, K. R. M., G. L. van Dijken, S. Mazloom, A. M. Erhardt, J. Ryan, K. R. Arrigo, and A. Paytan (2010) Influence of atmospheric nutrients on primary productivity in a coastal upwelling region, Global Biogeochem. Cycles, 24, GB4027, doi:10.1029/2009GB003737

Ryan, JP, MA McManus, JM Sullivan (2010) Interacting physical, chemical and biological forcing of phytoplankton thin-layer variability in Monterey Bay, California, Continental Shelf Research 30:7-16.

Ryan, JP, AM Fischer, RM Kudela, MA McManus, JS Myers, JD Paduan, CM Ruhsam, CB Woodson, Y Zhang (2010) Recurrent frontal slicks of a coastal ocean upwelling shadow, J. Geophys. Res., 115, C12070, doi:10.1029/2010JC006398.

Ryan, JP, SB Johnson, A Sherman, K Rajan, F Py, H Thomas, JBJ Harvey, L Bird, JD Paduan, RC Vrijenhoek (2010) Mobile autonomous process sampling within coastal ocean observing systems. Limnol. Oceanogr. Methods 8: 394–402.

Sullivan, J.M., M.A. McManus, O.M. Cheriton, K.J. Benoit-Bird, L. Goodman, Z. Wang, J. Ryan, M. Stacey, D.V. Holliday, C. Greenlaw, M.A. Moline, and M. McFarland (2010) Layered organization in the coastal ocean: An introduction to planktonic thin layers and the LOCO project. Continental Shelf Research, 30: 1-6.

Zhang, Y, RS McEwen, JP Ryan, JG Bellingham (2010) Design and Tests of an Adaptive Triggering Method for Capturing Peak Samples in a Thin Phytoplankton Layer by an Autonomous Underwater Vehicle. IEEE Journal of Oceanic Engineering 35:785-796, dio:10.1109/JOE.2010.2081031

Zhang, Y., Bellingham, J.G., Godin, M., Ryan, J., McEwen, R.S., Kieft, B., Hobson, B., Hoover, T., (2010). Thermocline tracking based on peak-gradient detection by an autonomous underwater vehicle. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Conference.


Chien, S., J Doubleday, D Tran, D Thompson, G Mahoney, Y Chao, R Castano, J Ryan, R Kudela, D Foley, A Balasuriya, H Schmidt, O Schofield, M Arrott, M Meissinger, D Mandl, S Frye, L Ong, P Cappelaere (2009) Towards an Autonomous Space In-situ Marine Sensorweb. 47th Meeting of the American Institute of Aeronautics and Astronautics, Orlando.

Dunagan, S, B Baldauf, P Finch, L Guild, E Hochberg, B Jaroux, L Johnson, B Lobitz, J Ryan, S Sandor-Leahy, J Shepanski (2009) Small satellite and UAS assets for coral reef and algal bloom monitoring. 33rd International Symposium on Remote Sensing of Environment, Lago Magglore, Italy.

Jessup, DA, MA Miller, JP Ryan, HM Nevins, HA Kerkering, A Mekebri, DB Crane, TA Johnson, RM Kudela (2009) Mass Stranding of Marine Birds Caused by a Surfactant-Producing Red Tide, PLoS ONE 4(2): e4550. doi:10.1371/journal.pone.0004550.

Rajan, K., Py, F., McGann, C., Ryan, J., O’Reilly, T., Maughan, T., Roman, B., (2009). Onboard adaptive control of AUV’s using automated planning and execution. Proceedings of the International Symposium on Unmanned Untethered Submersible Technology.

Ryan, JP, AM Fischer, RM Kudela, JFR Gower, SA King, R Marin III, FP Chavez (2009) Influences of upwelling and downwelling winds on red tide bloom dynamics in Monterey Bay, California, Continental Shelf Research, 29: 785–795.

Steinbuck, J, MT Stacey, MA McManus, OM Cheriton, JP Ryan (2009) Observations of turbulent mixing in a phytoplankton thin layer: Implications for formation, maintenance, and breakdown. Limnology and Oceanography, 54:1353–1368, doi: 10.4319/lo.2009.54.4.1353.

Woodson, CB, L Washburn, JA Barth, DJ Hoover, AR Kirincich, MA McManus, JP Ryan, J Tyburczy (2009) The northern Monterey Bay upwelling shadow front: Observations of a coastally- and surface-trapped buoyant plume. Journal of Geophysical Research, 114, C12013, doi:10.1029/2009JC005623.

Zhang, Y., McEwen, R.S., Ryan, J., Bellingham, J.G., (2009). An adaptive triggering method for capturing peak samples in a thin phytoplankton layer by an autonomous underwater vehicle. Proceedings of the Marine Technology Society/Institute of Electrical and Electronics Engineers Oceans Conference.


Kudela, RM, JP Ryan, MD Blakely, JQ Lane1, TD Peterson (2008) Linking the physiology and ecology of Cochlodinium to better understand harmful algal bloom events: a comparative approach. Harmful Algae, 7:278-292.

McGann C., F. Py K. Rajan, J. Ryan, R. Henthorn (2008) Adaptive Control for Autonomous Underwater Vehicles. In AAAI 23rd Conference on Artificial Intelligence, Integrated Intelligence Special Track, Chicago, July 13-17, 2008.

Rienecker, ER, JP Ryan, R Marin, M Blum, C Dietz, FP Chavez (2008) Mapping phytoplankton in situ using a laser-scattering sensor. Limnology and Oceanography: Methods, 6:153-161.

Ryan, JP, JFR Gower, SA King, WP Bissett, AM Fischer, RM Kudela, Z Kolber, F Mazzillo, EV Rienecker, FP Chavez (2008) A coastal ocean extreme bloom incubator. Geophysical Research Letters, 35, L12602, doi:10.1029/2008GL034081.

Ryan, JP, MA McManus, JD Paduan, and FP Chavez (2008) Phytoplankton thin layers within coastal upwelling system fronts. Marine Ecology Progress Series, 354:21-34.


Fox, M, D Long, F Py, K Rajan, J Ryan (2007) In situ analysis for intelligent control. Proceedings of IEEE/OES OCEANS Conference. 2007, ISBN:1-4244-0635-8, Aberdeen, Scotland.

Bird, LE, AD Sherman, JP Ryan (2007) Development of an Active, Large Volume, Discrete Seawater Sampler for Autonomous Underwater Vehicles, Proceedings of the Oceans MTS/IEEE Conference, Vancouver, Canada.


Carr, M-E, and 37 others (2006) A comparison of global estimates of marine primary production from ocean color. Deep-Sea Research II, 53:741-770.

Dierssen, HM, RM Kudela, JP Ryan, and RC Zimmerman (2006) Red and black tides: Quantitative analysis of water-leaving radiance and perceived color for phytoplankton, colored dissolved organic matter, and suspended sediments. Limnology and Oceanography, 51(6): 2646-2659.

Ryan, JP, I Ueki, Y Chao, H Zhang, P Polito, and FP Chavez (2006) Western Pacific modulation of large phytoplankton blooms in the central and eastern equatorial Pacific. Journal of Geophysical Research, Biogeosciences, 111, GO2013, doi:10.1029/2005JG000084.


Ryan, JP, HM Dierssen, RM Kudela, CA Scholin, KS Johnson, JM Sullivan, AM Fischer, EV Rienecker, PR McEnaney and FP Chavez (2005) Coastal ocean physics and red tides, an example from Monterey Bay, California. Oceanography, 18:246-255.

Ryan, JP, FP Chavez, and JG Bellingham (2005) Physical-biological coupling in Monterey Bay, California: topographic influences on phytoplankton ecology. Marine Ecology Progress Series, 287:23-32.


Sakamoto, C., et al. (2004) Influence of Rossby waves on nutrient dynamics and the plankton community structure in the North Pacific subtropical gyre. Journal of Geophysical Research, 109, C05032.


Chavez, FP, J Ryan, SE Lluch-Cota and M Niquen (2003) From anchovies to sardines and back: multidecadal change in the Pacific Ocean, Science 299(5604):217-221.

Fitzwater, SE , KS Johnson, VA Elrod, JP Ryan, LJ Coletti, SJ Tanner, RM Gordon, FP Chavez (2003) Iron, nutrient and phytoplankton biomass relationships in upwelled waters of the California coastal system, Continental Shelf Research, 23:1523-1544.


Campbell, J., and 22 others (2002) Comparison of algorithms for estimating ocean primary production from surface chlorophyll, temperature, and irradiance. Global biogeochemical cycles, 16(3), 10.1029/2001GB001444.

Chavez, FP, JT Pennington, CG Castro, JP Ryan, RP Michisaki, B Schlining, P Walz, KR Buck, A McFadyen and CA Collins (2002) Biological and chemical consequences of the 1997-98 El Niño in central California waters. Progress in Oceanography, 54:205-232.

Ryan, JP, PS Polito, PG Strutton and FP Chavez (2002) Unusual Large-scale blooms in the equatorial Pacific. Progress in Oceanography, 55:263-285.


McGillicuddy, D. J., V. K. Kosnyrev, J. P. Ryan, and J. A. Yoder (2001) Covariation of mesoscale ocean color and sea surface temperature patterns in the Sargasso Sea. Deep-Sea Research II, 48:1823-1836.

Polito, P. S., J. P. Ryan, W. T. Liu and F. P. Chavez (2001) Oceanic and atmospheric anomalies of tropical instability waves, Geophysical Research Letters, 28(11):2233-2236.

Ryan, JP, JA Yoder, and DW Townsend (2001) Influence of a Gulf Stream warm-core ring on water mass and chlorophyll distributions along the southern flank of Georges Bank. Deep-Sea Research II, 48:159-178.

Strutton, P. G., J. P. Ryan and F. P. Chavez (2001) Enhanced chlorophyll associated with tropical instability waves in the equatorial Pacific. Geophysical Research Letters, 28:2005-2008.


Goyet, C, RJ Healy, and JP Ryan (2000) Global distribution of total inorganic carbon and total alkalinity below the deepest winter mixed layer depths. ORNL/CDIAC-127, NDP-076. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, 40 pp. CDIAC NDP-076


Ryan, JP, JA Yoder, PC Cornillon, and JA Barth (1999) Chlorophyll enhancement and mixing associated with meanders of the shelfbreak front in the Mid-Atlantic Bight. Journal of Geophysical Research, 104:23,479-23,493.

Ryan, JP, JA Yoder, and PC Cornillon (1999) Enhanced chlorophyll at the shelfbreak of the Mid-Atlantic Bight and Georges Bank during the spring transition. Limnology and Oceanography, 44:1-11.


Ryan, JP and JA Yoder (1996) Long-term mean and event-related pigment distributions during the unstratified period in South Atlantic Bight outer margin and middle shelf waters. Continental Shelf Research, 16:1165-1183.