Publications


Le, K. T., Yuan, Z., Syed, A., Ratelle, D., Orenstein, E. C., Carter, M. L., Strang, S., Kenitz, K. M., Morgado, P., Franks, P. J. S., Vasconcelos, N., & Jaffe, J. S. (2022). Benchmarking and Automating the Image Recognition Capability of an In Situ Plankton Imaging System. Frontiers in Marine Science, 9, 869088. https://doi.org/10.3389/fmars.2022.869088
Giddings, A., Franks, P. J. S., & Baumann-Pickering, S. (2022). Monthly to Decadal Variability of Mesoscale Stirring in the California Current System: Links to Upwelling, Climate Forcing, and Chlorophyll Transport. Journal of Geophysical Research-Oceans, 127(6). https://doi.org/10.1029/2021jc018180
Franks, P. J. S., Inman, B. G., MacKinnon, J. A., Alford, M. H., & Waterhouse, A. F. (2021). Oceanic turbulence from a planktonic perspective. Limnology and Oceanography, 16. https://doi.org/10.1002/lno.11996
Villamana, M., Franks, P. J. S., Castro, B. F., Gilcoto, M., Maranon, E., & Mourino-Carballido, B. (2021). A pseudo-Lagrangian transformation to study a chlorophyll-a patch in the Ria de Vigo (NW Iberian Peninsula). Journal of Geophysical Research-Oceans, 126(10), 16. https://doi.org/10.1029/2021jc017455
Zaba, K. D., Franks, P. J. S., & Ohman, M. D. (2021). The California Undercurrent as a source of upwelled waters in a coastal filament. Journal of Geophysical Research-Oceans, 126(2). https://doi.org/10.1029/2020jc016602
Orenstein, E. C., Kenitz, K. M., Roberts, P. L. D., Franks, P. J. S., Jaffe, J. S., & Barton, A. D. (2020). Semi- and fully supervised quantification techniques to improve population estimates from machine classifiers. Limnology and Oceanography-Methods. https://doi.org/10.1002/lom3.10399
Orenstein, E. C., Ratelle, D., Briseno-Avena, C., Carter, M. L., Franks, P. J. S., Jaffe, J. S., & Roberts, P. L. D. (2020). The Scripps Plankton Camera system: A framework and platform for in situ microscopy. Limnology and Oceanography-Methods. https://doi.org/10.1002/lom3.10394
Garwood, J. C., Lucas, A. J., Naughton, P., Roberts, P. L. D., Jaffe, J. S., DeGelleke, L., & Franks, P. J. S. (2020). Larval cross-shore transport estimated from internal waves with a background flow: The effects of larval vertical position and depth regulation. Limnology and Oceanography. https://doi.org/10.1002/lno.11632
Briseno-Avena, C., Prairie, J. C., Franks, P. J. S., & Jaffe, J. S. (2020). Comparing Vertical Distributions of Chl-a Fluorescence, Marine Snow, and Taxon-Specific Zooplankton in Relation to Density Using High-Resolution Optical Measurements. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.00602
Kenitz, K. M., Orenstein, E. C., Roberts, P. L. D., Franks, P. J. S., Jaffe, J. S., Carter, M. L., & Barton, A. D. (2020). Environmental drivers of population variability in colony-forming marine diatoms. Limnology and Oceanography. https://doi.org/10.1002/lno.11468
Inman, B. G., Davies, C. J., Torres, C. R., & Franks, P. J. S. (2020). Deformation of ambient chemical gradients by sinking spheres. Journal of Fluid Mechanics, 892. https://doi.org/10.1017/jfm.2020.191
Zhang, Y., Chen, C. S., Xue, P. F., Beardsley, R. C., & Franks, P. J. S. (2020). A view of physical mechanisms for transporting harmful algal blooms to Massachusetts Bay. Marine Pollution Bulletin, 154. https://doi.org/10.1016/j.marpolbul.2020.111048
Sathyendranath, S., Platt, T., Kovac, Z., Dingle, J., Jackson, T., Brewin, R. J. W., Franks, P., Maranon, E., Kulk, G., & Bouman, H. A. (2020). Reconciling models of primary production and photoacclimation Invited. Applied Optics, 59(10), C100–C114. https://doi.org/10.1364/ao.386252
Garwood, J. C., Lucas, A. J., Naughton, P., Alford, M. H., Roberts, P. L. D., Jaffe, J. S., DeGelleke, L., & Franks, P. J. S. (2019). A novel cross-shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field. Limnology and Oceanography. https://doi.org/10.1002/lno.11400
Franks, P. J. S., Garwood, J. C., Ouimet, M., Cortes, J., Musgrave, R. C., & Lucas, A. J. (2019). Stokes drift of plankton in linear internal waves: Cross-shore transport of neutrally buoyant and depth-keeping organisms. Limnology and Oceanography. https://doi.org/10.1002/lno.11389
de Verneil, A., Franks, P. J. S., & Ohman, M. D. (2019). Frontogenesis and the creation of fine-scale vertical phytoplankton structure. Journal of Geophysical Research-Oceans, 124(3), 1509–1523. https://doi.org/10.1029/2018jc014645
Lennert-Cody, C. E., Clarke, S. C., Aires-da-Silva, A., Maunder, M. N., Franks, P. J. S., Roman, M., Miller, A. J., & Minami, M. (2019). The importance of environment and life stage on interpretation of silky shark relative abundance indices for the equatorial Pacific Ocean. Fisheries Oceanography, 28(1), 43–53. https://doi.org/10.1111/fog.12385
Lee, K. H., Jeong, H. J., Lee, K., Franks, P. J. S., Seong, K. A., Lee, S. Y., Lee, M. J., Jang, S. H., Potvin, E., Lim, A. S., Yoon, E. Y., Du Yoo, Y., Kang, N. S., & Kim, K. Y. (2019). Effects of warming and eutrophication on coastal phytoplankton production. Harmful Algae, 81, 106–118. https://doi.org/10.1016/j.hal.2018.11.017
Levy, M., Franks, P. J. S., & Smith, K. S. (2018). The role of submesoscale currents in structuring marine ecosystems. Nature Communications, 9. https://doi.org/10.1038/s41467-018-07059-3
Carranza, M. M., Gille, S. T., Franks, P. J. S., Johnson, K. S., Pinkel, R., & Girton, J. B. (2018). When mixed layers are not mixed. Storm-driven mixing and bio-optical vertical gradients in mixed layers of the Southern Ocean. Journal of Geophysical Research-Oceans, 123(10), 7264–7289. https://doi.org/10.1029/2018jc014416
Chenillat, F., Franks, P. J. S., Capet, X., Riviere, P., Grima, N., Blanke, B., & Combes, V. (2018). Eddy properties in the Southern California Current System. Ocean Dynamics, 68(7), 761–777. https://doi.org/10.1007/s10236-018-1158-4
Cohen, R. E., James, C. C., Lee, A., Martinelli, M. M., Muraoka, W. T., Ortega, M., Sadowski, R., Starkey, L., Szesciorka, A. R., Timko, S. E., Weiss, E. L., & Franks, P. J. S. (2018). Marine host-pathogen dynamics: Influences of global climate change. Oceanography, 31(2), 182–193. https://doi.org/10.5670/oceanog.2018.201
Briseno-Avena, C., Franks, P. J. S., Roberts, P. L. D., & Jaffe, J. S. (2018). A diverse group of echogenic particles observed with a broadband, high frequency echosounder. Ices Journal of Marine Science, 75(2), 471–482. https://doi.org/10.1093/icesjms/fsx171
Li, Q. P., Franks, P. J. S., & Landry, M. R. (2017). Recovering growth and grazing rates from nonlinear dilution experiments. Limnology and Oceanography, 62(5), 1825–1835. https://doi.org/10.1002/lno.10536
Snyder, S., Franks, P. J. S., Talley, L. D., Xu, Y., & Kohin, S. (2017). Crossing the line: Tunas actively exploit submesoscale fronts to enhance foraging success. Limnology and Oceanography Letters, 2(5), 187–194. https://doi.org/10.1002/lol2.10049
Jaffe, J. S., Franks, P. J. S., Roberts, P. L. D., Mirza, D., Schurgers, C., Kastner, R., & Boch, A. (2017). A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics. Nature Communications, 8, 14189. https://doi.org/10.1038/ncomms14189
Chenillat, F., Franks, P. J. S., & Combes, V. (2016). Biogeochemical properties of eddies in the California Current System. Geophysical Research Letters, 43(11), 5812–5820. https://doi.org/10.1002/2016gl068945
Cavole, L. M., Demko, A. M., Diner, R. E., Giddings, A., Koester, I., Pagniello, C., Paulsen, M. L., Ramirez-Valdez, A., Schwenck, S. M., Yen, N. K., Zill, M. E., & Franks, P. J. S. (2016). Biological impacts of the 2013-2015 warm-water anomaly in the Northeast Pacific. Oceanography, 29(2), 273–285. https://doi.org/10.5670/oceanog.2016.32
Snyder, S., & Franks, P. J. S. (2016). Quantifying the effects of sensor coatings on body temperature measurements. Animal Biotelemetry, 4(1), 8. https://doi.org/10.1186/s40317-016-0100-0
Fang, H. Z., de Callafon, R. A., & Franks, P. J. S. (2015). Smoothed estimation of unknown inputs and states in dynamic systems with application to oceanic flow field reconstruction. International Journal of Adaptive Control and Signal Processing, 29(10), 1224–1242. https://doi.org/10.1002/acs.2529
Chenillat, F., Franks, P. J. S., Riviere, P., Capet, X., Grima, N., & Blanke, B. (2015). Plankton dynamics in a cyclonic eddy in the Southern California Current System. Journal of Geophysical Research-Oceans, 120(8), 5566–5588. https://doi.org/10.1002/2015jc010826
de Verneil, A., & Franks, P. J. S. (2015). A pseudo-Lagrangian method for remapping ocean biogeochemical tracer data: Calculation of net Chl-a growth rates. Journal of Geophysical Research-Oceans, 120(7), 4962–4979. https://doi.org/10.1002/2015jc010898
Jeong, H. J., Lim, A. S., Franks, P. J. S., Lee, K. H., Kim, J. H., Kang, N. S., Lee, M. J., Jang, S. H., Lee, S. Y., Yoon, E. Y., Park, J. Y., Yoo, Y. D., Seong, K. A., Kwon, J. E., & Jang, T. Y. (2015). A hierarchy of conceptual models of red-tide generation: Nutrition, behavior, and biological interactions. Harmful Algae, 47, 97–115. https://doi.org/10.1016/j.hal.2015.06.004
Franks, P. J. S. (2015). Has Sverdrup’s critical depth hypothesis been tested? Mixed layers vs. turbulent layers. Ices Journal of Marine Science, 72(6), 1897–1907. https://doi.org/10.1093/icesjms/fsu175
Brzezinski, M. A., Krause, J. W., Bundy, R. M., Barbeau, K. A., Franks, P., Goericke, R., Landry, M. R., & Stukel, M. R. (2015). Enhanced silica ballasting from iron stress sustains carbon export in a frontal zone within the California Current. Journal of Geophysical Research-Oceans, 120(7), 4654–4669. https://doi.org/10.1002/2015jc010829
Briseño-Avena, C., Roberts, P. L. D., Franks, P. J. S., & Jaffe, J. S. (2015). ZOOPS-O2: A broadband echosounder with coordinated stereo optical imaging for observing plankton in situ. Methods in Oceanography, 12(Supplement C), 36–54. https://doi.org/10.1016/j.mio.2015.07.001
Taniguchi, D. A. A., Franks, P. J. S., & Poulin, F. J. (2014). Planktonic biomass size spectra: an emergent property of size-dependent physiological rates, food web dynamics, and nutrient regimes. Marine Ecology Progress Series, 514, 13–33. https://doi.org/10.3354/meps10968
Taniguchi, D. A. A., Landry, M. R., Franks, P. J. S., & Selph, K. E. (2014). Size-specific growth and grazing rates for picophytoplankton in coastal and oceanic regions of the eastern Pacific. Marine Ecology Progress Series, 509, 87–101. https://doi.org/10.3354/meps10895
Lim, A. S., Jeong, H. J., Jang, T. Y., Jang, S. H., & Franks, P. J. S. (2014). Inhibition of growth rate and swimming speed of the harmful dinoflagellate Cochlodinium polykrikoides by diatoms: Implications for red tide formation. Harmful Algae, 37, 53–61. https://doi.org/10.1016/j.hal.2014.05.003
Rossini, G. P. (2014). Modeling of Harmful Algal Blooms: Advances in the Last Decade. In Gian Paolo Rossini (Ed.), Toxins and biologically active compounds from microalgae. Volume 2, Biological effects and risk management. CRC Press.
Di Lorenzo, E., Combes, V., Keister, J. E., Strub, P. T., Thomas, A. C., Franks, P. J. S., Ohman, M. D., Furtado, J. C., Bracco, A., Bograd, S. J., Peterson, W. T., Schwing, F. B., Chiba, S., Taguchi, B., Hormazabal, S., & Parada, C. (2013). Synthesis of Pacific Ocean climate and ecosystem dynamics. Oceanography, 26(4), 68–81.
Franks, P. J. S., Di Lorenzo, E., Goebel, N. L., Chenillat, F., Riviere, P., Edward, C. A., & Miller, A. J. (2013). Modeling physical-biological responses to climate change in the California Current system. Oceanography, 26(3), 26–33.
Ohman, M. D., Barbeau, K., Franks, P. J. S., Goericke, R., Landry, M. R., & Miller, A. J. (2013). Ecological transitions in a coastal upwelling ecosystem. Oceanography, 26(3), 210–219.
Rippy, M. A., Franks, P. J. S., Feddersen, F., Guza, R. T., & Warrick, J. A. (2013). Beach nourishment impacts on bacteriological water quality and phytoplankton bloom dynamics. Environmental Science & Technology, 47(12), 6146–6154. https://doi.org/10.1021/es400572k
Chenillat, F., Riviere, P., Capet, X., Franks, P. J. S., & Blanke, B. (2013). California coastal upwelling onset variability: Cross-shore and bottom-up propagation in the planktonic ecosystem. PLOS ONE, 8(5). https://doi.org/10.1371/journal.pone.0062281
Rippy, M. A., Franks, P. J. S., Feddersen, F., Guza, R. T., & Moore, D. F. (2013). Physical dynamics controlling variability in nearshore fecal pollution: Fecal indicator bacteria as passive particles. Marine Pollution Bulletin, 66(1–2), 151–157. https://doi.org/10.1016/j.marpolbul.2012.09.030
Rippy, M. A., Franks, P. J. S., Feddersen, F., Guza, R. T., & Moore, D. F. (2013). Factors controlling variability in nearshore fecal pollution: The effects of mortality. Marine Pollution Bulletin, 66(1–2), 191–198. https://doi.org/10.1016/j.marpolbul.2012.09.003
Taniguchi, D. A. A., Franks, P. J. S., & Landry, M. R. (2012). Estimating size-dependent growth and grazing rates and their associated errors using the dilution method. Limnology and Oceanography-Methods, 10, 868–881. https://doi.org/10.4319/lom.2012.10.868
Omand, M. M., Feddersen, F., Guza, R. T., & Franks, P. J. S. (2012). Episodic vertical nutrient fluxes and nearshore phytoplankton blooms in Southern California. Limnology and Oceanography, 57(6), 1673–1688. https://doi.org/10.4319/lo.2012.57.6.1673
Li, Q. P., Franks, P. J. S., Ohman, M. D., & Landry, M. R. (2012). Enhanced nitrate fluxes and biological processes at a frontal zone in the southern California current system. Journal of Plankton Research, 34(9), 790–801. https://doi.org/10.1093/plankt/fbs006