Quigley, L., Franks, P., Thompson, A., Field, J., & Santora, J. (2024). Quantifying the fates and retention of larval rockfish through Lagrangian analyses. Marine Ecology Progress Series, 749, 109–125. https://doi.org/10.3354/meps14718

McBride, K., MacKinnon, J., Franks, P. J. S., McSweeney, J. M., Waterhouse, A. F., Palóczy, A., Colosi, J., & MacMahan, J. (2024). A juvenile journey: Using a highly resolved 3D mooring array to investigate the roles of wind and internal tide forcing in across‐shore larval transport. Limnology and Oceanography, lno.12675. https://doi.org/10.1002/lno.12675

Franks, P. J. S., & Inman, B. G. (2024). Shortcomings of the dissipation rate for understanding the turbulent environment of plankton—And a potential solution. Limnology and Oceanography, lno.12501. https://doi.org/10.1002/lno.12501

Schoenbeck, C. M., Solsona‐Berga, A., Franks, P. J. S., Frasier, K. E., Trickey, J. S., Aguilar, C., Schroeder, I. D., Širović, A., Bograd, S. J., Gopalakrishnan, G., & Baumann‐Pickering, S. (2024). Ziphius cavirostris presence relative to the vertical and temporal variability of oceanographic conditions in the Southern California Bight. Ecology and Evolution, 14(7), e11708. https://doi.org/10.1002/ece3.11708

Pereira, F., Da Silveira, I. C. A., Tandon, A., Franks, P. J. S., Luko, C. D., Santos, D. M. C., Pompeu, M., Michelazzo, L. S., Chuqui, M. G., & Brandini, F. P. (2024). Phytoplankton Responses to Mesoscale and Submesoscale Processes in a Tropical Meander. Journal of Geophysical Research: Oceans, 129(6), e2023JC020685. https://doi.org/10.1029/2023JC020685

Zheng, B., Lucas, A. J., Franks, P. J. S., Schlosser, T. L., Anderson, C. R., Send, U., Davis, K., Barton, A. D., & Sosik, H. M. (2023). Dinoflagellate vertical migration fuels an intense red tide. Proceedings of the National Academy of Sciences, 120(36), e2304590120. https://doi.org/10.1073/pnas.2304590120

Kenitz, K. M., Orenstein, E. C., Anderson, C. R., Barth, A. J., Briseño‐Avena, C., Caron, D. A., Carter, M. L., Eggleston, E., Franks, P. J. S., Fumo, J. T., Jaffe, J. S., McBeain, K. A., Odell, A., Seech, K., Shipe, R., Smith, J., Taniguchi, D. A. A., Venrick, E. L., & Barton, A. D. (2023). Convening Expert Taxonomists to Build Image Libraries for Training Automated Classifiers. Limnology and Oceanography Bulletin. https://doi.org/10.1002/lob.10584

Broullón, E., Franks, P. J. S., Fernández Castro, B., Gilcoto, M., Fuentes‐Lema, A., Pérez‐Lorenzo, M., Fernández, E., & Mouriño‐Carballido, B. (2023). Rapid phytoplankton response to wind forcing influences productivity in upwelling bays. Limnology and Oceanography Letters, lol2.10309. https://doi.org/10.1002/lol2.10309

Kenitz, K. M., Anderson, C. R., Carter, M. L., Eggleston, E., Seech, K., Shipe, R., Smith, J., Orenstein, E. C., Franks, P. J. S., Jaffe, J. S., & Barton, A. D. (2023). Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy. Limnology and Oceanography. https://doi.org/https://doi.org/10.1002/lno.12297

Gangrade, S., & Franks, P. J. S. (2023). Phytoplankton Patches at Oceanic Fronts Are Linked to Coastal Upwelling Pulses: Observations and Implications in the California Current System. Journal of Geophysical Research: Oceans, 128(3), e2022JC019095. https://doi.org/10.1029/2022JC019095

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

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

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

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

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

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

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

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

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

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

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.