Harding, K. J., Nagarkar, M., Wang, M., Ramsing, K., Anidjar, N., Giddings, S., Brahamsha, B., & Palenik, B. (2025). Temporal and Spatial Dynamics of Synechococcus Clade II and Other Microbes in the Eutrophic Subtropical San Diego Bay. Environmental Microbiology, 27(2), e70043. https://doi.org/10.1111/1462-2920.70043

Rammel, T., Nagarkar, M., & Palenik, B. (2024). Temporal and spatial diversity and abundance of cryptophytes in San Diego coastal waters. Journal of Phycology, jpy.13451. https://doi.org/10.1111/jpy.13451

Wen, B., Wu, Y., Guo, Y., Gasparrini, A., Tong, S., Overcenco, A., Urban, A., Schneider, A., Entezari, A., Vicedo-Cabrera, A. M., Zanobetti, A., Analitis, A., Zeka, A., Tobias, A., Nunes, B., Alahmad, B., Armstrong, B., Forsberg, B., Pan, S.-C., … Li, S. (2024). Comparison for the effects of different components of temperature variability on mortality: A multi-country time-series study. Environment International, 187, 108712. https://doi.org/10.1016/j.envint.2024.108712

Nagarkar, M., & Palenik, B. (2023). Diversity and putative interactions of parasitic alveolates belonging to Syndiniales at a coastal Pacific site. Environmental Microbiology Reports, 1758-2229.13138. https://doi.org/10.1111/1758-2229.13138

Moreno, I. J., Brahamsha, B., Donia, M. S., & Palenik, B. (2023). Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River. Microbial Ecology. https://doi.org/10.1007/s00248-023-02186-x

Valencia, B., Stukel, M. R., Allen, A. E., McCrow, J. P., Rabines, A., Palenik, B., & Landry, M. R. (2021). Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export. Environmental Microbiology, 15. https://doi.org/10.1111/1462-2920.15736

Yoo, Y. D., & Palenik, B. (2021). Growth and grazing of the chlorarachniophyte Bigelowiella natans (Chlorarachniophyceae) on the marine cyanobacterium Synechococcus. Phycologia. https://doi.org/10.1080/00318884.2021.1941567

Lee, M. J., Yoo, Y. D., Palenik, B., Lee, G. G., Yih, W., & Jeong, H. J. (2021). Vitamin B-12 auxotrophy of the red tide dinoflagellate Heterocapsa rotundata and the effects of feeding on Synechococcus and vitamin B-12 availability upon phagotrophic activity. Phycologia. https://doi.org/10.1080/00318884.2021.1936996

Hong, K., Beld, J., Davis, T. D., Burkart, M. D., & Palenik, B. (2021). Screening and characterization of polyhydroxyalkanoate granules, and phylogenetic analysis of polyhydroxyalkanoate synthase gene PhaC in cyanobacteria. Journal of Phycology. https://doi.org/10.1111/jpy.13123

Nagarkar, M., Wang, M., Valencia, B., & Palenik, B. (2020). Spatial and temporal variations in Synechococcus microdiversity in the Southern California coastal ecosystem. Environmental Microbiology. https://doi.org/10.1111/1462-2920.15307

Bradley, J. M., Svistunenko, D. A., Pullin, J., Hill, N., Stuart, R. K., Palenik, B., Wilson, M. T., Hemmings, A. M., Moore, G. R., & Le Brun, N. E. (2019). Reaction of O-2 with a diiron protein generates a mixed-valent Fe2+/Fe3+ center and peroxide. Proceedings of the National Academy of Sciences of the United States of America, 116(6), 2058–2067. https://doi.org/10.1073/pnas.1809913116

Nagarkar, M., Countway, P. D., Du Yoo, Y., Daniels, E., Poulton, N. J., & Palenik, B. (2018). Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site. The ISME Journal. https://doi.org/10.1038/s41396-018-0172-3

Yoo, Y. D., Seong, K. A., Kim, H. S., Jeong, H. J., Yoon, E. Y., Park, J., Kim, J. I., Shin, W., & Palenik, B. (2018). Feeding and grazing impact by the bloom-forming euglenophyte Eutreptiella eupharyngea on marine eubacteria and cyanobacteria. Harmful Algae, 73, 98–109. https://doi.org/10.1016/j.hal.2018.02.003

Shi, X. G., Lin, X., Li, L., Li, M. Z., Palenik, B., & Lin, S. J. (2017). Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. Isme Journal, 11(10), 2209–2218. https://doi.org/10.1038/ismej.2017.81

Stuart, R. K., Bundy, R., Buck, K., Ghassemain, M., Barbeau, K., & Palenik, B. (2017). Copper toxicity response influences mesotrophic Synechococcus community structure. Environmental Microbiology, 19(2), 756–769. https://doi.org/10.1111/1462-2920.13630

Paerl, R. W., Bouget, F.-Y., Lozano, J.-C., Verge, V., Schatt, P., Allen, E. E., Palenik, B., & Azam, F. (2016). Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. Isme Journal. https://doi.org/10.1038/ismej.2016.145

Foflonker, F., Ananyev, G., Qiu, H., Morrison, A., Palenik, B., Dismukes, G. C., & Bhattacharya, D. (2016). The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Research-Biomass Biofuels and Bioproducts, 16, 465–472. https://doi.org/10.1016/j.algal.2016.04.003

Wang, S. Y., Shi, X. G., & Palenik, B. (2016). Characterization of Picochlorum sp use of wastewater generated from hydrothermal liquefaction as a nitrogen source. Algal Research-Biomass Biofuels and Bioproducts, 13, 311–317. https://doi.org/10.1016/j.algal.2015.11.015

Yoo, Y. D., Seong, K. A., Myung, G., Kim, H. S., Jeong, H. J., Palenik, B., & Yih, W. (2015). Ingestion of the unicellular cyanobacterium Synechococcus by the mixotrophic red tide ciliate Mesodinium rubrum. Algae, 30(4), 281–290. https://doi.org/10.4490/algae.2015.30.4.281

Xia, X. M., Vidyarathna, N. K., Palenik, B., Lee, P., & Liu, H. B. (2015). Comparison of the seasonal variations of synechococcus assemblage structures in estuarine waters and coastal waters of Hong Kong. Applied and Environmental Microbiology, 81(21), 7644–7655. https://doi.org/10.1128/aem.01895-15

Johnson, T. L., Brahamsha, B., Palenik, B., & Muhle, J. (2015). Halomethane production by vanadium-dependent bromoperoxidase in marine Synechococcus. Limnology and Oceanography, 60(5), 1823–1835. https://doi.org/10.1002/lno.10135

Foflonker, F., Price, D. C., Qiu, H., Palenik, B., Wang, S. Y., & Bhattacharya, D. (2015). Genome of the halotolerant green alga Picochlorum sp reveals strategies for thriving under fluctuating environmental conditions. Environmental Microbiology, 17(2), 412–426. https://doi.org/10.1111/1462-2920.12541

Paerl, R. W., Bertrand, E. M., Allen, A. E., Palenik, B., & Azam, F. (2015). Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling. Limnology and Oceanography, 60(1), 215–228. https://doi.org/10.1002/lno.10009

Ma, Y. F., Allen, L. Z., & Palenik, B. (2014). Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environmental Microbiology Reports, 6(6), 583–594. https://doi.org/10.1111/1758-2229.12160

Palenik, B. (2014). Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment. Annual Review of Marine Science, Vol 7, 7, 325–340. https://doi.org/10.1146/annurev-marine-010814-015639

Dupont, C. L., McCrow, J. P., Valas, R., Moustafa, A., Walworth, N., Goodenough, U., Roth, R., Hogle, S. L., Bai, J., Johnson, Z. I., Mann, E., Palenik, B., Barbeau, K. A., Craig Venter, J., & Allen, A. E. (2014). Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. Isme Journal, 9(5), 1076–1092. https://doi.org/10.1038/ismej.2014.198

Taton, A., Unglaub, F., Wright, N. E., Zeng, W. Y., Paz-Yepes, J., Brahamsha, B., Palenik, B., Peterson, T. C., Haerizadeh, F., Golden, S. S., & Golden, J. W. (2014). Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. Nucleic Acids Research, 42(17). https://doi.org/10.1093/nar/gku673

Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J., Beszteri, B., Bidle, K. D., Cameron, C. T., Campbell, L., Caron, D. A., Cattolico, R. A., Collier, J. L., Coyne, K., Davy, S. K., … Worden, A. Z. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol, 12(6), e1001889. https://doi.org/10.1371/journal.pbio.1001889

Hamilton, T. J., Paz-Yepes, J., Morrison, R. A., Palenik, B., & Tresguerres, M. (2014). Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour. Conservation Physiology, 2(1). https://doi.org/10.1093/conphys/cou020

Gutierrez-Rodriguez, A., Slack, G., Daniels, E. F., Selph, K. E., Palenik, B., & Landry, M. R. (2014). Fine spatial structure of genetically distinct picocyanobacterial populations across environmental gradients in the Costa Rica Dome. Limnology and Oceanography, 59(3), 705–723. https://doi.org/10.4319/lo.2014.59.3.0705

Wang, S. Y., Lambert, W., Giang, S., Goericke, R., & Palenik, B. (2014). Microalgal assemblages in a poikilohaline pond. Journal of Phycology, 50(2), 303–309. https://doi.org/10.1111/jpy.12158

Bradley, J. M., Hill, N., Le Brun, N. E., Stuart, R. K., & Palenik, B. (2014). Spectroscopic investigation of iron mineralisation by a cyanobacterial ferritin. Journal of Biological Inorganic Chemistry, 19, S291–S291.

Tetu, S. G., Johnson, D. A., Varkey, D. R., Phillippy, K., Stuart, R. K., Dupont, C., Hassan, K. A., Palenik, B., & Paulsen, I. T. (2013). Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Frontiers in Microbiology, 4. https://doi.org/10.3389/fmicb.2013.00232

Paz-Yepes, J., Brahamsha, B., & Palenik, B. (2013). Role of a Microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proceedings of the National Academy of Sciences of the United States of America, 110(29), 12030–12035. https://doi.org/10.1073/pnas.1306260110

Stuart, R. K., Brahamsha, B., Busby, K., & Palenik, B. (2013). Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress. Isme Journal, 7(6), 1139–1149. https://doi.org/10.1038/ismej.2012.175

Prather, K. A., Bertram, T. H., Grassian, V. H., Deane, G. B., Stokes, M. D., DeMott, P. J., Aluwihare, L. I., Palenik, B. P., Azam, F., Seinfeld, J. H., Moffet, R. C., Molina, M. J., Cappa, C. D., Geiger, F. M., Roberts, G. C., Russell, L. M., Ault, A. P., Baltrusaitis, J., Collins, D. B., … Zhao, D. F. (2013). Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol. Proceedings of the National Academy of Sciences of the United States of America, 110(19), 7550–7555. https://doi.org/10.1073/pnas.1300262110

Dupont, C. L., Johnson, D. A., Phillippy, K., Paulsen, I. T., Brahamsha, B., & Palenik, B. (2012). Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102. Applied and Environmental Microbiology, 78(22), 7822–7832. https://doi.org/10.1128/aem.01739-12

Ma, Y., Paulsen, I. T., & Palenik, B. (2012). Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environmental Microbiology, 14(2), 453–466. https://doi.org/10.1111/j.1462-2920.2011.02633.x

Palenik, B. (2012). Recent functional genomics studies in marine synechococcus. In R. L. V. W. F. J. Burnap (Ed.), Functional Genomics and Evolution of Photosynthetic Systems (Vol. 33, pp. 103–118).

Moore, M. J. K., Furutani, H., Roberts, G. C., Moffet, R. C., Gilles, M. K., Palenik, B., & Prather, K. A. (2011). Effect of organic compounds on cloud condensation nuclei (CCN) activity of sea spray aerosol produced by bubble bursting. Atmospheric Environment, 45(39), 7462–7469. https://doi.org/10.1016/j.atmosenv.2011.04.034

Johnson, T. L., Palenik, B., & Brahamsha, B. (2011). Characterization of a functional vanadium-dependent bromoperoxidase in the marine cyanobacterium Synechococcus sp. CC9311. Journal of Phycology, 47(4), 792–801. https://doi.org/10.1111/j.1529-8817.2011.01007.x

Apple, J. K., Strom, S. L., Palenik, B., & Brahamsha, B. (2011). Variability in protist grazing and growth on different marine Synechococcus isolates. Applied and Environmental Microbiology, 77(9), 3074–3084. https://doi.org/10.1128/aem.02241-10

Lucas, A. J., Dupont, C. L., Tai, V., Largier, J. L., Palenik, B., & Franks, P. J. S. (2011). The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf. Limnology and Oceanography, 56(2), 611–626. https://doi.org/10.4319/lo.2011.56.2.0611

Tai, V., Burton, R. S., & Palenik, B. (2011). Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays. Marine Ecology-Progress Series, 426, 133-U164. https://doi.org/10.3354/meps09030

Tai, V., Poon, A. F. Y., Paulsen, I. T., & Palenik, B. (2011). Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. PLOS ONE, 6(9), e24249.

Rynearson, T. A., & Palenik, B. (2011). Learning to read the oceans: Genomics of marine phytoplankton. In M. Lesser (Ed.), Advances in Marine Biology, Vol 60 (Vol. 60, pp. 1–39).

Urbano, R., Palenik, B., Gaston, C. J., & Prather, K. A. (2011). Detection and phylogenetic analysis of coastal bioaerosols using culture dependent and independent techniques. Biogeosciences, 8(2), 301–309. https://doi.org/10.5194/bg-8-301-2011

Ostrowski, M., Mazard, S., Tetu, S. G., Phillippy, K., Johnson, A., Palenik, B., Paulsen, I. T., & Scanlan, D. J. (2010). PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus. Isme Journal, 4(7), 908–921. https://doi.org/10.1038/ismej.2010.24

Mao, X., Olman, V., Stuart, R., Paulsen, I. T., Palenik, B., & Xu, Y. (2010). Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. Bmc Genomics, 11. https://doi.org/10.1186/1471-2164-11-291

Dupont, C. L., Buck, K. N., Palenik, B., & Barbeau, K. (2010). Nickel utilization in phytoplankton assemblages from contrasting oceanic regimes. Deep-Sea Research Part I-Oceanographic Research Papers, 57(4), 553–566. https://doi.org/10.1016/j.dsr.2009.12.014