Monterey Bay Aquarium Research Institute
John Ryan - Publications

Coastal Oceanography
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. 2014c. 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.
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.
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
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
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
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
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.
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.
Harvey, J.B.J., J.P. Ryan, R. Marin III, C.M. Preston, N. Alvarado, C.A. Scholin, R.C. Vrijenhoek (2011). Robotic sampling, in situ monitoring and molecular detection of marine zooplankton. J. Exp. Mar. Biol. Ecol., doi:10.1016/j.jembe.2011.11.022.
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.
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.
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.
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
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.
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
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
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.
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.
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.
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.
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, in press.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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, 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.
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.
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, 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.
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.
Large-Scale Oceanography
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.
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.
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.
Ryan, JP, PS Polito, PG Strutton and FP Chavez. 2002. Unusual Large-scale blooms in the equatorial Pacific. Progress in Oceanography, 55:263-285.
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.
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.
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.
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.
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.


Last updated: Feb. 20, 2009