Publications

A full list is also available on Google Scholar and ORCID.

Note

Citations follow Limnology & Oceanography reference style: authors (initials unspaced, “and” before the final author), year, sentence-case title, italicized journal, volume: pages, then DOI.

2026

• Hu, S.K., A. Adams, A. Day, M. Ellis, N.A. Faz, F. Haro, M. Lerma, K.A. Nedd, S. Seshampally, M. Sonsel, and C.L. Wiederwohl. 2026. Riverine input and eddy edge effects on microeukaryotic biodiversity in the Northern Gulf. bioRxiv 2026.07.20.739614. link

• Rizzo, G., N.M. Scott, B.C. Kubik, S.K. Hu, J.A. Huber, and J.F. Holden. 2026. Methanothermococcus jasoni sp. nov., a novel thermophilic methanogen from subseafloor hydrothermal vent fluids of Axial Seamount, Juan de Fuca Ridge. International Journal of Systematic and Evolutionary Microbiology 76(3). link

2025

• Gleich, S.J., L.Y. Mesrop, J.A. Cram, J.L. Weissman, S.K. Hu, Y.-C. Yeh, J.A. Fuhrman, and D.A. Caron. 2025. With a little help from my friends: importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel. mSystems 10(2): e0104524. link

2024

• Krinos, A.I., M. Mars Brisbin, S.K. Hu, N.R. Cohen, T.A. Rynearson, M.J. Follows, F. Schulz, and H. Alexander. 2024. Missing microbial eukaryotes and misleading meta-omic conclusions. Nature Communications 15(1): 9873. link

• S.K. Hu, R.E. Anderson, M.G. Pachiadaki, V.P. Edgcomb, M.H. Serres, S.P. Sylva, C.R. German, J.S. Seewald, S.Q. Lang, and J.A. Huber. 2024. Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. ISME Journal 18(1): wrae004. link

• Gleich, S.J., S.K. Hu, A.I. Krinos, and D.A. Caron. 2024. Protistan community composition and metabolism in the North Pacific Subtropical Gyre: influences of mesoscale eddies and depth. Environmental Microbiology 26: e16556. link

• Beckett, S.J., D. Demory, A.R. Coenen, J.R. Casey, M. Dugenne, C.L. Follett, P. Connell, M.C.G. Carlson, S.K. Hu, and 12 others. 2024. Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre. Nature Communications 15: 2105. link

2023

• Ollison, G.A., S.K. Hu, J.V. Hopper, B.P. Stewart, J.L. Beatty, and D.A. Caron. 2023. Physiology governing diatom vs. dinoflagellate bloom and decline in coastal Santa Monica Bay. Frontiers in Microbiology 14: 1287326. link

• Alexander, H., S.K. Hu, A.I. Krinos, M. Pachiadaki, B.J. Tully, C.J. Neely, and T. Reiter. 2023. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 14: e01676-23. link

2022

• S.K. Hu, A.R. Smith, R.E. Anderson, S.P. Sylva, M. Setzer, M. Steadmon, K.L. Frank, E.W. Chan, D.S.S. Lim, C.R. German, J.A. Breier, S.Q. Lang, D.A. Butterfield, C.S. Fortunato, J.S. Seewald, and J.A. Huber. 2022. Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents. Molecular Ecology 31: 4830–4848. link code

• Hammond, S.W., L. Lodolo, S.K. Hu, and A.L. Pasulka. 2022. Methodological ‘lenses’ influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem. Environmental Microbiology Reports. link

• Ollison, G.A., S.K. Hu, J.V. Hopper, B.P. Stewart, J. Smith, J.L. Beatty, and others. 2022. Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight). Environmental Microbiology 1462-2920.16137. link

• Cohen, N.R., H. Alexander, A.I. Krinos, S.K. Hu, and R.H. Lampe. 2022. Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. Frontiers in Marine Science 9: 867007. link

2021

• Tully, B.J., J. Buongiorno, A.B. Cohen, J.A. Cram, A.I. Garber, S.K. Hu, and others. 2021. The Bioinformatics Virtual Coordination Network: an open-source and interactive learning environment. Frontiers in Education: STEM Education. link

• Ollison, G., S.K. Hu, L.Y. Mesrop, E. Delong, and D.A. Caron. 2021. Come rain or shine: depth not season shapes the protistan community at Station ALOHA in the North Pacific Subtropical Gyre. Deep-Sea Research Part II. link

• S.K. Hu, E.L. Herrera, A.R. Smith, M.G. Pachiadaki, V.P. Edgcomb, S.P. Sylva, E.W. Chan, J.S. Seewald, C.R. German, and J.A. Huber. 2021. Protistan grazing impacts microbial communities and carbon cycling in the deep-sea hydrothermal vent environment. Proceedings of the National Academy of Sciences USA. link code

• Coesel, S.N., B.P. Durham, R.D. Groussman, S.K. Hu, D.A. Caron, R.L. Morales, and others. 2021. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences USA 118: 12. link

• Krinos, A., S. Hu, N. Cohen, and H. Alexander. 2021. EUKulele: taxonomic annotation of the unsung eukaryotic microbes. Journal of Open Source Software 6: 2817. link

2020

• Goordial, J., S. Hu, and B. Tully. 2020. C-DEBI NextGen 2019 Early Career perspective on ‘What’s next?’: upcoming challenges and opportunities. link

• Coenen, A.R., S.K. Hu, E. Luo, D. Muratore, and J.S. Weitz. 2020. A primer for microbiome time-series analysis. Frontiers in Genetics 11: 310. link

• Lim, D.S.S., N.A. Raineault, J.A. Brier, E. Chan, J. Chernov, T. Cohen, M. Deans, A. Garcia, C.R. German, M. Hauer, S.K. Hu, J.A. Huber, R. Kane, S. Kobs Nawotniak, D. Lees, J. Lowe, M. Lubetkin, L. Marsh, V. Milesi, M. Miller, Z. Miramalek, M. Saunders, K. Sharif, A. Shields, E. Shock, A.R. Smith, and S. Sylva. 2020. SUBSEA 2019 expedition to the Gorda Ridge. Oceanography 33(1), Supplement: 36–37. link

2019

• Boeuf, D., B.R. Edwards, J.M. Eppley, S.K. Hu, K.E. Poff, A.E. Romano, and others. 2019. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proceedings of the National Academy of Sciences USA: 11824–11832. link

• Liu, Z., L.Y. Mesrop, S.K. Hu, and D.A. Caron. 2019. Transcriptome of Thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship. Frontiers in Marine Science 6: 284. link

• Pasulka, A., S.K. Hu, P.D. Countway, K.J. Coyne, S.C. Cary, K.B. Heidelberg, and D.A. Caron. 2019. SSU rRNA gene sequencing survey of benthic microbial eukaryotes from Guaymas Basin hydrothermal vent. Journal of Eukaryotic Microbiology jeu.12711. link

• Caron, D.A., and S.K. Hu. 2019. Are we overestimating protistan diversity in nature? Trends in Microbiology 27: 197–205. link

2018

• S.K. Hu, Z. Liu, H. Alexander, V. Campbell, P.E. Connell, S.T. Dyhrman, and others. 2018. Shifting metabolic priorities among key protistan taxa within and below the euphotic zone: depth-related protistan metatranscriptomes. Environmental Microbiology 20: 2865–2879. link

• S.K. Hu, P.E. Connell, L.Y. Mesrop, and D.A. Caron. 2018. A hard day’s night: diel shifts in microbial eukaryotic activity in the North Pacific Subtropical Gyre. Frontiers in Marine Science 5: 251. link

2017

• Liu, Z., S.K. Hu, V. Campbell, A.O. Tatters, K.B. Heidelberg, and D.A. Caron. 2017. Single-cell transcriptomics of small microbial eukaryotes: limitations and potential. The ISME Journal 11: 1282–1285. link

• Connell, P.E., V. Campbell, A.G. Gellene, S.K. Hu, and D.A. Caron. 2017. Planktonic food web structure at a coastal time-series site: II. spatiotemporal variability of microbial trophic activities. Deep Sea Research Part I Oceanographic Research Papers 121: 210–223. link

2016

• S.K. Hu, V. Campbell, P. Connell, A.G. Gellene, Z. Liu, R. Terrado, and D.A. Caron. 2016. Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific. FEMS Microbiology Ecology fiw050. link

2015

• S.K. Hu, Z. Liu, A.A.Y. Lie, P.D. Countway, D.Y. Kim, A.C. Jones, and others. 2015. Estimating protistan diversity using high-throughput sequencing. Journal of Eukaryotic Microbiology 62: 688–693. link

2014

• Lie, A.A.Y., Z. Liu, S.K. Hu, A.C. Jones, D.Y. Kim, P.D. Countway, and others. 2014. Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes. Applied and Environmental Microbiology 80: 4363–4373. link