Fischer, Alexis D., Hayashi, K., McGaraghan, A., and Kudela, R., 2020. Return of the "age of dinoflagellates" in Monterey Bay: Drivers of dinoflagellate dominance examined using automated imaging flow cytometry and long-term time series analysis. Limnology and Oceanography 9999, 1-17

Houskeeper, H. F. and Kudela, R. M., 2019. Ocean Color Quality Control Masks Contain the High Phytoplankton Fraction of Coastal Ocean Observations. Remote Sensing, 11(18), 2167

Kudela, R.M, Hooker, S. B., Houskeeper, H. F., and McPerson, M., 2019. The influence of signal to noise ration of legacy airborne and satellite sensors for simulating next-generation coastal and inland water products. Remote Sensing, 11(18), 2071

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., and Benoit-Bird, K., 2019. Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific. PloS one, 14(9), p.e0222456

Anderson, C.R., Berdalet, E., Kudela, R.M., Cusack, C.K., SIlke, J., O'Rourke, E., Dugan, D., McCammon, M., Newton, J.A., Moore, S.K., and Paige, K., 2019. Scaling up from regional case studies to a global harmful algal bloom observing system. Frontiers in Marine Science, 6, p250

Berg, G.M., Driscoll, S., Hayashi, K., and Kudela, R., 2019. Effects of nitrogen source, concentration, and irradiance on growth rates of two diatoms endemic to northern San Francisco Bay. Aquatic Biology, 28, p33-43

Stauffer, B.A., Bowers, H.A., Buckley, E., Davis, T., Johengen, T.H., Kudela, R.M., McManus, M.A., Purcell, H., Smith, G.J., VanderWoude, A., and Tamburri, M., 2019. Considerations in Harmful Algal Bloom Research and Monitoring: Perspectives from a Consensus-Building Workshop and Technology Testing. Frontiers in Marine Science, 6, p.399

Tatters, A.O., Howard, M.D., Nagoda, C., Fetscher, A.E., Kudela, R.M., and Caron, D.A., 2019. Heterogeneity of Toxin-Producing Cyanobacteria and Cyanotoxins in Coastal Watersheds of Southern California. Estuaries and Coasts, 42(4), p958-975.

Shultz, D, Campbell, L, and Kudela, RM, 2019. Trends in Dinophysis abundance and diarrhetic shellfish toxin levels in California mussels (Mytilus californianus) in Monterey Bay, California. Harmful Algae 88

Trainer, V.L., Moore, S.K., Hallegraeff, G., Kudela, R.M., Clement, A., Mardones, J.I., and Cochlan, W.P. 2019. Pelagic harmful algal blooms and climate change: Lessons from nature's experiments with extremes. Harmful Algae.

Bausell, J. and Kudela, R., 2019. Comparison of two in-water optical profiles in a dynamic coastal marine ecosystem. Applied Optics, 58(27), 7319-7330

Paerl, HW, TG Otten, and RM Kudela, 2018. Mitigating the expansion of harmful algal blooms across the freshwater-to-marine continuum. Environmental Science and Technology vol 52

Peacock, MB, et al. 2018. Blurred Lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California. Harmful Algae, Vol 73 (2018).

Anderson, DM, SFE Boerlage, MB Dixon (Eds). Harmful Algal Blooms (HABs) and Desalination: A Guide to Impacts, Monitoring, and Management. Paris, Intergovernmental Oceanographic Commission of UNESCO, 2017. 538pp. (IOC Manuals and Guides #78)

Schulien, JA, et al. 2017. Phytoplankton and microbial abundance and bloom dynamics in the upwelling shadow of Monterey Bay, CA, from 2006-2013. Marine Ecology Progress Series, Vol 572.

Gibble, CM, MB Peacock, and RM Kudela, 2016. Evidence of freshwater algal toxins in marine shellfish: Implications for human and aquatic health. Harmful Algae 59 (2016).

McCabe, RM, et al. 2016. An unprecedented coastwide toxic algal bloom linked to anomalous ocean conditions. Geophysical Research Letters. 10.1002/2016GL070023

Andersen, C., et al. 2015. Living with Harmful Algal Blooms in a changing world: Strategies for modeling and mitigating their effects in coastal marine ecosystems. Coastal and Marine Hazards, Risks, and Disasters, p. 495-561, 2015.

Davis, KA, NS Banas, SN Giddings, SA Siedlecki, P MacCready, EJ Lessard, RM Kudela, and BM Hickey. 2015. Estuary-enhanced upwelling of marine nutrients fuels coastal productivity in the U.S. Pacific Northwest. Journal of Geophysical Research, 119.12: 8778-8799.

Kudela, RM, Bickel, A, Carter, ML, Howard, MDA, Rosenfeld, L. 2015. The Monitoring of Harmful Algal Blooms through Ocean Observing: the Development of the California Harmful Algal Bloom Monitoring and Alert Program. Invited chapter to Coastal Ocean Observing Systems, Y. Liu, H. Kerkering, R.H. Weisberg (eds.). Elsevier, Chapter 5, pp. 58-75. ISBN 978-0-12-802022-7.

Kudela RM, Lucas AJ, Hayashi K, Howard M, and McLaughlin, K, 2015. Death from below: investigation of inhibitory factors in bloom development during a wastewater efflvent diversion. Estuarine, Coastal and Shelf Science. doi: 10.1016/j.ecss.2015.07.021.

Kudela RM, Palacios SL, Austerberry DC, Accorsi EK, Guild LS, Torres-Perez, J, 2015 . Application of hyperspectral remote sensing to cyanobacterial blooms in inland waters. Remote Sensing of Environment 167 (2015) 196–205.

Lucas, AJ and RM Kudela. 2015. The fine-scale vertical variability of a wastewater plume in shallow, stratified coastal waters. Estuar. Coast. Shelf Sci. doi:10.1016/j.ecss.2015.08.010

Palacios, SL, Kudela RM, Guild LS, Negrey KH, Torres-Perez J, and Broughton J, 2015. Remote sensing of phytoplankton functional types in the coastal ocean from the HyspIRI Preparatory Flight Campaign. Remote Sensing Environment, 167: 269-280.

Sverdrup, Keith A, and Raphael M. Kudela. 2014. Investigating Oceanography, 1st Ed. McGraw-Hill New York. 472 p.

Thompson, D. R., Seidel, F. C., Gao, B. C., Gierach, M. M., Green, R. O., Kudela, R. M., & Mouroulis, P. 2015. Optimizing Irradiance Estimates for Coastal and Inland Water Imaging Spectroscopy. Geophysical Research Letters 42(10): 4116-4123.

Gibble, CM, RM Kudela. 2014. Detection of persistent microcystin toxins at the land-sea interface in Monterey Bay, California. Harmful Algae, 39: 146-153.

Giddings, SN, P MacCready, BM Hickey, NS Banas, KA Davis, SA Siedlecki, VL Trainer, RM Kudela, NA Pelland, TP Connolly. 2014. Hindcasts of potential harmful algal bloom transport pathways on the Pacific Northwest coast. Journal of Geophysical Research, 119: 2439-2461, doi:10.1002/2013JC009622

Jacox, MG, CA Edwards, M Kahru, DL Rudnick, and RM Kudela. 2014. Improving remote estimation of primary productivity in the southern California Current System.  Deep-Sea Research II, doi:10.1016/j.dsr2.2013.12.008

Kahru, M, MG Jacox, ZP Lee, RM Kudela, M Manzano-Sarabia, and BG Mitchell. 2014. Optimized multi-satellite merger of primary production estimates in the California Current using inherent optical properties. J. Marine Systems, http://dx.doi.org/10.1016/j.marsys.2014.06.003.

Lucas, AJ, GC Pitcher, TA Probyn, and RM Kudela. 2014. The influence of diurnal winds on phytoplankton dynamics in a coastal upwelling system off southwestern Africa. Deep-Sea Research II, 101: 50-62.

Peacock, Misty. Bloom Watch. Estuary News, December 2014, vol 23 No. 4.

Peacock, MDB, and RM Kudela. 2014. Evidence for active vertical migration by two dinoflagellates experiencing iron, nitrogen, and phosphorus limitation. Limnology and Oceanography, 59(3): 660-673.

Ryan, JP, CO Davis, NB Tufillaro, RM Kudela, and B-C Gao. 2014. Application of the Hyperspectral Imager for the Coastal Ocean to phytoplankton ecology studies in Monterey Bay, California. Remote Sensing 6, 1007-1025.

Seltenrich, N. Remote sensing applications for environmental health research. Environmental Health Perspectives, October 2014, vol 122 No. 10.

Kahru, Mati, et al. 2014. Evaluation of satellite retrievals of chlorophyll-a in the California Current. Remote Sensing 2014, 6, 8524-8540.

Peacock, Misty. Revealing plankton pigments: New technique for identifying plankton by color. Estuary News, September 2014, vol 23 No. 3.

Ryan, JP, et al. 2014. Application of the hyperspectral imager for the coastal ocean to phytoplankton ecology studies in Monterey Bay, CA, USA. Remote Sensing 2014, 6, 1007-1025; doi:10.3390/rs6021007

Jacox, M. G., C. A. Edwards, M. Kahru, D. L. Rudnick, and R. M. Kudela (2013), The potential for improving remote primary productivity estimates through subsurface chlorophyll and irradiance measurement, Deep-Sea Res. II, doi:10.1016/j.dsr2.2013.12.008.

Boyd, PW, et al., 2013. Marine phytoplankton temperature versus growth responses from polar to tropical waters - outcome of a scientific community-wide study. PLOS ONE vol 8 issue 5.

Calleja, MLI, et al. 2013. Changes in compound specific δ15N amino acid signatures and D/L ratios in marine
dissolved organic matter induced by heterotrophic bacterial reworking. Marine Chemisty 149, 32-44.

Peacock, MB and RM Kudela, 2013. Alkaline phosphatase activity detected in distinct phytoplankton communities in the northern Gulf of Alaska. Marine Ecology Progress Series v 473, 79-90.

Jacox, M. G., and C. A. Edwards, 2012. Upwelling source depth in the presence of nearshore wind stress curl. J. Geophys. Res., 117, C05008, doi:10.1029/2011JC007856.

Harvey, J, et al, 2012. Robotic sampling, in situ monitoring and molecular detection of marine zooplankton. Journal of Experimental Marine Biology and Ecology 413 (2012), 60-70.

Peacock, MB, and RM Kudela, 2012. A method for determining alkaline phosphatase activity in marine phytoplankton using spectrofluorometry. Journal of Microbiological Methods. doi:10.1016/j.mimet.2012.03.007

McGaraghan, AR, and RM Kudela, 2012. Estimating labile particulate iron concentrations in coastal waters from remote sensing data. Journal of Geophysical Research 117, C02004, doi:10,1029/2011JC006977

Jacox, MG, and CA Edwards, 2011. Effects of stratification and shelf slope on nutrient supply in coastal upwelling regions. Journal of Geophysical Research 116, C03019, doi:10.1029/2010JC006547

Anderson, CR, et al., 2011. Detecting toxic diatom blooms from ocean color and a regional ocean model. Geophysical Research Letter 38, L04603, doi:10.1029/2010GL045858. Aux 1, aux 2, aux 3.

Zehr, JP, and RM Kudela, 2011. Nitrogen cycle of the open ocean: From genes to ecosystems. Annual Review of Marine Science 3:197-225.

Jacox, MG, and ML Powers, 2010. Science on Sunday: The prospective graduate student workshop in Ocean Sciences. Astronomical Society of the Pacific Conference Series 436, Learning from Inquiry in Practice, eds. L. Hunter and AJ Metevier (San Francisco, CA: ASP), pp. 247-257.

Ryan, JP, AM Fisher, RM Kudela, MA McManus, JS Myers, JD Paduan, CM Ruhsam, CB Woodson, and Y Zhang, 2010. Recurrent frontal slicks of a coastal ocean upwelling shadow. Journal of Geophysical Research 115, C12070, doi:10.1029/2010JC006398.

Kudela, RM, 2010. Does horizontal mixing explain phytoplankton dynamics? Proceedings of the National Academy of Sciences 107:18235-18236.

Lane JQ, Roddam CM, Langlois GW, Kudela RM, 2010. Application of Solid Phase Adsorption Toxin Tracking (SPATT) for field detection of domoic acid and saxitoxin in coastal California. Limnology and Oceanography Methods 8:645-660

Benoit, MD, Kudela RM, and AR Flegal, 2010. Modeled trace element concentrations and partitioning in the San Francisco Estuary, based on suspended solids concentrations. Environmental Science and Technology.

Kudela RM, Seeyave S, Cochlan WP, 2010. The role of nutrients in regulation and promotion of harmful algal blooms in upwelling systems. Progress in Oceanography 85: 122-135.

Kudela RM, Howard MDA, Jenkins BD, Miller PE, Smith GJ, 2010. Using the molecular toolbox to compare harmful algal blooms in upwelling systems. Progress in Oceanography 85: 108-121.

Kudela, RM, AR Horner-Devine, NS Banas, BM Hickey, TD Peterson, RM McCabe, EJ Lessard, E Frame, KW Bruland, DA Jay, JO Peterson, WT Peterson, PM Kosro, SL Palacios, MC Lohan, and EP Dever, 2010. Multiple trophic levels fueled by recirculation in the Columbia River plume. Geophys. Res. Lett., doi:10.1029/2010GL044342

Zehr, JP, and RM Kudela, 2009. Photosynthesis in the open ocean. Science 326:945-946.

Palacios, S., T. Peterson, and R. Kudela, 2009. Development of synthetic salinity from remote sensing for the Columbia River plume, Journal of Geophysical Research, 114, C00B05, doi: 10.1029/2008JC004895.

Lane, J., P Raimondi, and RM Kudela, 2009. Development of a logistic regression model for the prediction of toxigenic Pseudo-nitzschia blooms in Monterey Bay, California. Marine Ecology Progress Series, 383, 37-51.

Anderson, CR, Siegel, DA, Kudela, RM and MA Brzezinski, 2009. Empirical models of toxigenic Pseudo-nitzschia blooms: Potential use as a remote detection tool in the Santa Barbara Channel. Harmful Algae, 8, 478-492

Howard, M.D., Smith, G.J, and Kudela, R.M. Phylogenetic Relationships of Yessotoxin-Producing Dinoflagellates, Based on the Large Subunit and Internal Transcribed Spacer Ribosomal DNA Domains. Applied and Environmental Microbiology, Jan. 2009, P. 54-63.